TW202227108A - Use of bacteria in bodyweight regulation - Google Patents

Abstract

The present invention resides in the discovery that the presence and quantity of certain bacterial species is significantly altered in the gastrointestinal tract of overweight individuals, especially those who fail to achieve weight loss after receiving fecal microbiota transplantation (FMT) treatment. Thus, methods are provided for promoting weight loss by way of modulating recipients' gastrointestinal tract bacteria profile as well as for predicting the likelihood of success in achieving weight loss following FMT treatment in certain individuals. Also provided are kits and compositions for use in these methods.

Description

Use of bacteria in body weight regulation

Related applications

This application claims priority from US Provisional Patent Application No. 63/067,217, filed on August 18, 2020, and US Provisional Patent Application No. 63/169,481, filed on April 1, 2021, the contents of each of which are for all purposes The purpose is hereby incorporated by reference in its entirety. This case concerns methods for promoting weight loss by modulating the recipient's gastrointestinal bacterial profile and for predicting the likelihood of successful weight loss following FMT treatment in certain individuals. This case is also about kits and compositions for use in these methods.

As living standards continue to improve, the number of overweight or even obese individuals is rapidly increasing globally. Since serious health risks are directly related to being overweight, this trend toward an increasing proportion of overweight people in the general population has led to a significant increase in the incidence of many diseases, including type 2 diabetes (T2D), heart disease, hypertension, and stroke. . For example, the World Health Organization (WHO) estimates that by 2030, the number of people living with diabetes will exceed 350 million worldwide. Due to the rising incidence of obesity-related diseases, its severe health impacts, and its profound economic consequences, there is an urgent need for new and effective means of treating individuals who are already overweight or obese, or at risk of becoming overweight or obese, in order to Help them reduce or maintain their weight to a lower and healthier amount to achieve or maintain normal cholesterol levels, including low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL- C) amount) and triglyceride amounts, and ultimately reduce or eliminate their subsequent risk of serious diseases such as diabetes and cardiovascular disease. The present invention fulfills this and other related needs by providing novel methods and compositions that are effective in regulating the body weight of patients and which are useful in treating obesity or T2D or reducing the risk of obesity or T2D. risk.

The present invention relates to novel methods for promoting weight loss in overweight or obese patients, for treating or reducing the risk of developing obesity or T2D, and for assessing the likelihood that a patient can successfully achieve weight loss by FMT Methods and compositions. In particular, the inventors of the present application have discovered that depending on whether an individual is able to successfully reduce their body weight following an FMT procedure, certain microbial species, especially certain bacteria, are present in the individual's gastrointestinal (GI) tract as Significantly different amounts exist. Health benefits associated with weight loss, such as improvements in blood sugar, triglycerides, and/or by modulating the amount of relevant microbes in the patient's gut, such as by fecal microbiota transplantation (FMT) treatment or oral administration of beneficial bacteria, can be achieved cholesterol, and thus reduce the risk of serious medical conditions such as heart disease, high blood pressure, stroke and diabetes. These findings also provide new ways to assess or predict whether an individual will successfully achieve weight loss goals with FMT. Accordingly, in a first aspect, the present invention provides a novel method for weight loss comprising reducing the amount of one or more of the bacterial species specified in Table 1 in the gastrointestinal tract of an overweight individual, reducing overweight or obesity-related health risks.

In some embodiments, the introducing step comprises orally administering to the individual a composition comprising an effective amount of one or more species. In some embodiments, the introducing step comprises delivering a composition comprising an effective amount of one or more species to the small intestine, ileum, or large intestine of the individual. In some embodiments, the introducing step comprises fecal microbial phase transplantation (FMT). In some embodiments, the FMT comprises administering to the recipient a composition comprising the processed donor fecal material. In some embodiments, the composition is administered orally; or the composition is deposited directly into the recipient's gastrointestinal tract. In some embodiments, the composition administered to an individual consists essentially of one or more species and one or more pharmaceutically acceptable excipients. In some embodiments, the amount or relative abundance of one or more bacterial species is determined in a first stool sample obtained from the recipient prior to the introducing step and a second stool sample obtained from the recipient after the introducing step. In some embodiments, the amount of one or more species is determined by polymerase chain reaction (PCR), especially quantitative PCR. In some embodiments, the species administered to the recipient comprises one or more selected from the group consisting of Anaerostipes hadrus , Collinsella tanakaei , and Roseburia hominis .

