WO2022051610A1

WO2022051610A1 - Microbiota restoration therapy (mrt) compositions and methods of manufacture

Info

Publication number: WO2022051610A1
Application number: PCT/US2021/049041
Authority: WO
Inventors: Lee A. Jones
Original assignee: Ferring B.V.
Priority date: 2020-09-04
Filing date: 2021-09-03
Publication date: 2022-03-10

Abstract

Methods for treating and/or preventing a recurrent Clostridioides difficile infection are disclosed. An example comprises administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection. The oral microbiota restoration composition comprises a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

Description

MICROBIOTA RESTORATION THERAPY (MRT) COMPOSITIONS AND METHODS OF MANUFACTURE

Field

The present disclosure pertains to compositions and methods for treating patients.

Background

A wide variety of compositions and methods have been developed for treating diseases and/or conditions of the digestive track. Of the known compositions and methods, each has certain advantages and disadvantages. There is an ongoing need to provide alternative compositions and methods for treating diseases and/or conditions of the digestive track.

Brief Summary

This disclosure provides design, material, manufacturing method, and use alternatives for compositions and methods for treating patients. A method for treating a recurrent Clostridioides difficile infection is disclosed. The method comprises: administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection; and wherein the oral microbiota restoration composition comprises a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering two doses of the oral microbiota restoration composition.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering two doses of the oral microbiota restoration composition two times per day for two days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition. Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for two days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for four days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least eight doses of the oral microbiota restoration composition over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering eight or fewer doses of the oral microbiota restoration composition over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least sixteen doses of the oral microbiota restoration composition over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering sixteen or fewer doses of the oral microbiota restoration composition over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least sixteen doses of the oral microbiota restoration composition over at least four days.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering sixteen or fewer doses of the oral microbiota restoration composition over at least four days.

Alternatively or additionally to any of the embodiments above, each dose includes one or more capsules, and the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to

1 x 10¹⁰ colony forming units per capsule.

Alternatively or additionally to any of the embodiments above, each dose includes one or more capsules, and the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to

2 x 10⁹ colony forming units per capsule.

A method for treating a recurrent Clostridioides difficile infection is disclosed. The method comprises: administering one or more capsules containing a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin to a patient with one or more episodes of a recurrent Clostridioides difficile infection.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering two capsules.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering two capsules two times per day for two days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering four capsules.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering four capsules two times per day for two days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering four capsules two times per day for four days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering at least eight capsules over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering eight or fewer capsules over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering at least sixteen capsules over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering sixteen or fewer capsules over at least two days. Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering at least sixteen capsules over at least four days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering sixteen or fewer capsules over at least four days.

Alternatively or additionally to any of the embodiments above, the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x 10¹⁰ colony forming units per capsule.

Alternatively or additionally to any of the embodiments above, the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units per capsule.

A method for preventing a recurrent Clostridioides difficile infection is disclosed. The method comprises: administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection; and wherein the oral microbiota restoration composition comprises a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition.

Alternatively or additionally to any of the embodiments above, administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for two days.

Alternatively or additionally to any of the embodiments above, each dose includes one or more capsules, and the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x 10¹⁰ colony forming units per capsule. Alternatively or additionally to any of the embodiments above, each dose includes one or more capsules, and the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units per capsule.

A method for preventing a recurrent Clostridioides difficile infection is disclosed. The method comprises: administering one or more capsules containing a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin to a patient with one or more episodes of a recurrent Clostridioides difficile infection.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering sixteen or fewer capsules over at least two days.

Alternatively or additionally to any of the embodiments above, administering one or more capsules includes administering at least sixteen capsules over at least four days.

Alternatively or additionally to any of the embodiments above, the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x 10¹⁰ colony forming units per capsule. Alternatively or additionally to any of the embodiments above, the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units per capsule.

A composition for treating a recurrent Clostridioides difficile infection is disclosed. The composition comprises: a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

Alternatively or additionally to any of the embodiments above, the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x 10¹⁰ colony forming units.

Alternatively or additionally to any of the embodiments above, the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units.

A composition for preventing a recurrent Clostridioides difficile infection is disclosed. The composition comprises: a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

The above summary of some embodiments is not intended to describe each disclosed embodiment or every implementation of the present disclosure. The Figures and Detailed Description which follow more particularly exemplify these embodiments.

Brief Description Of The Drawings

The disclosure may be more completely understood in consideration of the following detailed description of various embodiments of the disclosure in connection with the accompanying drawings, in which:

FIG. 1 is a flowchart depicting an overall process for manufacturing a standardized FMT composition; and,

FIG. 2 is a flowchart depicting further steps in a representative manufacturing process.

FIG. 3 is a flowchart depicting further steps in another representative manufacturing process.

FIG. 4 is a flowchart depicting further steps in another representative manufacturing process. FIG. 5 is a flowchart depicting further steps in another representative manufacturing process.

While the disclosure is amenable to various modifications and alternative forms, specifics thereof have been shown by way of example in the drawings and will be described in detail. It should be understood, however, that the intention is not to limit the disclosure to the particular embodiments described. On the contrary, the intention is to cover all modifications, equivalents, and alternatives falling within the spirit and scope of the disclosure.

Detailed Description

For the following defined terms, these definitions shall be applied, unless a different definition is given in the claims or elsewhere in this specification.

All numeric values are herein assumed to be modified by the term “about,” whether or not explicitly indicated. The term “about” generally refers to a range of numbers that one of skill in the art would consider equivalent to the recited value (i.e., having the same function or result). In many instances, the terms “about” may include numbers that are rounded to the nearest significant figure.

The recitation of numerical ranges by endpoints includes all numbers within that range (e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, and 5).

As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the content clearly dictates otherwise. As used in this specification and the appended claims, the term “or” is generally employed in its sense including “and/or” unless the content clearly dictates otherwise.

It is noted that references in the specification to “an embodiment”, “some embodiments”, “other embodiments”, etc., indicate that the embodiment described may include one or more particular features, structures, and/or characteristics. However, such recitations do not necessarily mean that all embodiments include the particular features, structures, and/or characteristics. Additionally, when particular features, structures, and/or characteristics are described in connection with one embodiment, it should be understood that such features, structures, and/or characteristics may also be used connection with other embodiments whether or not explicitly described unless clearly stated to the contrary The following detailed description should be read with reference to the drawings in which similar elements in different drawings are numbered the same. The drawings, which are not necessarily to scale, depict illustrative embodiments and are not intended to limit the scope of the disclosure.

"Mammal" as used herein refers to any member of the class Mammalia, including, without limitation, humans and nonhuman primates such as chimpanzees, and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs, and the like. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be included within the scope of this term.

The term “cryopreservation,” as used herein, refers to the process of cooling and storing biological cells, tissues, or organs at very low temperatures to maintain their viability. As a non- limiting example, cryopreservation can be the technology of cooling and storing cells at a temperature below the freezing point (e.g., 196 K) that permits high rates of survivability of the cells upon thawing.

The term “cryoprotectant,” as used herein, refers to a substance that is used to protect biological cells or tissues from the effects of freezing.

As used herein, the term “microbiota” can refer to the human microbiome, the human microbiota or the human gut microbiota. The human microbiome (or human microbiota) is the aggregate of microorganisms that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal, genito-urinary, or vaginal tracts of humans. The human microbiome is comprised of bacteria, fungi, and archaea. Some of these organisms perform tasks that are useful for the human host, but the function of the majority of the organisms that make up the human microbiome is unknown. Under normal circumstances, these microorganisms do not cause disease to the human host, but instead participate in maintaining health. Hence, this population of organisms is frequently referred to as “normal flora.”

The population of microorganisms living in the human gastrointestinal tract is commonly referred to as “gut flora” or “gut microbiota.” The microbial flora of the human gut encompasses a wide variety of microorganisms that aid in digestion, the synthesis of vitamins, and creating enzymes not produced by the human body.

The phrase “microbiota restoration therapy,” as used herein, refers to a composition which may include, but is not limited to, human fecal material containing viable gut flora from a patient or donor, a diluent, and a cryoprotectant. Additional compositions include equivalent freeze-dried and reconstituted feces or a “synthetic” fecal composition. The human fecal material is screened for the presence of pathogenic microorganisms prior to its use in the microbiota restoration therapy. The human fecal material is screened for the presence of Clostridium species including C. difficile, Norovirus, Adenovirus, enteric pathogens, antigens to Giardia species, Cryptosporidia species and other pathogens, including acid-fast bacteria, enterococci, including but not limited to vancomycin-resistant enterococci (VRE), methicillin- resistant Staphylococcus aureus (MSRA), as well as any ova or parasitic bodies, or sporeforming parasites, including but not limited to Isospora, Clyslospora, and Cryptospora.

The process of fecal bacteriotherapy can include introducing a fecal sample of a healthy donor, or a donor having one or more desired characteristics, into a gastrointestinal tract of a patient to repopulate a healthy or desirable gut microbiota. In certain examples, prior to introduction of the fecal sample, the patient's intestinal flora can be disrupted using antibiotics, such that the healthy or desirable gut microbiota, once introduced into the patient, can easily populate the gastrointestinal tract.

The human fecal material is optionally filtered prior to its use in the microbiota restoration therapy.

The present disclosure is directed to compositions, methods of manufacture and methods of treatment utilizing microbiota restoration therapy (MRT) for the treatment of Clostridium difficile infections (CDI). CDI is a common nosocomial infection and is frequently associated with severe morbidity and mortality, especially in elderly patients. While CDI treatment is one example use for the MRT compositions disclosed herein, this is not intended to be limiting. Other diseases and/or conditions are contemplated. Some of the medical conditions that may be desirably impacted by treatment with MRT compositions may include cardiovascular and/or peripheral vascular disease, allergies, obesity, hypoglycemia, constipation, celiac sprue (e.g., celiac disease), gastrointestinal cancer (e.g. gastrointestinal cancer is at least one of stomach cancer, esophageal cancer, colon cancer gallbladder cancer, liver cancer, pancreatic cancer, colorectal cancer, anal cancer, and gastrointestinal stromal tumors), melanoma, non-squamous cell lung cancer, squamous cell lung cancer, renal cell carcinoma, head and neck tumors, bladder cancer, Hodgkin lymphoma, non-Hodgkin lymphoma, gastric cancer, colorectal cancer, multiple myeloma, esophageal cancer, breast cancer, glioblastoma, mediastinal B-cell lymphoma, other hematologic malignancies, testicular cancer, pancreatic cancer, lymphoma, cervical cancer, ovarian cancer, basal cell carcinoma, neuroblastoma, leukemia, sarcoma, other cancers, myoclonus dystonia, sacrolileitis, spondyloarthropathy, spondylarthritis, proximal myotonic myopathy; an autoimmune disease nephritis syndrome, autism, travelers’ diarrhea, small intestinal bacterial overgrowth, chronic pancreatitis, a pancreatic insufficiency, chronic fatigue syndrome, benign myalgic encephalomyelitis, chronic fatigue immune dysfunction syndrome, Parkinson’s Disease (PD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), degenerative neurological diseases, Grand mal seizures or petitmal seizures, Steinert’s disease, chronic infectious mononucleosis, epidemic myalgic encephalomyelitis, idiopathic thrombocytopenic purpura (ITP), an acute or chronic allergic reaction obesity, anorexia, irritable bowel syndrome (IBS or spastic colon) Crohn’s disease, irritable bowel disease (IBD), colitis, ulcerative colitis or Crohn’s colitis, chronic infectious mononucleosis, epidemic myalgic encephalomyelitis, acute or chronic urticarial, lupus, rheumatoid arthritis (RA) or juvenile idiopathic arthritis (JIA), pre-diabetic syndrome, fibromyalgia (FM), Type I or Type II diabetes, acute or chronic insomnia, migraines, and attention deficit/hyperactivity disorder (ADHD).