In a second aspect, the present invention provides kits for the treatment of overweight or obese individuals for the purpose of facilitating their weight loss efforts. The set comprises: a first container and a second container, the first container contains a first composition, the first composition contains an effective amount of one of the bacterial species shown in Table 1, the second The container contains a second composition comprising an effective amount of another of the species shown in Table 1.

In some embodiments, the first composition comprises processed donor fecal material for FMT, eg, the material has been processed and formulated for oral administration, such as dried, frozen or lyophilized, and placed in capsules suitable for oral ingestion. In some embodiments, the second composition is formulated for oral administration. In some embodiments, both the first composition and the second composition are formulated for oral administration. In some cases, a kit may comprise two or more compositions, each comprising an effective amount of at least one, possibly two or even three different species independently selected from those shown in Table 1 , namely, Corynebacterium thaliana, Collins tanaka and Rhosbyllium hominis. In some embodiments, each composition consists essentially of one or more species and one or more pharmaceutically acceptable excipients. The compositions of the kit may each comprise a physiologically acceptable carrier or excipient suitable for the intended method of administration (eg, oral ingestion or rectal suppository).

In a third aspect, methods are provided for determining the likelihood of an individual achieving weight loss by an FMT procedure to be performed. The method comprises the steps of: (1) determining the amount or relative abundance of one or more bacterial species shown in Table 2 in a stool sample from the individual; (2) determining the same bacteria in a stool sample from a reference group The amount or relative abundance of the species, the reference cohort comprising individuals with FMT-induced weight loss after receiving the FMT program and individuals without FMT-induced weight loss after receiving the FMT program; (3) using the method from step (2) The obtained data generates a decision tree by a random forest model, and runs the amount or relative abundance of one or more bacterial species from step (1) along the decision tree to generate a score; and (4) will score greater than 0.5. Individuals judged to be likely to achieve weight loss by an FMT procedure planned to be performed on the individual at a later time, and individuals with a score of 0.5 or less were judged to be less likely to achieve weight loss by FMT performed on the individual at a later time Treatment achieves weight loss. In some cases, the one or more species comprises any two or three species shown in Table 2.

In a fourth aspect, a kit for assessing the likelihood of weight loss in an individual by the FMT procedure to be performed is provided. The kits contain reagents for the detection of one or more of the species shown in Table 2. In some embodiments, the reagents comprise a set of oligonucleotide primers for amplifying polynucleotide sequences from any of the species shown in Table 2, preferably unique to the species , thus allowing qualitative and quantitative detection of bacterial species. In some cases, the amplification reaction is PCR, preferably quantitative PCR.

In some embodiments, the one or more species comprise or consist of the candidate clade TM7 single cell isolate TM7c, Bacteroides stercoris , or Bacteroides dorei . In some embodiments, the one or more species comprise or consist of two species of the candidate clade TM7 single cell isolate TM7c, Bacteroides faecalis and Bacteroides donovani. In some embodiments, the one or more species comprise or consist of the candidate clade TM7 single cell isolate TM7c, Bacteroides faecalis, or Bacteroides donovani.

definition

The term "fecal microbiota transplantation (FMT)" or "fecal transplant" refers to a medical procedure during which fecal matter obtained from a healthy individual containing live fecal microorganisms (bacteria, fungi, viruses, etc.) is transferred into the recipient's gastrointestinal tract to restore a healthy gut microflora that has been disrupted or destroyed by any of a variety of medical conditions, such as overweight or obesity and related disorders. Typically, fecal matter from healthy donors is first processed into a suitable form for transplantation, which can be by direct deposition into the lower gastrointestinal tract, such as by colonoscopy, or by nasal cannula, or by Oral ingestion of packaged materials containing processed (eg, dried and frozen or lyophilized) fecal material is accomplished.