In the case of humans, the present disclosure encompasses methods of treatment of chronic disorders associated with the presence of abnormal enteric micro flora. Such disorders include but are not limited to those conditions in the following categories: gastro-intestinal disorders including irritable bowel syndrome or spastic colon, functional bowel disease (FBD), including constipation predominant FBD, pain predominant FBD, upper abdominal FBD, nonulcer dyspepsia (NUD), gastro-oesophageal reflux, inflammatory bowel disease including Crohn’s disease, ulcerative colitis, indeterminate colitis, collagenous colitis, microscopic colitis, chronic Clostridium difficile infection, pseudemembranous colitis, mucous colitis, antibiotic associated colitis, idiopathic or simple constipation, diverticular disease, AIDS enteropathy, small bowel bacterial overgrowth, coeliac disease, polyposis coil, colonic polyps, chronic idiopathic pseudo obstructive syndrome; chronic gut infections with specific pathogens including bacteria, viruses, fungi and protozoa; viral gastrointestinal disorders, including viral gastroenteritis, Norwalk viral gastroenteritis, rotavirus gastroenteritis, AIDS related gastroenteritis; liver disorders such as primary biliary cirrhosis, primary sclerosing cholangitis, fatty liver or cryptogenic cirrhosis; rheumatic disorders such as rheumatoid arthritis, non-rheumatoid arthritidies, non rheumatoid factor positive arthritis, ankylosing spondylitis, Lyme disease, and Reiter’s syndrome; immune mediated disorders such as glomeruionephritis, haemolytic uraemic syndrome, juvenile diabetes mellitus, mixed cryoglobulinaemia, polyarteritis, familial Mediterranean fever, amyloidosis, scleroderma, systemic lupus erythematosus, and Behcets syndrome; autoimmune disorders including systemic lupus, psoriasis, idiopathic thrombocytopenic purpura, Sjogren’s syndrome, haemolytic uremic syndrome or scleroderma; neurological syndromes such as chronic fatigue syndrome, migraine, multiple sclerosis, amyotrophic lateral sclerosis, myasthenia gravis, Guillain-Barre syndrome, Parkinson’s disease, Alzheimer’s disease, Chronic Inflammatory Demyelinating Polyneuropathy, and other degenerative disorders; psychiatric disorders including chronic depression, schizophrenia, psychotic disorders, manic depressive illness; regressive disorders including, Asbergers syndrome, Rett syndrome, attention deficit hyperactivity disorder (ADHD), and attention deficit disorder (ADD); the regressive disorder, autism; sudden infant death syndrome (SIDS), anorexia nervosa; dermatological conditions such as chronic urticaria, acne, dermatitis herpetiformis and vasculitis disorders; and cardiovascular and/or vascular disorders and diseases.

Globally, the increase in the prevalence of drug resistant organisms has created many challenges for clinicians that may pose public health risks. Infections by drug resistant organisms (e.g., vancomycin-resistant Enterococcus (VRE)) and Clostridium difficile infection share similar risk factors. VRE is a nosocomial pathogen that can be a complication among transplant and immune compromised patients. VRE carriers may also be at increased risk for infection due to VRE and also be a potential source of VRE transmissions to others. VRE shedding in stool increases with antimicrobial exposures and decreases with normalization of the intestinal microbiota after antimicrobials are discontinued. Accordingly, normalization of intestinal microbiota may not only be useful for treating Clostridium difficile infections (including chronic infections and/or recurrent infections), these treatments may also be useful for treating infections by drug resistant organisms (e.g., VRE and/or other drug resistant organisms including those disclosed herein).

In some instances, the microbiota restoration therapy compositions (and/or fecal bacteriotherapy compositions) disclosed herein may be used to treat patients with infections by drug resistant organisms and/or multi-drug resistant organisms (MDRO). The drug resistant organisms may be resistant to antimicrobial agents (e.g., antibiotics, antivirals, antifungals, antiparasitics, other drugs, combinations thereof, and the like) and may include drug resistant micro-organisms such as bacteria, viruses, fungi, parasites, etc. The infections that can be treated by the microbiota restoration therapy compositions disclosed herein may be along the digestive tract or along other systems of the patient.

The microbiota restoration therapy compositions may be used to treat infections by a variety of drug resistant organisms such as vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), extended- spectrum P-lactamase producing gram-negative bacteria, Klebsiella pneumoniae carbapenemase producing gramnegative bacteria, multi-drug resistant gram negative rods bacteria (e.g., such as Enterobacter species, E.coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa'), drug resistant Enterobacter species, multi-drug resistant tuberculosis (e.g., Mycobacterium tuberculosis), drug resistant staphylococci, drug resistant enterococci, drug resistant gonococci, drug resistant streptococci (e.g., including Streptococcus pneumoniae), drug resistant salmonella, drug resistant gram negative bacteria, drug resistant Candida, drug resistant HIV, drug resistant influenza virus, drug resistant cytomegalovirus, drug resistant herpes simplex virus, drug resistant malaria, drug resistant Plasmodium vivax, drug resistant Plasmodium falciparum, drug resistant Toxoplasma gondii, and the like, and/or other drug resistant organisms. These are just examples.

The microbiota restoration therapy compositions may be used to treat other infections including urinary tract infections.

The microbiota restoration therapy compositions may be used to treat recurrent Clostridium difficile infections. For example, the microbiota restoration therapy compositions may be used to treat recurrent Clostridium difficile infections in patients with one or more prior episodes of a recurrent Clostridium difficile infection. The microbiota restoration therapy compositions may be used to prevent recurrent Clostridium difficile infections. For example, the microbiota restoration therapy compositions may be used to prevent recurrent Clostridium difficile infections in patients with one or more prior episodes of a recurrent Clostridium difficile infection.

Treatment of infections by drug resistant organisms with the microbiota restoration therapy compositions disclosed herein may include treating patients with no prior history of infection with a drug resistant organism, treating patients with a single prior infection by a drug resistant organism, treating patients with two or more (e.g., two, three, four, five, six, or more) prior infections by a drug resistant organism, etc. In some instances, the microbiota restoration therapy compositions may be used to treat a patient with three prior infections by a drug resistant organism. In other instances, the microbiota restoration therapy compositions may be used to treat a patient with two prior infections by a drug resistant organism if the prior infections resulted in hospitalization, if the prior or current infections require treatment with toxic drugs, or if the prior infections were all from the same organism.

In some instances, MRT compositions can be administered to a patient using an enema or other suitable technique. However, it may be desirable to orally administer an MRT composition. In order to prepare an MRT composition in a form suitable for oral administration, a number of steps may be carried out. Generally, these steps may include collecting a fecal sample, processing the fecal sample, lyophilizing or “freeze-drying” the processed fecal sample (or otherwise converting the processed fecal sample from a liquid to a solid), adding one or more additives and/or excipients, and forming an oral form of the MRT composition from the lyophilized material and additives (e.g., a tablet, capsule, liquid preparation, or the like). Some additional details regarding at least some of these steps are disclosed herein.

Figure 1 is a flow chart depicting a portion of an example MRT production process. This is just an example. Other examples of screening donors, obtaining human stool samples, and processing the stool samples to a MRT product are disclosed in commonly assigned U.S. Patent Publication 2014/0363398, which is herein incorporated by reference. More particularly, Figure 1 schematically depicts a process for collecting and inspecting a donor fecal sample. As a first step in the collecting/inspecting process, potential stool donors are screened. Screening/prescreening is described in more detail herein. Once the donor passes the screening, step two may include collecting the donor’s stool using a human stool collection kit as defined herein, whether at home or at a collection facility. The kit can include, but is not limited to, a clean human stool collection container with lid, a large closeable/sealable bag, a donation form and a human stool collection instruction sheet. The time and date of collection, along with donor identity and method of transport, can be recorded in order to track the time from collection to processing, and the conditions of transport. As a non-limiting example, the collection container can include an indicator of the minimum and the maximum temperature to which the sample is exposed. As another non-limiting example, one or more temperature sensitive stickers that changes color at temperatures below about 4° C and temperatures greater than about room temperature (about 22-29° C.) can be affixed to the container.

Step three may involve transporting the sample to a processing facility. It can be appreciated that if the sample is collected at the processing facility, transporting the sample is not necessary. In some instances it may be desirable to collect the sample at the processing facility in order to more clearly establish the chain of custody of the sample. With the receipt of the first stool donation for any individual, a profile will be established for each donor. Subsequent stool samples can be subjected to a human stool test, which is utilized to match and confirm the identity of the donor with the donation. Based on prior collected samples, a human stool profile for the donor is generated and can be maintained or enhanced over repeated donations. Any new sample will be compared with this profile to confirm it is the same donor. Differentiation can be made to confirm donor identity based on the representation of Bacterioides species in the human stool. In a non-limiting example, the base set of stool samples used to create the profile is collected at the processing facility to assure donor identity in the profile samples. In another non-limiting example, the base set of stool samples used to create the profile can be collected in locations other than the processing facility, with donor identity assurance protocols appropriate to the situation or location.

Step four of the method may include labeling the donation “Quarantine” and holding the donation in quarantine at or below room temperature for no longer than in the range of 24 hours to five days prior to processing. Donations may be rejected in situations where the temperature indicator has been activated or where the time between donation and receipt exceeds 24 hours. In addition, where applicable, the human stool test results must match the donor profile. If the human stool test does not match the donor profile, the donation collected for that day will be discarded and the donor will be disqualified.

In one method of the disclosure, the human stool sample is processed within about 24 hours of collection. In another method of the application, the time of collection is recorded at the time of arrival of the stool sample at the processing facility. Step six may include inspecting the stool donation. Visual inspection can be completed upon arrival of the stool sample at the processing facility. In the event the human stool sample is loose, unformed, is not of sufficient weight (e.g., less than about 50 g), or for any other reason, including but not limited to evidence indicating poor sample quality or concerns about donor health, the sample may be rejected, labeled “Inspection - Rejected” and the donation is discarded. Further, answers to questions on the human stool collection form can be reviewed by trained personnel. Certain answers in the collection form may require ample rejection. If the sample is accepted, it may be labeled “Inspection - Accepted” and may be moved to a manufacturing process.

Figure 2 is a flow chart depicting a portion of a generic illustrative method for preparing a stool sample for MRT as an oral dosage. It is contemplated that an intermediate product within the method for preparing a stool sample for MRT as an oral dosage may be suitable for MRT via an enema or gastro-nasal tube. The stool sample may first be collected and screened 100, for example, in the method described with respect to Figure 1. Once the sample has been accepted, the sample may be purified and concentrated 102. The sample may be purified using centrifugation, membrane filtration, or a combination thereof to remove fecal material above a certain particle size. It is contemplated that since most bacteria of interest are in the range of 0.3 microns (pm) to 30 pm, the sample may be processed to remove particles greater than 50- 70 pm. The sample may be processed to obtain a 75% to 90% concentration of the bacteria. This may allow for an increased flexibility in the ratio of formulation excipients to bacteria for further processing.

The sample may be membrane filtered in a number of different ways, including, but not limited to the use of filter bags, pressure filters, and/or vacuum filters. In some instances, the sample may be filtered multiple times using a smaller filter membrane with each subsequent filtering. In some instances, saline may be added as a diluent in a ratio of 1:3 (stool to saline), although this is not required. In other instances, a mixture of saline and a cryoprotectant (e.g., polyethylene glycol (PEG) 3350) may be used as a diluent. The PEG concentration of the diluent can be approximately about 30-90 g/liter (or about 10-90 g/liter). The PEG concentration of the diluent can also be approximately between about 25-75 g/liter. In one example, the ratio of saline/PEG mixture to stool sample is 2:1, or 2 mL saline/PEG mixture to 1 gram human stool. As a non-limiting example, approximately 100 mL of saline/PEG mixture can be used for 50 g of human stool. In another example, the ratio of saline/PEG mixture to stool sample is 3:1, or 3 mL saline/PEG mixture to 1 gram human stool. As a non-limiting example, approximately 150 mL of saline/PEG mixture can be used for 50 g of human stool. While saline/PEG may be suitable for use as a diluent (and/or cryoprotectant), this is not intended to be limiting. Other cryoprotectants may also be utilized. For example, dextrose, betaine, glycine, sucrose, polyvinyl alcohol, Pluronic F-127, mannitol, tween 80, ethylene glycol, 1,3-propanediol, hydroxypropyl cellulose, glycerol, PEG/glycerol mix, propylene glycol, or combinations thereof may be used as cryoprotectants. These materials may be used alone or in combination with a solvent such as saline.

In one example, the sample may be placed in a 500 pm filter bag, with or without a diluent, and agitated using, for example, Stomacher agitation at 230 rpm for approximately 2 minutes to obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be placed in a filter bag having a pore size smaller than 500 pm, for example, 280 pm. The sample may be agitated again using, for example, Stomacher agitation at 230 rpm with or without a diluent for approximately 4 minutes to obtain a filtrate having a particle size of approximately 280 pm or less. This filtrate may be placed in another filter bag having a pore size smaller than, for example, 280 pm, such as, but not limited to 60 pm. The sample may be agitated again using, for example, Stomacher agitation at 230 rpm with or without a diluent for approximately 4 minutes to produce a filtrate having a particle size of approximately 50-70 pm or less.

In another example, the sample may be placed in a 500 pm filter bag, with or without a diluent, and agitated using, for example, Stomacher agitation obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be processed using a pressure filter having a pore size of approximately 160 pm and the resulting filtrate processed using a pressure filter having a pore size of approximately 60 pm. In some instances, the sample may be need to be processed a second time using a bag filter having a pores size between 160 pm and 500 pm prior to using the pressure filter. In another example, the sample may be placed in a 500 pm filter bag, with or without a diluent, and agitated using, for example, Stomacher agitation obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be processed using a vacuum filter having a pore size of approximately 160 pm and the resulting filtrate processed using a vacuum filter having a pore size of approximately 60 pm. In some instances, the sample may be need to be processed a second time using a bag filter having a pores size between 160 pm and 500 pm prior to using the pressure filter.

Once the sample has been processed to have a particle size of approximately 60 pm or less, the sample may then be washed and further concentrated using a centrifuge. In some instances, centrifuge tubes may have a volume in the range of 50 to 500 mL, or more. The filtered suspension is filled to approximately 20 to 80% of the volume of the centrifuge tube. In one example, the samples may be centrifuged at 1100 to 3600 revolutions per minute (rpm) for 10 to 15 minutes cycles. In another example, the samples may be centrifuged at a rate such that the centrifugal force is in the range of about 8-12,000 g (e.g., about 10,000 g) for 15 - 45 minutes or 20 - 30 minutes. The centrifuge may be ramped up or gradually accelerated to the speed needed to create a centrifugal force in the range of about 8-12,000 g (e.g., about 10,000 g). It is further contemplated that the centrifuge may also be slowly ramped down or decelerated when the centrifugation process is complete. In some instances, it may be desirable to decelerate the centrifuge as slowly as possible so that the return to atmospheric pressure is slow so as to protect the bacterial cells from potentially bursting. The supernatant is removed and the remaining material in the tube is the purified intermediate MRT composition. This may result in a product that has been concentrated by approximately 60%. In some instances, the centrifugation process may be a 2-tiered process. For example, the product may first undergo a “pre-spin”, (e.g., about 300-2000xg or about l,400xg for 1-5 minutes or for about 2 minutes) to remove fecal fibrous material and then may undergo a longer centrifugation to concentrate the product. For example, following the “pre-spin”, the supernatant may be transferred to a new centrifuge tube/bottle and then spun at a higher speed (e.g., about 5,000- 12,000xg or about 10,000xg for 30-60 minutes or for about 45 minutes). After the high-speed spin, the supernatant may be discarded and the recovered microbiota can be further processed. It is further contemplated that volumes of up to 300 mL may be centrifuged without resulting in a drop in the amount of concentration. The resulting MRT composition is a bacterial suspension having a particle size of 70 pm or less and a bacterial concentration on the order of approximately IxlO¹⁰ CFU/g. The resulting MRT composition may also be stable for 3 weeks at refrigeration conditions.

In some embodiments, centrifugation alone can be used multiple times for purification and concentration. However, the particle size of the bacterial suspension may still be in a range (e.g. greater than 60 pm) that clogs pipet tips. However, in some instances, wide pipette tips may be used. Whether this is successful or not is dependent on the input fecal material, which is variable. It is further contemplated that a system of separators and decanters could be used if the batch size was in the range of several tens of liters, or more. However, this may not be required if the starting product has been previously processed.

In other embodiments, density gradient centrifugation may be used for purification and concentration of a fecal sample. Density gradient centrifugation may be used in combination with the filtering techniques described above, or alone. Density gradient centrifugation may separate strictly by density, whereas differential centrifugation may separate by particle size and density. To perform density gradient centrifugation, a density gradient media may be added to the sample (e.g. diluted raw sample or diluted, filtered sample). The density gradient media may be a solution of varying concentration (e.g. a sucrose having varying concentrations). For example, a density gradient media may be created by overlaying lower concentrations of a solution on higher concentrations of the solution in a centrifuge tube. The sample may be placed on top of the density gradient media and subsequently centrifuged. The particles in the sample may travel through the density gradient media until they reach the point in the gradient at which their density matches that of the surrounding solution. For example, the target material (e.g. bacteria) may settle in the middle of the centrifuge tube due to the density of the bacteria and the density gradient media. A wide variety of density gradient media may be used for the centrifugation, including, but not limited to, polyhydric (sugar) alcohols, polysaccharides, inorganic salts, iodinated compounds, colloidal silica, etc. Other density gradient materials may include iohexols such as Nycodenz ® (manufactured by Axis-Shield), iodixanol solutions, such as OptiPrep ™ (manufactured by Axis Shield), and/or various molecular weight PEGs. It is contemplated that concentrations in the range of 40% to 80% weight/volume (w/v) of Nycodenz® may be used. The media may be pharmaceutical grade, biologically inert, and/or isosmotic. In some instances, density gradient centrifugation may purify bacteria from stool more efficiently that differential centrifugation.

In some embodiments, tangential flow filtration (or crossflow filtration) may be used in combination with density gradient centrifugation to further remove any undesired soluble material. In tangential flow filtration, the majority of the feed flow may flow tangentially across a surface of a filter than into the filter. Tangential flow filtration of the target material (e.g. bacteria) may further remove soluble impurities from the target material. During the tangential flow filtration, additional fibrous material may be pushed out as the bacterial suspension (obtained from traditional centrifugation and/or density gradient centrifugation) is passed across the surface of the filter. In some instances, each pass of the bacterial suspension through the tangential flow filtration system may be followed by a buffer. It is contemplated that larger volumes (e.g. up to about 10 L) of bacterial suspension may be processed at one time through a tangential flow filtration system. In some instances, the filtrate from the tangential flow filtration process may be used as the purified intermediate fecal sample. It is contemplated that the filtered suspension (e.g. filtrate) may be diluted with saline and/or phosphate-buffered saline (PBS). In other instances, the filtrate from the tangential flow filtration process may be further processed using, for example, but not limited to, differential centrifugation and/or dead-end filtration.

In some embodiments, it may be desirable to stabilize the processed sample in suspension 104 at refrigeration conditions for a period of time in the range of one to two weeks. In some instances, removal of the fecal material and replacement with carriers or excipients which are soluble in an aqueous solution may allow the bacteria to be suspended in the liquid and further processed without stability concerns. Considerations for these excipient solutions may be pH, concentration, and isotonicity or isosmolality. Excipients may be selected based on protein and monoclonal antibody formulations and their proposed role in stabilizing biologies. Some example excipients that may be used to provide liquid stabilization 104 of the sample may include, but are not limited to: salt (NaCl), sucrose, trehalose, L-arginine monohydrochloride, and/or PEG 3350, as summarized in Table 1 below. Lists of other potential excipients can be found in tables I and III in Seong Hoon Jeong, Arch Pharm Res Vol 35, No 11, 1871 - 1886, 2012 and in Tables in Pramanick et al. Pharma Times, Vol 45, No. 3, March 2013.

Table 1: Summary of illustrative excipients.

In some instances, the excipient may include 2-20% sucrose, 0.1-5% L-arginine monohydrochloride, 0.5-20% PEG 3550, or combinations thereof.

Combinations of excipients may be used to protect biological cells or tissues from the effects of freezing and/or to provide stability (e.g. minimize cell death) to the product during storage. Table 2 below illustrates some example excipient formulations that may provide cryoprotection and stability during storage. However, the formulations listed in Table 2 are not intended to be limiting. Other combinations and/or quantities of excipients may also be used.

Table 2: Excipient Solution Compositions Prior to Adding to the Drug Substance

In some instances, the excipient (e.g., the lyophilization excipient) may include polyethylene glycol (e.g., about 1-5%, or about 2-3%, or about 2.3%), trehalose (e.g., about 1- 25%, or about 5-15%, or about 10%), sucrose (e.g., about 1-25%, or about 5-15%, or about 10%) and glycerin (e.g., about 0.1-5%, or about 0.5-2%, or about 1%) in purified water.

It is contemplated that the above excipient formulations, when added to the drug substance (e.g. fecal sample or processed fecal sample) may provide cryoprotection and stability during storage to the biological cells in a liquid and/or solid formulation. In some instances, the excipient formulations may be added to the drug substance in a ratio of 1 : 1. This is just an example. Other excipient to drug substance ratios are also contemplated, for example, but not limited to 0.25:1, 0.5:1, 1.5:1, 2:1, etc.

In some of these and in other instances, the excipient formulations may include:

(a) 0.5-20% PEG, (b) 0.1-5% glycerin, (c) 10-30% PVP, (d) 40-80% trehalose, (e) 40- 80% sucrose, (f) 10-30% phosphate buffer solution, or (g) combinations thereof. Other formulations are contemplated.

It is contemplated that similar excipients may also be used to protect the bacteria during membrane filtration. For example, Farber and Sharpe in Applied and Environmental Microbiology, Aug 1984, P. 441 - 443 state that bacterial recovery is improved in the presence of certain food debris (carrots, cheese, peaches, tuna) - pH may be important - pH 5.88 to 6.40 for carrots, pH 4.75 - 5.02 for cheese, pH 5.9 to 6.2 for tuna, pH 3.3 to 4.05 for peaches. The presence of sugars, carbohydrates, or proteins may be important, properties of these foods that coat the bacteria, support bacterial growth (pre-biotic activity) or support the bacterial cell wall during filtration may be important.

Suitable carriers may vary with the desired form and mode of administration of the composition. For example, they may include diluents or excipients such as fillers, binders, wetting agents, disintegrators, surface- active agents, glidants, lubricants, and the like. Typically, the carrier may be a solid (including powder), liquid, or combinations thereof. Each carrier is preferably “acceptable” in the sense of being compatible with the other ingredients in the composition and not injurious to the subject. The carrier may be biologically acceptable and inert (e.g., it permits the composition to maintain viability of the biological material until delivered to the appropriate site).

Oral compositions may include an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g., gelatin capsules. Oral compositions can also be prepared by combining a composition of the present disclosure with a food. In one embodiment a food used for administration is chilled, for instance, ice cream. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, primogel, or corn starch; a lubricant such as magnesium stearate or sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, orange flavoring, or other suitable flavorings. These are for purposes of example only and are not intended to be limiting.

Once the purified sample has been purified and stabilized in an aqueous suspension which may be suitable for delivery via a gastro-nasal tube or an enema, the sample may be further processed to be suitable for an oral delivery, such as in the form of tablets, troches, or capsules. For example, the aqueous solution may be converted to a solid 106. A list of bacterial processing techniques can be found in Martin et al., Innovative Food Science and Emerging Technologies, 27 (2015) 15 - 25.

In some instances, lyophilization, or freeze-drying, may be used to convert the sample from a liquid to a solid. The sample may be provided with a cryoprotectant such as, but not limited to PEG, skim milk, charcoal, ascorbic acid or a combination thereof to protect the bacteria from the effects of freezing. The sample may also be provided with a lyoprotectant such as, but not limited to sucrose, inositol, trehalose, glycerol, or a combination thereof. In some instances, the sample may also be provided with an enrichment material which may provide acid buffering. Alternatively or additionally, the enrichment material may also keep the bacteria more active which may facilitate analytical testing. Some example enrichment materials may include, but are not limited to skim milk, charcoal, gelatin, ascorbic acid, GI media, or combinations thereof. Alternatively or additionally, an oxygen scavenger may be added to the sample prior to and/or after lyophilization. While not wishing to be bound by theory, it is believed that an oxygen scavenger may improve the stability and/or viability of the sample. It is contemplated that lyophilization tubes may include an insert that can be used to expel a lyophilized pellet from the lyophilization tube after freeze-drying. The width of the lyophilization tube may be smaller than the width of a capsule shell for oral treatment. This may allow for the displacement of a tray of pellets directly into the capsule shells. It is contemplated that this may reduce or eliminate the need for particle sizing of the formulation or blending it further 108 for improvement in flow properties into the capsule. The dose may also be determined by pellet size. In some instances, a pellet produced in the lyophilization process may include approximately 4.5xl0⁸ CFU (CDC). A size 0 capsule may accommodate three pellets. Thus, a capsule may include approximately 6.7xl0⁹ CFU (CDC). Eight capsules taken twice a day may be required to be equivalent to one enema dose. Further, there may be no need to test for homogeneity of the batch of pellets that are mixed together prior to capsule filling. In some instances, tamping may allow for a greater concentration or number of pellets within each capsule. For example, tamping of the pellets within the capsule may allow for about 2-4 times (e.g., about 2.5 times) the number of pellets in each capsule (e.g., without tamping each capsule may accommodate 2-4 or about 3 pellets whereas with tamping each capsule may accommodate about 7-10 or about 8 pellets). This may help to reduce the number of capsules a patient may need to take in order to achieve the desired dose. In some instances, the pellets may be ground prior to tamping them into the capsule. If the pellets are ground, it may be desirable for the powder to have a Carr’s Index value in the range of 15 to 30 to facilitate capsule filling. Alternatively, the pellets may be ground and compressed into a tablet form. An enteric powder may then be pressed over the tablet to generate an oral dosage that may be stable in the acid environment of the stomach but dissolves in the intestinal tract.