The term "inhibiting" or "inhibition" as used herein refers to any inhibitory effect on a target biological process such as RNA/protein expression of a target gene, biological activity of a target protein, cell signaling, cell proliferation, etc. Detection of negative effects. Typically, inhibition is reflected in the target process (eg, growth or proliferation of certain species of microorganisms, eg, one or more of the bacteria shown in Table 2), or in the downstream parameters mentioned above, when compared to a control A reduction of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more of any one. "Inhibition" also includes a 100% reduction, ie the complete elimination, prevention or abrogation of the target biological process or signal. Other related terms such as "suppressing", "suppression", "reducing", "reduction", "decrease", "decreasing", " "lower" and "less" are used in a similar manner in this disclosure to refer to a reduction of various amounts (eg, at least 10%, 20%, compared to a control amount (ie, the amount prior to inhibition) %, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more) until the target biological process or signal is completely eliminated. On the other hand, terms such as "activate", "activating", "activation", "increase", "increasing", "promote", " "promoting," "enhance," "enhancing," "enhancement," "higher," and "more" are used in this disclosure to encompass differences in the target process or signal A positive change in amount (e.g., at least 10%, 20%, 30%, 40%, 50%, 60% compared to a control amount (before activation), such as a control amount of one or more species shown in Table 1 %, 70%, 80%, 90%, 100%, 200% or greater, such as 3-fold, 5-fold, 8-fold, 10-fold, 20-fold increase). In contrast, the terms "substantially the same" or "substantially unchanged" mean little or no change in the amount from a comparison basis (eg, a standard control value), usually within ±10% of the comparison basis, or within ±10% of the comparison basis Within 5%, 4%, 3%, 2%, 1%, or even less variation.

The term "antibacterial agent" refers to any substance capable of inhibiting, inhibiting or preventing the growth or proliferation of bacterial species, especially those shown in Table 2, respectively. Known agents with antibacterial activity include various antibiotics that generally inhibit the proliferation of a broad spectrum of bacterial species as well as agents capable of inhibiting the proliferation of specific bacterial species, such as antisense oligonucleotides, small inhibitory RNAs, and the like. The term "antibacterial agent" is similarly defined to encompass agents that have broad-spectrum activity to kill nearly all species, as well as agents that specifically inhibit the proliferation of target species. Such specific antibacterial agents can be naturally short polynucleotides (eg, small inhibitory RNAs, microRNAs, miniRNAs, lncRNAs, or antisense oligonucleotides) that are capable of disrupting the life cycle of the target species The expression of key genes can therefore only specifically inhibit or eliminate this species without significantly affecting other closely related species.

"Percent relative abundance," when used in the context of describing the presence of a particular species (eg, any of those shown in either of Tables 1 or 2) in relation to all species present in the same environment, is Refers to the relative amount of the species in the amount of all species expressed as a percentage. For example, the relative abundance percentage of a particular species can be determined by comparing the amount of DNA specific for that species in a given sample (eg, as determined by quantitative polymerase chain reaction) with the amount of DNA from all bacteria in the same sample (eg, by quantitative polymerase chain reaction PCR and 16s rRNA sequence-based sequencing decisions).

"Absolute abundance," when used in the context of describing the presence of a particular species (eg, any of those shown in Tables 1 or 2) in stool, refers to the amount of all DNA in a stool sample from the species amount of DNA. For example, the absolute abundance of a bacterium can be determined by comparing the amount of species-specific DNA in a given sample (eg, as determined by quantitative PCR) to the amount of all fecal DNA in the same sample.