In other instances, it may be desirable to preserve the sample through vaporization foam drying. It is contemplated that traditional excipients and equipment may be used with this process. Higher excipient concentrations and optimal process parameters to produce foam during processing may result in low water content formulations. The lower the water content; the greater the probability of stability at room temperature. Once the sample has been dried 106, the sample may be further processed to achieve a desired particle size and/or blending 108 in order to prepare the sample for oral product processing.

In yet other embodiments the liquid sample may be microencapsulated by lipids to protect from bile, alginates, and/or polymers. Once the sample has been encapsulated, the sample may be further processed to achieve a desired particle size and/or blending 108 in order to prepare the sample for oral product processing.

After the sample has been processed to a desired particle size and/or blended 106 in order to prepare the sample for oral product processing, the sample may be encapsulated 110. It is contemplated that the encapsulation process may provide for low pH protection 112. For example, the encapsulation process may prevent or substantially prevent capsule shells, tablets, and/or troches from breaking down in the acidic environment of the stomach such that the MRT composition is released in the desired portion of the intestinal tract. It is contemplated that an enteric coated capsule may be needed to provide for protection in the stomach and have disintegration of the capsule in the small and large intestine. In some instances, the capsules may be pan coated with the enteric coating. Enteric coating materials may include fatty acids, waxes, shellac, plastics, and plant fibers. Pan coating of hydroxypropyl methylcellulose (HPMC), or also called Hypromellose capsules, will protect at low pH and also help to protect from moisture. Some suitable capsules may include DRcaps™ and Vcaps™ available from Capsugel®. Likewise, AR caps having a composition of 60% HPMC and 40% HPMCP (hypromellose phthalate) may have the same properties. Capsule types that are not gelatin may contain less water (gelatin caps usually 10 to 12% water, versus other polymer capsules have 3-4% or less water). Banding of the capsule with polymers that are insoluble in low pH environments may be required, as will be discussed in more detail below. In other instances, the capsules may be stacked such that 2 or more capsules are used to enclose the sample. For example, the sample may be placed in a capsule and then that capsule placed in another larger capsule. A stacked (e.g. two or more capsules) and/or banded capsule may survive in an acidic environment (e.g. the stomach) for at least two or more hours and dissolve in the more neutral intestinal tract.

In some instances, a capsule that has been banded with a low pH-resistant polymer may not fully disintegrate and/or release the product for 5 or more hours. This may allow the capsule to pass through the stomach intact and allow the product to be released into the intestines where the bacteria is desired. It is further contemplated that releasing the MRT composition into the more neutral environment of the intestines, as opposed to the acidic environment of the stomach (in the range of a pH of 1.2) may allow more bacteria to survive. Banding the capsule may include placing a band of low pH-resistant polymer over the region where the first capsule portion and the second capsule portion overlap. In other instances, two capsules (e.g., double encapsulation), where one capsule is disposed within another capsule, may allow the capsule to pass through the stomach intact and/or so that a desirable quantity of viable bacteria may reach the target region.

In some embodiments, superdisintegrants may be used to expand the dosage form (e.g. capsule or tablet) to improve the probability of bacteria contacting the intestinal wall. For example, cross-linked cellulose swells 4 to 8 times in 10 seconds, cross-linked starch swells 7 to 12 times in less than 30 seconds, and cross-linked alginic acid experiences rapid swelling in an aqueous medium or wicking action.

The presence of pre-biotics may be desired to ensure bacterial growth at site of action in the intestine. These are materials that can be added to the capsule formulation or dosed separately at the same administration time. Some suitable additives may include galactooligosaccharides, inulin-derivatives such as fructo-oligosaccharides, cellulose, dextrins, chitins, pectins, beta- glucans, waxes, lignin, phytochemicals (bioactive non-nutrient plant compounds present in fruits, vegetables, grains, and other plant foods), carotenoids, phenolics, alkaloids, nitrogen-containing and organosulfur compounds. It is contemplated that L-arginine and PEG excipients, in certain concentration ranges, may produce water and electrolyte secretion when the drug product is delivered. This may enhance the bacteria’s ability to attach and grow in the intestine. Other excipients that produce this effect may also improve the therapeutic effect. An oral product may be packaged in a number of different ways including, but not limited to, blister packaging or a bottle. In some instances, an oxygen scavenger and/or a desiccant may be placed in the bottle and/or blister packaging. The blister packaging and/or bottle may include features configured to make the packing child resistant. For example, a bottle may be provided with a child resistant cap and the blister pack may be provided with a child resistant outer sleeve. In some instances, the blister pack may include graphics designed to guide the patient on how to use the pack. For example, the blister pack may provide guidance on how many pills to take on a given day and/or what time of day to take the pills. The packaging may include monitoring devices to monitor the shipping conditions. As a nonlimiting example, the packaging containers can include an indicator of the minimum and the maximum temperature to which the product is exposed. As another non- limiting example, one or more temperature sensitive stickers that changes color at temperatures below about 4° C and temperatures greater than about room temperature (about 22-29° C.) can be affixed to the container.

Figures 3 and 4 are a flow charts depicting two illustrative methods 201, 300 for preparing a stool sample for MRT as an oral dosage. In some embodiments, the oral dosage may be prepared from a fresh stool sample (Figure 3) and in other embodiments, the oral dosage may be prepared from a substance that has already been processed (Figure 4). As used herein a fresh stool sample will be referred to as Drug Substance A and a sample that has been previously processed will be referred to as Drug Substance B. Other drug substances are contemplated includes substances derived from cultures of fecal microbiota. Referring first to Figure 3, the stool sample may first be collected and screened, for example, in the method described with respect to Figure 1. Once the sample has been accepted, the sample may be weighed into a filtration bag, as shown at step 200. It is contemplated that multiple collection containers (e.g. same or different donors and collected at various times) that are within their expiration data may be used (e.g. pooled together). The sample may be purified using centrifugation, membrane filtration, or a combination thereof to remove fecal material above a certain particle size. It is contemplated that since most bacteria of interest are in the range of 0.3 microns (pm) to 30 pm, the sample may be processed to remove particles greater than in the range of 50-70 pm. The sample may be processed to obtain an approximately 60% concentration of the bacteria. This may allow for an increased flexibility in the ratio of formulation excipients to bacteria for further processing.

A filter solution, or diluent, may be added to the filter bag, as shown at step 202. In some instances saline may be used as a diluent. For example a solution of 0.9% sodium chloride (NaCl) may be added to the filter bag at a ratio of approximately 3 milliliters (mL) per gram of Drug Substance A. In other instances, phosphate buffered saline may be added to the filter bag at a ratio of 1:1 (by weight). It is contemplated that other diluents, other diluent concentrations, and dilution rates may be used, as desired. For example, a mixture of saline and a cryoprotectant (e.g., polyethylene glycol (PEG) 3350) may be used as a diluent. The PEG concentration of the diluent can be approximately about 30-90 g/liter (or about 10-90 g/liter). The PEG concentration of the diluent can also be approximately between about 25-75 g/liter. In one example, the ratio of saline/PEG mixture to stool sample is 2:1, or 2 mL saline/PEG mixture to 1 gram human stool. However, in some instances, such as when Drug Substance A is being processed specifically for lyophilization, the diluent may not include a cryoprotectant. The sample may then be membrane filtered in a number of different ways, including, but not limited to the use of filter bags, pressure filters, and/or vacuum filters, as shown at step 204. In some instances, the sample may be filtered multiple times using a smaller filter membrane with each subsequent filtering. In one example, the sample may be placed in a 500 pm filter bag and agitated using, for example, Stomacher agitation at 230 rpm for approximately 2 minutes to obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be placed in a filter bag having a pore size smaller than 500 pm, for example, 280 pm. The sample may be agitated again using, for example, Stomacher agitation at 230 rpm with or without a diluent for approximately 4 minutes to obtain a filtrate having a particle size of approximately 280 pm or less. This filtrate may be placed in another filter bag having a pore size smaller than, for example, 280 pm, such as, but not limited to SO- VO pm. The sample may be agitated again using, for example, Stomacher agitation at 230 rpm with or without a diluent for approximately 4 minutes to produce a filtrate having a particle size of approximately 50-70 pm or less.

In another example, the sample may be placed in a 500 pm filter bag, with or without a diluent, and agitated using, for example, Stomacher agitation obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be processed using a pressure filter having a pore size of approximately 160 pm and the resulting filtrate processed using a pressure filter having a pore size of approximately 60 pm. In some instances, the sample may be need to be processed a second time using a bag filter having a pores size between 160 pm and 500 pm prior to using the pressure filter.

In another example, the sample may be placed in a 500 pm filter bag, with or without a diluent, and agitated using, for example, Stomacher agitation obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be processed using a vacuum filter having a pore size of approximately 160 pm and the resulting filtrate processed using a vacuum filter having a pore size of approximately 60 pm. In some instances, the sample may be need to be processed a second time using a bag filter having a pores size between 160 pm and 500 pm prior to using the pressure filter.

Once the sample has been processed to have a particle size of approximately 50-70 pm or less, the sample may then be placed into intermediate storage containers, as shown at step 206. An example of an acceptable intermediate storage container is a 250 mL sterile plastic container with lid. In some instances, the filtered suspension may be stored in the refrigerator at 5 ± 3°C for up to 5 days, although this is not required. The filtered suspension may be combined and mixed into larger containers, as shown at step 208. An example of an acceptable immediate storage container is a multiple liter sterile plastic container with lid.

Aliquots of the mixed filtered suspension may then be placed into centrifuge tubes, 50 to 500 mL in volume, as shown at step 210. The filtered suspension is filled to approximately 20 to 80% of the volume of the centrifuge tube. In some instances, centrifuge tubes having a volume of greater than 500 mL may be used. The filtered suspension may then be washed and further concentrated using a centrifuge, as shown at step 212. In one example, the samples may be centrifuged at 1100 to 3600 revolutions per minute (rpm) for 10 to 15 minutes cycles. In another example, the samples may be centrifuged at a rate such that the centrifugal force is in the range of about 8-12,000 g (e.g., about 10,000 g) for 15 - 45 minutes or 20 - 30 minutes. The centrifuge may be ramped up or gradually accelerated to the speed needed to create a centrifugal force in the range of about 8-12,000 g (e.g., about 10,000 g). It is further contemplated that the centrifuge may also be slowly ramped down or decelerated when the centrifugation process is complete. In some instances, it may be desirable to decelerate the centrifuge as slowly as possible so that the return to atmospheric pressure is slow so as to protect the bacterial cells from potentially bursting. The supernatant is removed and the remaining material in the tube is the purified intermediate MRT composition. This may result in a product that has been concentrated by approximately 60%.

In some instances, the centrifugation process may be a 2-tiered process. For example, the product may first undergo a “pre-spin”, (e.g., about 300-2000xg or about l,400xg for 1-5 minutes or for about 2 minutes) to remove fecal fibrous material and then may undergo a longer centrifugation to concentrate the product. For example, following the “pre-spin”, the supernatant may be transferred to a new centrifuge tube/bottle and then spun at a higher speed (e.g., about 5,000- 12, OOOxg or about 10,000xg for 30-60 minutes or for about 45 minutes). After the high-speed spin, the supernatant may be discarded and the recovered microbiota can be further processed. It is further contemplated that volumes of up to 300 mL may be centrifuged without resulting in a drop in the amount of concentration. In some instances, volumes of greater than 300 mL may be centrifuged. For example, as discussed above, the centrifuge volume may be selected as a percentage (for example, in the range of 60%) of the container volume. The resulting MRT composition is a bacterial suspension having a particle size of 70 pm or less and a bacterial concentration on the order of approximately IxlO¹⁰ CFU/g. The purified intermediate bacterial viability may be measured via a propidium monoazide (PMA) quantitative polymerase chain reaction (qPCR) method. The resulting MRT composition may also be stable for 3 weeks at refrigeration conditions.

In some embodiments, centrifugation alone can be used multiple times for purification and concentration. However, the particle size of the bacterial suspension may still be in a range (e.g. greater than 60 pm) that clogs pipet tips. Whether this is successful or not is dependent on the input fecal material, which is variable. It is further contemplated that a system of separators and decanters could be used if the batch size was in the range of several tens of liters, or more.

The intermediate MRT composition may be optionally transferred to an intermediate tube and, if necessary, shipped to a lyophilization facility, as shown at step 214. Purified intermediate may be shipped in a pre-qualified shipper for refrigeration conditions, 5 ± 3°C to the contract lyophilizer, if necessary, for lyophilization.

The purified intermediate may be mixed at a 1:1 ratio with a lyophilization excipient solution, as shown at step 216. The lyophilization excipient solution may be comprised of 2.3 % PEG 3350, 1% glycerin, 10% trehalose, and 10% sucrose. However, other lyophilization excipients may be used. Prior to adding the excipient solution to the purified intermediate, the lyophilization excipient solution (without glycerin) is filtered through a 0.2 pm filter. The glycerin is autoclaved at 121°C for a minimum of 15 minutes and added aseptically. Once the lyophilization excipients and purified intermediate have been mixed (lyophilization suspension), a single two hundred microliter (200 pL) aliquot of the lyophilization suspension is placed in each well of a 96-well plate, as shown at step 218 and lyophilized, as shown at step 220.

The lyophilization process will be described with further reference to Figure 5, which illustrates a flow chart of an illustrative lyophilization process 220. To perform the lyophilization, once filled, the 96-well plate may be wrapped in sterile bio shield, as shown at step 402. Other plate sizes are also contemplated. After all plates are wrapped, they may be immediately transported and loaded into the lyophilizer, as shown at step 404. The lyophilizer may be sealed and the lyophilization cycle initiated. Product is frozen by lowering the product shelf temperature to a range of approximately -40°C to -45°C, as shown at step 406. After the product is frozen, primary drying (sublimation) occurs by applying vacuum and elevating the shelf temperature up to 0°C, as shown at step 408. A secondary drying step is initiated to further reduce water content and bring the product to ambient temperature (approximately 25°C), as shown at step 410. The vacuum is released at the end of the secondary drying step and the product is removed from the lyophilizer, as shown at step 412. Product may be placed inside an anaerobic chamber for collection of the lyophilized aliquots. The lyophilized aliquots may be in pellet form and are transferred to a packaging with desiccant, as shown at step 414. Filled packages may be purged with nitrogen gas and heat- sealed, as shown at step 416. Returning now to Figure 3, if the intermediate MRT composition has been shipped off- site for lyophilization, the lyophilized pellets may then be shipped back to the MRT composition manufacturer, in a pre-qualified shipper for refrigeration conditions, as shown at step 222.

In some instances, it may be desirable for the lyophilized material or pellets to have a glass transition temperature (T_g) of greater than 30 °C. In some examples, the glass transition temperature may be in the range of 30 - 75 °C. This may result in a final product that is stable at room temperature. The glass transition temperature may also be used as a tool for screening the product received form the lyophilization process and/or for verifying the stablility of the final product. For example, the T_g may be used to predict stability of the product during storage. In some instances, a T_g of 50 °C above the storage temperature may allow the lyophilized intermediate and/or the final oral drug product to be stored for a period of time without a significant loss of bacteria.

Upon receipt of the lyophilized intermediate, it may be removed from the packaging and filled into capsules, as shown at step 224. The lyophilized intermediate may also be sampled and the total viability is measured via a PMA-qPCR method. Encapsulation may be conducted in a nitrogen-purged area at ambient temperature to minimize the exposure of the lyophilized intermediate to oxygen. The lyophilization intermediates are encapsulated in a hypromellose capsule. Multiple lyophilized intermediates can be loaded into a hypromellose capsule depending on the capsule size (e.g., sizes 1, 0, or 00).

The capsule may then be banded, as shown at step 226. In some instances, the capsules may be banded with hypromellose. In some instances, the banding material may be an anionic copolymer based on methacrylic acid and methyl methacrylate, such as, but not limited to Eudragit® L100. In other instances, the banding material may be hypromellose phthalate or hypromellose acetate succinate. These are just examples. The banding material may be any material which is resistant to low pH environments (e.g. the stomach) and degrades in high pH environments (e.g. the intestinal tract). A consistent banding thickness is applied to each capsule so the disintegration performance meets the acceptance limit. Alternatively, the capsules may not be banded and/or are otherwise free of a banding material. Capsules are stored at refrigeration conditions, 5 ± 3°C in a nitrogen-purged bulk plastic container or packaged with desiccant. Encapsulated and banded drug product may be packaged with desiccant and heat-sealed, as shown at step 228. In some instances, the encapsulated and banded drug product may be packaged in individual dosage quantities in metallized polyester/polyethylene bonded film. This may minimize the exposure of the drug product to oxygen and/or moisture which may cause degradation of the product. The metallized polyester/polyethylene bonded film may have a moisture vapor transmission rate of 0.02 gr/100 in² and an oxygen transmission rate of 0.0402/mL/100 in² in 24 hours. The bonded film packets may be provided to the patient in a child-resistant container to meet the need for childresistant clinical supply packaging. The child-resistant container may be a 40 dram (2.5 ounces) green pharmacy vial with a child-resistant cap. The vial may be made of translucent, light resistant polypropylene. The low density polyethylene (LDPE) child-resistant cap helps prevent unauthorized access by requiring that the user push down and rotate the cap to open the container.

Referring now to Figure 4, an illustrative method 300 for preparing a previously purified stool sample (Drug Substance B) for MRT as an oral dosage. Drug Substance B may be a fecal microbiota frozen preparation, prepared as an enema dosage form including human stool and a solution of 2.3% polyethylene glycol 3350 (or other cryoprotectant) and 0.9% sodium chloride solution for irrigation in a ratio 1 g of stool to 3 mL of solution. For example, Drug Substance B may have been processed in a manner similar to steps 200 through 212 described above, with the addition of a cryoprotectant at step 202. After the centrifugation process outlined at step 212, the purified intermediate (e.g. now Drug Substance B) may be refrigerated, frozen, or used for treatment.

Beginning at step 302, the frozen preparation may be thawed, if necessary, and placed into a filtration bag. It is contemplated that multiple collection containers (e.g. same or different donors and collected at various times) that are within their expiration data may be used. The sample may be purified using centrifugation, membrane filtration, or a combination thereof to remove fecal material above a certain particle size. It is contemplated that since most bacteria of interest are in the range of 0.3 microns (pm) to 30 pm, the sample may be processed to remove particles greater than in the range of 50-70 pm. The sample may be processed to obtain an approximately 60% concentration of the bacteria. This may allow for an increased flexibility in the ratio of formulation excipients to bacteria for further processing.

A filter solution, or diluent, may be added to the filter bag, as shown at step 304. In some instances saline may be used as a diluent. For example a solution of 0.9% sodium chloride (NaCl) may be added to the filter bag at a ratio of approximately 3 milliliters (mL) per gram of Drug Substance B. It is contemplated that other diluents, other diluent concentrations, and dilution rates may be used, as desired. The sample may then be membrane filtered in a number of different ways, including, but not limited to the use of filter bags, pressure filters, and/or vacuum filters, as shown at step 306. In some instances, the sample may be filtered multiple times using a smaller filter membrane with each subsequent filtering. In one example, the sample may be placed in a 500 pm filter bag and agitated using, for example, Stomacher agitation at 230 rpm for approximately 2 minutes to obtain a filtrate having a particle size of approximately 500 pm or less. This filtrate may then be placed in a filter bag having a pore size smaller than 500 pm, for example, 280 pm. The sample may be agitated again using, for example, Stomacher agitation at 230 rpm with or without a diluent for approximately 4 minutes to obtain a filtrate having a particle size of approximately 280 pm or less. This filtrate may be placed in another filter bag having a pore size smaller than, for example, 280 pm, such as, but not limited to 50-70 pm. The sample may be agitated again using, for example, Stomacher agitation at 230 rpm with or without a diluent for approximately 4 minutes to produce a filtrate having a particle size of approximately 50-70 pm or less.

Once the sample has been processed to have a particle size of approximately 50-70 pm or less, the sample may then be placed into intermediate storage containers, as shown at step 308. An example of an acceptable intermediate storage container is a 250 mL sterile plastic container with lid. In some instances, the filtered suspension may be stored in the refrigerator at 5 ± 3°C for up to 5 days, although this is not required. The filtered suspension may be combined and mixed into larger containers, as shown at step 310. An example of an acceptable immediate storage container is a multiple liter sterile plastic container with lid.

Aliquots of the mixed filtered suspension may then be placed into centrifuge tubes, 50 to 500 mL in volume, as shown at step 312. The filtered suspension is filled to approximately 20 to 80% of the volume of the centrifuge tube. In some instances, centrifuge tubes having a volume of greater than 500 mL may be used. The filtered suspension may then be washed and further concentrated using a centrifuge, as shown at step 314. In one example, the samples may be centrifuged at 1100 to 3600 revolutions per minute (rpm) for 10 to 15 minutes cycles. In another example, the samples may be centrifuged at a rate such that the centrifugal force is in the range of about 8-12,000 g (e.g., about 10,000 g) for 15 - 45 minutes or 20 - 30 minutes. The centrifuge may be ramped up or gradually accelerated to the speed needed to create a centrifugal force in the range of about 8-12,000 g (e.g., about 10,000 g). It is further contemplated that the centrifuge may also be slowly ramped down or decelerated when the centrifugation process is complete. In some instances, it may be desirable to decelerate the centrifuge as slowly as possible so that the return to atmospheric pressure is slow so as to protect the bacterial cells from potentially bursting. The supernatant is removed and the remaining material in the tube is the purified intermediate MRT composition. This may result in a product that has been concentrated by approximately 60%.

In some instances, the centrifugation process may be a 2-tiered process. For example, the product may first undergo a “pre-spin”, (e.g., about 300-2000xg or about l,400xg for 1-5 minutes or for about 2 minutes) to remove fecal fibrous material and then may undergo a longer centrifugation to concentrate the product. For example, following the “pre-spin”, the supernatant may be transferred to a new centrifuge tube/bottle and then spun at a higher speed (e.g., about 5,000- 12, OOOxg or about 10,000xg for 30-60 minutes or for about 45 minutes). After the high-speed spin, the supernatant may be discarded and the recovered microbiota can be further processed. It is further contemplated that volumes of up to 300 mL may be centrifuged without resulting in a drop in the amount of concentration. In some instances, volumes of greater than 300 mL may be centrifuged. For example, as discussed above, the centrifuge volume may be selected as a percentage (for example, in the range of 60%) of the container volume. The resulting MRT composition is a bacterial suspension having a particle size of 70 pm or less and a bacterial concentration on the order of approximately IxlO¹⁰ CFU/g. The purified intermediate bacterial viability may be measured via a propidium monoazide (PMA) quantitative polymerase chain reaction (qPCR) method. The resulting MRT composition may also be stable for 3 weeks at refrigeration conditions. In some embodiments, centrifugation alone can be used multiple times for purification and concentration. However, the particle size of the bacterial suspension may still be in a range (e.g. greater than 60 pm) that clogs pipet tips. Whether this is successful or not is dependent on the input fecal material, which is variable. It is further contemplated that a system of separators and decanters could be used if the batch size was in the range of several tens of liters, or more.

The intermediate MRT composition may be optionally transferred to an intermediate tube and, if necessary, shipped to a lyophilization facility, as shown at step 316. Purified intermediate may be shipped in a pre-qualified shipper for refrigeration conditions, 5 ± 3°C to the contract lyophilizer, if necessary, for lyophilization.

The purified intermediate may be mixed at a 1:1 ratio with a lyophilization excipient solution, as shown at step 318. The lyophilization excipient solution may be comprised of 2.3 % PEG 3350, 1% glycerin, 10% trehalose, and 10% sucrose. However, other lyophilization excipients may be used. Prior to adding the excipient solution to the purified intermediate, the lyophilization excipient solution (without glycerin) is filtered through a 0.2 pm filter. The glycerin is autoclaved at 121°C for a minimum of 15 minutes and added aseptically. Once the lyophilization excipients and purified intermediate have been mixed (lyophilization suspension), a single two hundred microliter (200 pL) aliquot of the lyophilization suspension is placed in each well of a 96-well plate, as shown at step 320 and lyophilized, as shown at step 322.

The purified intermediate may be mixed at a suitable ration (e.g., a 1:1 ratio) with a lyophilization excipient solution, as shown at step 318. In some instances, the lyophilization excipient may include polyethylene glycol (e.g., about 1-5%, or about 2-3%, or about 2.3%), trehalose (e.g., about 1-25%, or about 5-15%, or about 10%), sucrose (e.g., about 1-25%, or about 5-15%, or about 10%) and glycerin (e.g., about 0.1-5%, or about 0.5-2%, or about 1%) in purified water. For example, the lyophilization excipient solution may be comprised of 2.3 % PEG 3350, 1% glycerin, 10% trehalose, and 10% sucrose. However, other lyophilization excipients may be used. Prior to adding the excipient solution to the purified intermediate, the lyophilization excipient solution (without glycerin) is filtered through a 0.2 pm filter. The glycerin is autoclaved at 121°C for a minimum of 15 minutes and added aseptically. Once the lyophilization excipients and purified intermediate have been mixed (lyophilization suspension), a single two hundred microliter (200 p L) aliquot of the lyophilization suspension is placed in each well of a 96-well plate, as shown at step 320 and lyophilized, as shown at step 322.