As used herein, the "total bacterial load" of a stool sample refers to the amount of all bacterial DNA in each of the amounts of all DNA in the stool sample. For example, the absolute abundance of bacteria can be determined by comparing the amount of bacterial-specific DNA (eg, 16 srRNA determined by quantitative PCR) in a given sample to the amount of all fecal DNA in the same sample.

The term "overweight" is used to describe individuals who are overweight and have a body mass index (BMI) greater than 25. The term encompasses "obesity" or "obesity," which describes a condition in which an individual has a BMI greater than 30.

The term "treat" or "treating" as used in this application describes an action that results in eliminating, reducing, alleviating, reversing, preventing and/or delaying the onset or recurrence of any symptoms of a predetermined medical condition. In other words, "treating" a condition encompasses both therapeutic and prophylactic interventions for the condition, including promoting a patient's recovery from the condition.

As used herein, the term "effective amount" refers to the use or administration of a substance (eg, an antibacterial agent) that results in a desired effect (eg, growth or The amount of the substance that inhibits or inhibits proliferation). Effects include preventing, inhibiting or delaying any relevant biological process during bacterial proliferation to any detectable extent. The exact amount will depend on the nature of the substance (active agent), the mode of use/administration, and the purpose of application, and will be determined by one of skill in the art using known techniques and those described herein. In another context, when an "effective amount" of one or more beneficial or desired species (eg, those listed in Table 1) is artificially introduced into the gastrointestinal tract of a patient, such as those to be used in FMT In the case of a composition, this means that the amount of the relevant bacteria introduced is sufficient to confer a health benefit to the recipient, such as reduced recovery time or reduced need for therapeutic intervention for related conditions such as overweight or obesity, including but not limited to drugs (eg appetite suppressants) and any of a variety of treatments such as behavior and communication therapy, educational therapy, family therapy, speech or physical therapy, etc.

A "pharmaceutically acceptable" or "pharmacologically acceptable" excipient is one that is not biologically deleterious or otherwise undesirable, ie, the excipient can be administered to an individual with the biologically active agent without Does not cause any undesired biological effects. The excipient also does not interact in a detrimental manner with any component of the composition containing it.

The term "excipient" refers to any substantially auxiliary substance that may be present in the final dosage form of the composition of the present invention. For example, the term "excipient" includes vehicles, binders, disintegrants, fillers (diluents), lubricants, glidants (flow enhancers), compression aids, colorants, sweeteners, preservatives agents, suspending/dispersing agents, film-forming/coating agents, flavoring agents and printing inks.

When used to describe a composition containing an active ingredient or ingredients, the term "consisting essentially of" refers to the fact that the composition does not contain any similar or related biological activity with the active ingredient or is capable of enhancing or inhibiting Active other ingredients, however one or more inactive ingredients such as physiologically or pharmaceutically acceptable excipients may be present in the composition. For example, substantially consist of an active agent (eg, Corynebacterium thaliana, Collins Tanaka, Collins Tanaka A composition consisting of one or more of R. hominis and R. hominis) is a composition that does not contain any detectable positivity that may be detected for the same target process (eg, inhibition of weight gain or progression of T2D) or any other agent that negatively affects or can increase the severity of disease in a recipient individual or can reduce the severity of disease in a recipient individual to any measurable degree.