Another example process may include manufacturing an MRT composition suitable for use as a drug administered via enema and/or suitable for use as the starting material for manufacturing a drug for oral administration. The process may include collecting a fresh human fecal sample from a pre-screened donor. Such processes may be similar to those disclosed herein and/or similar to those disclosed in U.S. Patent Nos. 9,675,648 and 9,629,881, which are herein incorporated by reference. In some instances, multiple samples from the same donor are collected and pooled. The pooled sample, which may also be termed the drug substance, may be stored at 5°C ± 3°C in a sterile microbiology container. One or more additional samples, and/or portions of the pooled sample, may be stored as a reserve samples in a sterile microbiology container in a -80°C freezer.

A portion of the pooled sample/drug substance (e.g., 50 ± 10g) may be taken from the pooled sample and disposed in a filter bag assembly. The filter bag assembly may include a filter bag within an outer closure bag. An excipient solution (e.g., which also may be understood to be a diluent, cryoprotectant, or other solution) may be added to the drug substance. The excipient solution may include 10-90g/L, or about 20-50g/L or about 30g/L polyethylene glycol (e.g., polyethylene glycol 3350 powder) in 0.9% sodium chloride. The excipient solution may be added at a suitable ratio such as l-5mL per 1g of drug substance (e.g., 3mL of the excipient solution per 1g of drug substance). The process of placing a portion/sample of pooled sample/drug substance into a filter bag assembly, followed by addition of the excipient solution, may be repeated until the pooled sample/drug substance is sufficiently used up. For example, if the weight of the remainder of the pooled sample/drug substance is 50 ± 10g or more, another sample of pooled sample/drug substance may be added to another filter bag assembly. Once the weight of the remainder of the pooled sample is less than 50 ± 10g, the remainder of the pooled sample/drug substance may be discarded and the filter bag assemblies may be closed.

One at a time, closed filter bag assemblies containing drug substance and excipient solution may be mixed. For example, the filter bag assemblies may be placed into the paddle mixer and processed (e.g., for about 2 minutes at a speed of about 230 RPM). The paddle mixer run time and speed may be electronically controlled, and the settings may be verified prior to manufacturing every batch.

The first filter bag assembly processed in the paddle mixer may be opened and the filtrate may be withdrawn and filled into cryo vials. The cryo vials can be submitted to quality control (QC) and stored in a -80°C freezer. Quality Control drug product release samples may be tested in a QC laboratory. Reserve samples may be stored in a -80°C freezer.

The fill tube cap of an ethylene vinyl acetate (EVA) enema bag may be removed and 150 ± 30g of the microbiota suspension (e.g., the filtered drug substance and excipient) may be withdrawn from the filter bag assembly and filled into the EVA bag through the fill port. When filling is complete, the fill tube cap is replaced, sealing the EVA bag prior to removal from the biosafety cabinet. The fill tube on the EVA bag may be sealed between the bag and fill cap using a tube sealer to prevent inadvertent opening of the container-closure. A tag labeled with drug product batch number, and a “quarantine” batch status sticker may be attached to every EVA enema bag.

The in-process drug product may be refrigerated at 5°C ± 3°C prior to freezing in a - 80°C freezer. The drug product can be held at 5 °C ± 3 °C for up to 24 hours prior to freezing in a -80°C freezer. The drug product (e.g., contained within the sealed enema bag) may be transferred from refrigerated storage to a designated -80°C drug product quarantine freezer. Quarantined drug product remains in this location until it is dispositioned by QC. If all donor and QC test results are acceptable the batch will be dispositioned as released. If results are not acceptable the batch will be dispositioned as rejected and discarded. Drug product dispositioned as accepted will be removed from the -80°C quarantine freezer, labelled “Accepted” and transferred to a designated released drug product -80°C freezer. The accepted, released drug product, which may be similar to Drug Substance B, may be thawed and administered to a patient (e.g., via enema). The released drug product may also be understood to be the suspended intermediate, suitable for use in manufacturing an oral MRT composition as described below.

Batch manufacturing of an oral MRT composition begins with selection of multiple bags of released drug product (e.g., where each bag of released drug product contains a frozen suspended intermediate manufactured as described above). Each of the bags of released drug product may be from the same donor. The selected bags may be thawed at a suitable temperature (e.g., room temperature) for a suitable time (e.g., about 2 hours) and a quantity (e.g., 500 g) of the suspended intermediate may be transferred into one or more 1-liter centrifuge bottles. A diluent may be added to the suspending intermediate. The diluent may be phosphate Buffered Saline (PBS) or another suitable diluent. The diluent may be added to the suspended intermediate in a suitable ratio (e.g., 1:1 ratio by weight), mixed by intermittent gentle shaking, and held for 30 minutes at 4°C. At this point, the sample may be termed the diluted intermediate.

The diluted intermediate may be differentially centrifuged. For example, the diluted intermediate may be centrifuged at a relatively low speed. For example, the diluted intermediate may be centrifuged for about 1-5 minutes (e.g., 2 min) at about 500-2, OOOxg, or about 1,000- l,500xg, or about l,400xg. The low speed centrifugation may occur at 4°C ± 3°C. The supernatant from this slow speed spin may be transferred into one or more new IL centrifuge bottles (e.g., containing bottle liners) for further processing, and the pelleted material may be discarded. The bottles containing the collected supernatant may then centrifuged at a relatively high speed. For example, the collected supernatant may be centrifuged at about 5,000-20,000, or about 8,000- 12, OOOxg, or about 10, OOOxg for about 15- 60 minutes (e.g., about 45 minutes). The high speed centrifugation may occur at 4°C ± 3°C. After the high-speed spin, the supernatant may discarded and the remaining pellet (e.g., which may be pellets if multiple bottles are centrifuged) are retained for further processing. The pellet(s) may be termed the recovered microbiota.

A lyophilization excipient/cryoprotectant may be added to the recovered microbiota in at a suitable ratio. For example, the lyophilization excipient may be added to the recovered mircrobiota at a 1:1 ratio (w/w). In some instances, the lyophilization excipient may include polyethylene glycol (e.g., about 1-5%, or about 2-3%, or about 2.3%), trehalose (e.g., about 1- 25%, or about 5-15%, or about 10%), sucrose (e.g., about 1-25%, or about 5-15%, or about 10%) and glycerin (e.g., about 0.1-5%, or about 0.5-2%, or about 1%) in purified water. For example, the lyophilization excipient solution may be comprised of 2.3 % PEG 3350, 1% glycerin, 10% trehalose, and 10% sucrose. The mixture contained in the bottle liner may be mixed using a paddle mixer to form a uniform suspension. The resuspended microbiota solution may be aliquoted into 96-well plates (e.g., 200 pl per well) and subjected to a lyophilization process. Other plate type may be utilized and/or a single well dish. An example lyophilization process will be described with further reference to Figure 5, which illustrates a flow chart of an illustrative lyophilization process 220/322. To perform the lyophilization, once filled, the 96- well plate may be wrapped in sterile bio shield, as shown at step 402. Other plate sizes are also contemplated. In some embodiments, a tray having zero wells may also be used. This may maximize the volume available to receive the lyophilized suspension, which may increase efficiency in the lyophilization process. After all plates are wrapped, they may be immediately transported and loaded into the lyophilizer, as shown at step 404. The lyophilizer may be sealed and the lyophilization cycle initiated. Product is frozen by lowering the product shelf temperature to a range of approximately -40°C to -45°C, as shown at step 406. After the product is frozen, primary drying (sublimation) occurs by applying vacuum and elevating the shelf temperature up to 0°C, as shown at step 408. A secondary drying step is initiated to further reduce water content and bring the product to ambient temperature (approximately 25°C), as shown at step 410. The vacuum is released at the end of the secondary drying step and the product is removed from the lyophilizer, as shown at step 412. Product may be placed inside an anaerobic chamber for collection of the lyophilized aliquots. The lyophilized aliquots may be in pellet form and are transferred to a packaging with desiccant, as shown at step 414. Filled packages may be purged with nitrogen gas and heat-sealed, as shown at step 416. If the intermediate MRT composition has been shipped off- site for lyophilization, the lyophilized pellets may then be shipped back to the MRT composition manufacturer, in a pre-qualified shipper for refrigeration conditions, as shown at step 324. In some instances, the lyophilized pellets may be termed the lyophilized intermediate.

In some instances, the composition of the lyophilized intermediate (% w/w) may include the processed microbiota (e.g., about 10-75%, or about 40-60%, or about 45-50%, or about 47.9%), polyethylene glycol (e.g., about 1-10%, or about 3-8%, or about 5.2%), glycerin (e.g., about 0.5-5%, or about 1-4%, or about 2.2%), trehalose (e.g., about 10-40%, or about 20- 30%, or about 22.4%), and sucrose (e.g., about 10-40%, or about 20-30%, or about 22.4%). The processed microbiota may include about 1 x 10⁵ to 1 x 10¹² viable bacteria, or about 1 x 10⁶ to 1 x 10¹¹ viable bacteria, or about 1 x 10⁷ to 1 x 10¹⁰ viable bacteria. It can be appreciated that the composition of the lyophilized intermediate, which may be mechanically processed prior to being placed into a capsule, represents the composition of the active ingredient of the oral MRT composition. The disclosed compositions result when the manufacturing process utilizes a lyophilization excipient that includes polyethylene glycol (e.g., about 1-5%, or about 2-3%, or about 2.3%), trehalose (e.g., about 1-25%, or about 5-15%, or about 10%), sucrose (e.g., about 1-25%, or about 5-15%, or about 10%) and glycerin (e.g., about 0.1-5%, or about 0.5-2%, or about 1%) in purified water.

In some instances, it may be desirable for the lyophilized pellets to have a glass transition temperature (T_g) of greater than 30 °C. In some examples, the glass transition temperature may be in the range of 30 - 75 °C. This may result in a final product that is stable at room temperature. The glass transition temperature may also be used as a tool for screening the product received form the lyophilization process and/or for verifying the stability of the final product. For example, the T_g may be used to predict stability of the product during storage. In some instances, a T_g of 50 °C above the storage temperature may allow the lyophilized intermediate and/or the final oral drug product to be stored for a period of time without a significant loss of bacteria.

Upon receipt of the lyophilized intermediate, it may be removed from the packaging, milled or otherwise broken into smaller particles and/or a powder-like consistency, and the milled material may be filled into capsules, as shown at step 326. The lyophilized intermediate may also be sampled and the total viability is measured via a PMA-qPCR method (e.g., example methods are disclosed in U.S. Patent Application Pub. No. US 2017/0327862, which is herein incorporated by reference). Encapsulation may be conducted in a nitrogen-purged area at ambient temperature to minimize the exposure of the lyophilized intermediate to oxygen. The lyophilization intermediates are encapsulated in one or more hypromellose capsules. Multiple lyophilized intermediates (e.g. multiple pellets) can be loaded into a hypromellose capsule depending on the capsule size (e.g., sizes 1, 0, or 00). For example, the milled drug product may be encapsulated in a size 0 capsule using manual capsule filling equipment within an NF-grade nitrogen purged glove box. Content uniformity among the capsules may be tested for the filled capsules. These capsules may be then filled into size 00 capsules. In other words, the drug product may be double encapsulated.

Optionally, the capsule may then be banded, as shown at step 328. In some instances, the capsules may be banded with hypromellose. In some instances, the banding material may be Eudragit E100, hypromellose phthalate, or hypromellose acetate/succinate. These are just examples. The banding material may be any material which is resistant to low pH environments (e.g. the stomach) and degrades in high pH environments (e.g. the intestinal tract). A consistent banding thickness is applied to each capsule so the disintegration performance meets the acceptance limit. Capsules are stored at refrigeration conditions, 5 ± 3°C in a nitrogen-purged bulk plastic container or packaged with desiccant. The capsules may be packaged with desiccant and heat-sealed, as shown at step 330. In some instances, the capsules may be packaged in individual dosage quantities in metallized polyester/polyethylene bonded film. This may minimize the exposure of the drug product to oxygen and/or moisture which may cause degradation of the product. The metallized polyester/polyethylene bonded film may have a moisture vapor transmission rate of 0.02 gr/100 in² and an oxygen transmission rate of 0.0402/mL/100 in² in 24 hours. The bonded film packets may be provided to the patient in a child-resistant container to meet the need for child-resistant clinical supply packaging. The child-resistant container may be a 40 dram (2.5 ounces) green pharmacy vial with a child-resistant cap. The vial may be made of translucent, light resistant polypropylene. The low density polyethylene (LDPE) child-resistant cap helps prevent unauthorized access by requiring that the user push down and rotate the cap to open the container.

In at least some instances, the moisture content of the encapsulated drug product (e.g., including the double encapsulated drug product) is less than or equal to about 10%, or about less than or equal to about 8%, or less than or equal to about 6%. In at least some instances, the encapsulated drug product is packaged to limit/minimize any further moisture update.

In at least some instances, the drug product may include about 10% or more bacteria from the class Bacteroidia, or about 15% or more bacteria from the class Bacteroidia, or about 20% or more bacteria from the class Bacteroidia.

The encapsulated drug product (e.g., the capsules) may be administered to a patient. This may include administering the capsules (e.g., which may also be termed doses) to a patient using a suitable dosing regimen. This may include administering one or more capsules to the patient. For example, the 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more capsules may be administered to the patient. In some of these and in other instances, the capsules may be administered to the patient on one or more days. For example, the capsules may be administered over 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more days. In some of these and in other instances, the capsules may be administered to the patient one or more times per day to the patient. For example, the capsules may be administered 1, 2, 3, 4, 5, 6, or more times per day to the patient.

One example dosing regimen may include administering two doses/capsules to the patient two times per day for two days. Another example dosing regimen may include administering four doses/capsules to the patient two times per day for two days. Another example dosing regimen may include administering four doses/capsules to the patient two times per day for four days. Another example dosing regimen may include two doses/capsules per day to the patient for four days. Another example dosing regimen may include one dose/capsule per day to the patient for eight days. There are just examples. In these examples, each dose/capsule may include a lyophilized material. The lyophilized material may include fecal microbiota. The viable bacterial content (e.g., the viable bacterial content of fecal microbiota in the lyophilized material) may be about 1 x 10⁶ to 1 x 10¹¹ colony forming units (CFU) per capsule (or more), or about 1 x 10⁷ to 1 x 10¹⁰ CFU/capsule, or about 1 x 10⁷ or more CFU/capsule, or about 1 x 10⁸ to 1 x 10¹⁰ colony forming units (CFU) per capsule or about 8 x 10⁸ to 2 x 10⁹ CFU/capsule (e.g., at the time of dosing). In some instances, the lyophilized material may include a lyophilization excipient. The lyophilization excipient may include one or more of polyethylene glycol, trehalose, sucrose, and glycerin (e.g., such as those lyophilization excipients described herein).

U.S. Patent Application Pub. No. US 2018/0289750 is herein incorporated by reference.

U.S. Patent No. 10,226,431 is herein incorporated by reference.

The disclosure may be further clarified by reference to the following Examples, which serve to exemplify some embodiments, and not to limit the disclosure.

for MRT Sample Formulations

The collapse temperature results for twelve sample microbiotia restorative therapy formulations were identified. The collapse temperature may be used to assist in developing optimal formulations and lyophilization cycle parameters to freeze-dry this type of product in a reasonable amount of time without compromising its physical or chemical integrity. A standard lyophilization cycle was executed for these formulations and contained anaerobic microbial cell suspensions.

Materials and Methods for Freeze

Twelve formulations were utilized for testing. Each base consisted of skim milk 10%, ascorbic acid 1%, gelatin 1.4% and charcoal 0.3%. Ingredients were food grade, USP or NF grade chemicals. The base was then supplemented with each of the following additives:

• Trehalose 10% and Sucrose 10%

• Sucrose 10% and Inositol 5%

• Trehalose 10% and Glycerol 1%

• Raffinose 10% and Inositol 5%

• Raffinose 10% and Glycerol 1%

• Glucose 5% and Inositol 5%

• PEG 1% and Sucrose 10%

• PEG 1% and Glycerol 1%

• Trehalose 10%, Sucrose 10% and Glycerol 1%

• Sucrose 10% and Lactose 8%

• Trehalose 10% and Inositol 5%

• PEG 1% and Lactose 8%

The formulations were prepared. The freeze-dry microscopy instrument consisted of a Olympus BX53 polarized light microscope with a Linkam FDCS196 thermal stage, a T 95 system controller, a LNP liquid nitrogen pump, and an Edwards E2M1.5 vacuum pump. A 20 microliter (pL) aliquot of a 100 milliliter (ml) sample was placed on a glass slide which had been placed on the thermal stage after applying a small drop of silicone oil. A small coverslip was placed over the sample and the chamber was sealed. The sample was then cooled to -45 degree Celsius (°C) at 10 °C/minute. The temperature at which the material became frozen during the cooling stage was recorded. Once the temperature dropped to -45 °C, the vacuum was initiated. The product sample was then warmed at l°C/minute. The product sample was monitored continuously during the cycle to observe the drying and sublimation fronts. Once evidence of collapse was observed the temperature was recorded. Table 3 is a summary of the freezing temperature and the collapse temperature for each of the formulations.

Table 3. Freezing temperatures and collapse temperatures recorded for each formulation.

Lyophilization cycles are influenced by a variety of factors including percent solids in the formulations, vial size and diameter, collapse temperatures, chamber pressures, shelf temperatures, product resistance, etc. The chamber pressure and shelf temperature necessary to complete the primary drying process is determined by the thermal characteristics of the formulation, mainly the collapse temperature. The primary drying temperature is colder than the collapse temperature to account for product warming that occurs from increased resistance from the growing dried layer. Three cycles were designed based on the combination of factors above. All cycle times were less than 48 hours to complete. Table 4 is a summary of the drying temperature and chamber pressures for the lyophilization cycles based on critical collapse temperatures.

Table 4. Primary drying temperatures and chamber pressures for the Lyophilization cycles based on critical collapse temperatures.

A lyophilization cycle was designed based on data collected during the freeze dry microscopy studies. A pilot lyophilization cycle was conducted for each of the formulations to test for cake structure and survival of a bacterial cell mixture. Harvesting of cells and dispensing of the suspension were completed based on protocols established by Gibson Bioscience to obtain microbial ranges of 10e7 to 10e8 colony forming units per 100 microliter aliquot of the mix. The microorganism stocks used were selected from the first phase of the study and included the following anaerobes: Bacteroides uniformis ATCC 8492™, Alistipes putredinis ATCC 29800™, Ruminococcus gnavus ATCC 29149™ and Bacteroides ovatus ATCC 8484™.

The number of viable cells (CFU) before and after lyophilization was determined by serial dilution method. Dilutions consisted of the following levels: 10e3, 10e5, 10e7, and 10e9. Pellet samples were rehydrated in ImL of Phosphate Buffered Saline. All samples were plated to pre-reduced CDC Anaerobic Blood Agar and selective Bacteroides Bile Esculin Agar in duplicate. Agar plates were incubated at 35-37 °C for 48 hours in an anaerobic atmosphere. The lyophilization cycles produced good quality cake structures for all formulations. Pellets were solid and uniform in appearance. Each lyophilized pellet dissolved within 30 seconds upon rehydration in 1.0 mL of Phosphate Buffered Saline. Survival rates were calculated as a percentage of the total number of bacterial colony forming units after freeze- 5 drying divided by the total number of bacterial colony forming units before freeze-drying. Colony Forming Units were based on the mix of the 4 organisms. The viability and percent survival of total colony forming units for each formulation are summarized in Tables 5 and 6.

* Based on Log Transformed Data

10 Table 5. Viability and percent survival of total colony forming units for each formulation inoculated directly to CDC Anaerobic Blood Agar.

Based on Log Transformed Data

Table 6. Viability and percent survival of total colony forming units for each formulation inoculated directly to selective Bacteroides Bile Esculin Agar.

5 Based on the data collected, the selected anaerobes showed the highest survival rate when the combination of Trehalose and Sucrose or Sucrose and Inositol were utilized in the base formulation. This was true for recovery on both CDC Anaerobic Blood Agar and selective Bacteroides Bile Esculin Agar. These results indicate that the combination of Trehalose and Sucrose or Sucrose and Inositol provide the best protection for Bacteroides sp. during 10 lyophilization.

Example 3: Bacterial stability of solid product during storage

A study was preformed to determine the stability of the packaged encapsulated capsule after manufacturing and upon storage. A standard microbiological plating method, a molecular non-culture PMA-qPCR method, and 16s rRNA gene sequencing of both PMA and 15 non-PMA treated samples were employed to characterize the active component (bacteria) present in the solid drug product. The plating and total viability stability data indicate that a lyophilized packaged, encapsulated product (using a first lyophilization process) is more stable at colder storage conditions (5 ± 3 °C) than at higher storage temperatures and relative humidity (25 ± 2°C/ 60% ± 5% RH and 30 ± 2°C/65% ± 5% RH). The plating and total viability stability data for a lyophilized packaged, encapsulated product (using a second lyophilization process) indicates that packaged, encapsulated product is stable at both 5 ± 3 °C and 25 ± 2°C storage temperatures.

suitable for use as a a enema and/or suitable for use as the

material for

for oral administration

NOTE: Steps 1-3 may be performed within a Type II Class B2 biosafety cabinet. All instruments used to manipulate drug substance, excipient solution or drug product formulation (i.e. tongue depressors, serological pipettes) are single use instruments provided pre- sterilized by the manufacturer. Filter bags, closure bags and EVA bags are also provided pre- sterilized by the manufacturer.

Step 1 - Collect Donor Pooled Drug Substance Test Sample and Drug Substance Reserve Samples

A fresh human fecal sample can be collected from a pre-screened donor. In some instances, multiple samples from the same donor are collected and pooled. The pooled sample may be stored at 5°C ± 3°C in a sterile microbiology container. One or more additional samples, and/or portions of the pooled sample, may be stored as a reserve samples in a sterile microbiology container in a -80°C freezer.

Step 2 - Dispense Drug Substance

A 50 ± 10g sample (e.g., the drug substance) may be taken from the pooled sample and disposed in a filter bag assembly. The filter bag assembly may include a filter bag within an outer closure bag.

Step 3 - Dispense Excipient Solution

An excipient solution (e.g., which also may be understood to be a diluent, cryoprotectant, or other solution) may be added to the drug substance. The excipient solution may include 30g/L polyethylene glycol (e.g., polyethylene glycol 3350 powder) in 0.9% sodium chloride. The excipient solution may be added at a ratio of 3mL of the excipient solution per 1g of drug substance. If the weight of the remainder of the pooled sample is 50 ± 10g or more, steps 2 and 3 may be repeated. If the weight of the remainder of the pooled sample is less than 50 ± 10g, the remainder of the pooled sample may be discarded and the filter bag assemblies may be closed.

Step 4 - Mixing and Filtration

One at a time, closed filter bag assemblies containing drug substance and excipient solution are placed into the paddle mixer and processed for 2 minutes at a speed of 230 RPM. The paddle mixer run time and speed are electronically controlled, settings are verified prior to manufacturing every batch.

NOTE: Steps 5-6 are performed within a Type II Class B2 biosafety cabinet.

Step 5 - Collect Drug Product Quality Control and Reserve Samples

The first filter bag processed in the paddle mixer is opened and the filtrate may be withdrawn and filled into cryo vials. The cryo vials can be submitted to quality control (QC) and stored in a -80°C freezer. QC samples are only collected from the first dose manufactured for each batch.

Step 5A - Drug Product Quality Control Release Testing

Quality Control drug product release samples are tested in a QC laboratory. Reserve samples may be stored in a -80°C freezer.

Step 6 - Filling

The fill tube cap of an ethylene vinyl acetate (EVA) enema bag may be removed and 150 ± 30g of the microbiota suspension (e.g., the filtered drug substance and excipient) is withdrawn from the filter bag assembly and filled into the EVA bag through the fill port. When filling is complete, the fill tube cap is replaced, sealing the EVA bag prior to removal from the biosafety cabinet.

Step 7 - Seal EVA Bag

The fill tube on the EVA bag may be sealed between the bag and fill cap using a tube sealer to prevent inadvertent opening of the container-closure.

Step 8 - Attach Batch Identification Tags and Quarantine Labels

A tag labeled with drug product batch number, and a “quarantine” batch status sticker is attached to every EVA enema bag.

Step 9 - Refrigerate Drug Product at 5°C ± 3°C The in-process drug product is refrigerated at 5°C ± 3°C prior to freezing in a -80°C freezer. The drug product can be held at 5 °C ± 3 °C for up to 24 hours prior to freezing in a -

80°C freezer.

Step 10 - Freeze Drug Product in a -80°C Freezer

The drug product (e.g., contained within the sealed enema bag) may be transferred from refrigerated storage to a designated -80°C drug product quarantine freezer. Quarantined drug product remains in this location until it is dispositioned by QC.

Step 11 - Drug Product Disposition

If all donor and QC test results are acceptable the batch will be dispositioned as released. If results are not acceptable the batch will be dispositioned as rejected and discarded.

Step 12 - Release Drug Product

Drug product dispositioned as accepted will be removed from the -80°C quarantine freezer, labelled “Accepted” and transferred to a designated released drug product -80°C freezer. The accepted, released drug product may be thawed and administered to a patient (e.g., via enema).

Example 5 : Example process for manufacturing an oral MRT composition from the released

Step 1 - Thaw Suspended Intermediate

Batch manufacturing of an oral MRT composition begins with selection of multiple bags of released drug product (e.g., where each bag of released drug product contains a frozen suspended intermediate manufactured as described in Example 4). Each of the bags of released drug product are from the same donor. The selected bags are thawed at room temperature for at least 2 hours and 500 g of suspended intermediate is transferred into 1 -liter centrifuge bottles.

Step 2 - Add Diluent

Phosphate Buffered Saline (PBS) may be added to the Suspended Intermediate in a 1:1 ratio by weight, mixed by intermittent gentle shaking, and held for 30 minutes at 4°C.

Step 3 - Differential Centrifugation

The diluted intermediate may be centrifuged for 2 min at l,400xg and 4 °C ± 3 °C. The supernatant from this slow speed spin may be transferred into new IL centrifuge bottles containing bottle liners for further processing, and the pelleted material is discarded. The bottles containing the collected supernatant may then centrifuged at 10,000xg for 45 mins at 4°C ± 3°C. After the high-speed spin, the supernatant may discarded and the recovered microbiota are retained for further processing.

Step 4 - Resuspend the recovered microbiota with lyophilization excipient solution A lyophilization excipient/cryoprotectant may be added to the recovered microbiota in a 1:1 ratio (w/w). The lyophilization excipient may include 2.3 % polyethylene glycol (e.g., PEG 3350), 10% trehalose, 10% sucrose, and 1% glycerin in purified water. The mixture may be mixed using a paddle mixer to form a uniform suspension.

Step 5 - Lyophilization The resuspended microbiota solution is aliquoted into 96-well plates (200 pl per well) and placed into a qualified lyophilizer. Lyophilization steps are described in the following table.

Table 7: Lyophilization Cycle Details

Step 6 - Milling Operation

Within a NF-grade-nitrogen purged glove box workstation, lyophilized drug pellets are milled through a low energy mill.

Step 7 - Double Encapsulate Milled drug is encapsulated in size 0 capsules using manual capsule filling equipment within an NF-grade nitrogen purged glove box. Content uniformity among the capsules is tested for the filled capsules. These capsules are then filled into size 00 capsules.

Step 7A - Fill Uniformity Testing (g/capsule)

A representative sample set of filled size 0 capsules is weighed to ensure uniformity of fill.

Step 8 - Bulk Pack and Label

Capsules are individually enclosed in aluminum- aluminum blister packaging with child resistant lidding foil. The blister packs are labeled and packed in dose cartons, then stored at 5°C ± 3°C.

Step 9 - Collet Final Drug Product QC, Stability and Reserve Samples

A representative sample of the filled size 00 capsules is tested for product release.

Step 9A: Final Drug Product Release Testing

The drug product may be tested for release.

Step 10 - Quarantine Hold

Bulk packed capsules are placed in refrigerated storage designated for quarantined drug product until packaging.

Step 11 - Final Product Disposition

If all QC test results and batch record review requirements are acceptable, the batch will be dispositioned as accepted. If results are not acceptable the batch will be dispositioned as rejected and discarded. Quality assurance will disposition Final Product batches as accepted or rejected.

Step 12 - Final Pack and Label

Step 13 - Release

Product batches dispositioned as accepted will be removed from quarantined drug product storage, labelled “Accepted” and transferred to designated released drug product storage at 5°C ± 3°C. Processing Hold Times: Hold times for each intermediate step are presented below in Table 8.

Table 8. Processing Hold Times

Example 6 - Batch Formula

Table 9. Batch Formula of Microbiota Capsule Prior to Encapsulation

NA - not applicable ^aComponent is removed during processing; trace amounts of sodium chloride and phosphate salts may remain after purification ^bComponent removed during lyophilization

The starting material for each batch is 60 released doses of the released drug product as described in Example 4, equivalent to approximately 9000 g starting material, and results in recovery of approximately 1700 g of microbiota resuspended in lyophilization medium. This material is lyophilized in 96 well plates is performed which results in approximately 7700 lyophilized pellets. After milling of the lyophilized pellets, the powder yield is approximately 300 g. With a fill weight of 235 mg for each capsule, the theoretical yield of capsules is approximately 1200 capsules/batch. Despite donor to donor variability in the starting material, the estimated bacteria per mg is similar among donors and lots manufactured to date. The product is controlled by the fill weight. Example 6 - Description and Composition of Drug Product

The drug product is a concentrated, lyophilized microbial powder that is encapsulated in an enteric capsule. The drug product is composed of the following (see Tables 10-12):

Table 10. Drug Product Components

NA - not applicable ^aComponent is removed during processing; trace amounts of sodium chloride and phosphate salts may remain after purification ^bReferred to as trehalose throughout this document but is formally trehalose dihydrate ^cComponent removed during lyophilization ^dRefer to VCaps® capsule section 3.2.P.4.1

Milled lyophilized intermediate powder is filled and tamped into size 0 capsules without any additional excipients and over-encapsulated with size 00 capsules. The expected formulation percent concentrations are the same as the pre-encapsulation material.

Table 11. Composition of Lyophilized Intermediate in Each Capsule

Table 12 depicts the drug product presentation.

Table 12. Drug Product Presentation

7 - Treatment of Recurrent Clostridioides

Infections and/or

rCDI Recurrence

A Phase I open-label trial assessed the safety, efficacy in preventing rCDI recurrence, and intestinal microbiome effects of an oral MRT composition (e.g., RBX7455, a room temperature- stable, orally administered investigational live bio therapeutic) manufactured as described in these examples (e.g., Example 5). Adult participants with one or more prior episodes of rCDI received: four RBX7455 capsules twice daily for four days (Group 1); four RBX7455 capsules twice daily for two days (Group 2); or two RBX7455 capsules twice daily for two days (Group 3). For all groups, the first dose was administered in clinic, with remaining doses self- administered at home. Adverse events were monitored during and for 6 months after treatment. Treatment success was defined as rCDI prevention through 8 weeks after treatment. Participants’ microbiome composition was assessed prior to and for 6 months after treatment.

Nine of 10 Group 1 patients (90%), 8 of 10 Group 2 patients (80%), and 10 of 10 Group 3 patients (100%) were recurrence- free at the 8-week endpoint with durability to 6 months. Seventy-five treatment-emergent adverse events were observed in 27 participants with no serious investigational product-related events. Prior to treatment, participants’ microbiomes were dissimilar from the RBX7455 composition with decreased Bacteroidia- and Clostridia- class bacteria, whereas after treatment, responders’ microbiomes showed increased Bacteroidia and Clostridia.

In this study, three dosing regimens of RBX7455 were shown to be safe and effective at preventing rCDI for 8 weeks after treatment, with no additional recurrences for up to 6 months post-treatment. In addition, treatment with RBX7455 appeared to modify the microbiome in patients responding to therapy such that it converged toward the composition of RBX7455.

It should be understood that this disclosure is, in many respects, only illustrative. Changes may be made in details, particularly in matters of shape, size, and arrangement of steps without exceeding the scope of the disclosure. The invention’s scope is, of course, defined in the language in which the appended claims are expressed.

Claims

What is claimed is:

1. A method for treating a recurrent Clostridioides difficile infection, the method comprising: administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection; and wherein the oral microbiota restoration composition comprises a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

2. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering two doses of the oral microbiota restoration composition.

3. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering two doses of the oral microbiota restoration composition two times per day for two days.

4. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition.

5. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for two days.

6. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent

58 Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for four days.

7. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least eight doses of the oral microbiota restoration composition over at least two days.

8. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering eight or fewer doses of the oral microbiota restoration composition over at least two days.

9. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least sixteen doses of the oral microbiota restoration composition over at least two days.

10. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering sixteen or fewer doses of the oral microbiota restoration composition over at least two days.

11. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least sixteen doses of the oral microbiota restoration composition over at least four days.

12. The method of claim 1, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent

59 Clostridioides difficile infection includes administering sixteen or fewer doses of the oral microbiota restoration composition over at least four days.

13. A method for treating a recurrent Clostridioides difficile infection, the method comprising: administering one or more capsules containing a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin to a patient with one or more episodes of a recurrent Clostridioides difficile infection.

14. The method of claim 13, wherein administering one or more capsules includes administering two capsules.

15. The method of claim 13, wherein administering one or more capsules includes administering two capsules two times per day for two days.

16. The method of claim 13, wherein administering one or more capsules includes administering four capsules.

17. The method of claim 13, wherein administering one or more capsules includes administering four capsules two times per day for two days.

18. The method of claim 13, wherein administering one or more capsules includes administering four capsules two times per day for four days.

19. The method of claim 13, wherein administering one or more capsules includes administering at least eight capsules over at least two days.

20. The method of claim 13, wherein administering one or more capsules includes administering eight or fewer capsules over at least two days.

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21. The method of claim 13, wherein administering one or more capsules includes administering at least sixteen capsules over at least two days.

22. The method of claim 13, wherein administering one or more capsules includes administering sixteen or fewer capsules over at least two days.

23. The method of claim 13, wherein administering one or more capsules includes administering at least sixteen capsules over at least four days.

24. The method of claim 13, wherein administering one or more capsules includes administering sixteen or fewer capsules over at least four days.

25. A method for preventing a recurrent Clostridioides difficile infection, the method comprising: administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection; and wherein the oral microbiota restoration composition comprises a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

26. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering two doses of the oral microbiota restoration composition.

27. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering two doses of the oral microbiota restoration composition two times per day for two days.

28. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent

61 Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition.

29. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for two days.

30. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering four doses of the oral microbiota restoration composition two times per day for four days.

31. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least eight doses of the oral microbiota restoration composition over at least two days.

32. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering eight or fewer doses of the oral microbiota restoration composition over at least two days.

33. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least sixteen doses of the oral microbiota restoration composition over at least two days.

34. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent

62 Clostridioides difficile infection includes administering sixteen or fewer doses of the oral microbiota restoration composition over at least two days.

35. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering at least sixteen doses of the oral microbiota restoration composition over at least four days.

36. The method of claim 25, wherein administering one or more doses of an oral microbiota restoration composition to a patient with one or more episodes of a recurrent Clostridioides difficile infection includes administering sixteen or fewer doses of the oral microbiota restoration composition over at least four days.

37. A method for preventing a recurrent Clostridioides difficile infection, the method comprising: administering one or more capsules containing a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin to a patient with one or more episodes of a recurrent Clostridioides difficile infection.

38. The method of claim 37, wherein administering one or more capsules includes administering two capsules.

39. The method of claim 37, wherein administering one or more capsules includes administering two capsules two times per day for two days.

40. The method of claim 37, wherein administering one or more capsules includes administering four capsules.

41. The method of claim 37, wherein administering one or more capsules includes administering four capsules two times per day for two days.

42. The method of claim 37, wherein administering one or more capsules includes administering four capsules two times per day for four days.

43. The method of claim 37, wherein administering one or more capsules includes administering at least eight capsules over at least two days.

44. The method of claim 37, wherein administering one or more capsules includes administering eight or fewer capsules over at least two days.

45. The method of claim 37, wherein administering one or more capsules includes administering at least sixteen capsules over at least two days.

46. The method of claim 37, wherein administering one or more capsules includes administering sixteen or fewer capsules over at least two days.

47. The method of claim 37, wherein administering one or more capsules includes administering at least sixteen capsules over at least four days.

48. The method of claim 37, wherein administering one or more capsules includes administering sixteen or fewer capsules over at least four days.

49. A composition for treating a recurrent Clostridioides difficile infection, the composition comprising: a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

50. The composition of claim 49, wherein the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x IO¹⁰ colony forming units.

51. The composition of claim 49, wherein the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units.

52. A composition for preventing a recurrent Clostridioides difficile infection, the composition comprising: a lyophilized material comprising fecal microbiota, polyethylene glycol, trehalose, sucrose, and glycerin.

53. The composition of claim 52, wherein the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x IO¹⁰ colony forming units.

54. The composition of claim 52, wherein the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units.

55. The method of any one of claims 1-12, wherein each dose includes one or more capsules, and wherein the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to

1 x IO¹⁰ colony forming units per capsule.

56. The method of any one of claims 1-12, wherein each dose includes one or more capsules, and wherein the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to

2 x 10⁹ colony forming units per capsule.

57. The method of any one of claims 13-24, wherein the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x IO¹⁰ colony forming units per capsule.

58. The method of any one of claims 13-24, wherein the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units per capsule.

59. The method of any one of claims 25-36, wherein each dose includes one or more capsules, and wherein the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x IO¹⁰ colony forming units per capsule.

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60. The method of any one of claims 25-36, wherein each dose includes one or more capsules, and wherein the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units per capsule.

61. The method of any one of claims 37-48, wherein the viable bacterial content of fecal microbiota may be about 1 x 10⁷ to 1 x IO¹⁰ colony forming units per capsule.

62. The method of any one of claims 37-48, wherein the viable bacterial content of fecal microbiota may be about 8 x 10⁸ to 2 x 10⁹ colony forming units per capsule.

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