As used herein, the term "about" refers to a range of values that is +/- 10% of the specified value. For example, "about 10" represents a range of values from 9 to 11 (10+/-1). Detailed description of the invention I. Introduction

The present invention provides new methods for achieving weight loss in an individual by altering the distribution of bacteria in the gastrointestinal tract of an individual, and assessing the likelihood of an individual achieving weight loss by fecal microbiological transplantation (FMT) treatment. In their studies, the inventors of the present application found that the presence and relative abundance of certain bacterial species were significantly altered in the gastrointestinal tract of overweight individuals who failed to lose weight following FMT treatment. For example, the presence and abundance of the species shown in Table 1 were found to be in elevated amounts in the gastrointestinal tract of those who successfully lost weight due to FMT, but not in the gastrointestinal tract of FMT recipients who failed to lose weight This increase was observed. On the other hand, it has been observed that the amount or relative abundance of certain bacterial species (such as those shown in Table 2) in individual stool samples correlates with the likelihood of successful weight loss after FMT. Thus, the results of this study provide a useful tool for promoting the effect of weight loss in overweight individuals and for assessing the prospects of overweight individuals achieving effective weight loss following FMT therapy. II. FMT Donor/Recipient Selection and Preparation

Overweight individuals suffering from a disrupted state of the gastrointestinal microflora are considered recipients of FMT therapy in order to restore the normal healthy distribution of microorganisms. As disclosed by the inventors of the present application, overweight individuals who have received FMT but have failed to lose weight tend to have reduced amounts of bacterial species in their gastrointestinal tract, as shown in Table 1, fecal material containing higher levels of these species An average amount of one or more of the FMT donors is particularly favored for subsequent FMT therapy for weight loss purposes. For example, for each of these species in the ideal donor stool sample, the ideal donor may preferably have about 0.01%, 0.02%, 0.05%, 0.10%, 0.20%, 0.40%, 0.50% higher than total bacteria %, 0.60%, 0.80%, 1.0%, 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 8.5%, 9.0% or higher relative abundance.

Fecal material used in FMT is obtained from healthy donors and then processed into the appropriate form for the intended means of delivery in the upcoming FMT procedure. While healthy individuals from the same family or family of recipients often serve as donors, donor microbial profile is an important consideration in practicing the present invention, and may instead favor the selection of unrelated donors. Methods of preparing donor material for transplantation include drying, freezing or lyophilization, and formulation or packaging steps, depending on the precise route of delivery to the recipient, eg, by oral ingestion or by rectal deposition.

Various methods for determining the amount of all bacterial species in a sample have been reported in the literature, for example, using sequence similarity in commonly shared 16S rRNA bacterial sequences to perform amplification of bacterial polynucleotide sequences (for example, by PCR) and sequencing. On the other hand, the quantity of any given species can be determined by the amplification and sequencing of its unique genomic sequence. Abundance percentage is often used as a parameter indicating the relative amount of bacterial species in a given environment. III. Therapeutic method by regulating bacterial load

The inventors' findings reveal a direct correlation between the prospect of an individual's weight loss and the presence and relative abundance of certain bacterial species, such as those shown in Tables 1 or 2, in an individual's gastrointestinal tract. This disclosure enables delivery of an effective amount of one or more of the species shown in Table 1 by adjusting or regulating the amount of these species in the gastrointestinal tract of these individuals via, eg, a subsequent FMT procedure or alternative means. Gastrointestinal tract of a patient for the treatment of overweight/obese individuals to lose weight, for the treatment of obesity or T2D or to reduce the risk of obesity or T2D, especially to help those who have failed in one or more previous FMT procedures Different methods for those who achieve weight loss.

When stool from a proposed FMT donor is tested and found to contain insufficient amounts of one or more beneficial bacteria species, as shown in Table 1 (eg, each less than about 0.01%, 0.05%, 0.10%, 0.20%, 0.40%, 0.50%, 0.80%, 1.0%, 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, or 8.0%), the proposed donor is considered to be Unsuitable donors for FMT in overweight/obese individuals treated for the purpose of successful weight control or loss. Or he may be disqualified as a donor in favor of another individual whose fecal samples exhibit a more favorable bacterial profile and whose fecal material should not be immediately used for FMT due to the lack of prospects for conferring such beneficial health effects , unless the fecal material is appropriately altered. In light of the findings of the inventors of the present application, in these cases where the expected lack of weight loss benefits of FMT therapy could be readily ameliorated, for example, one or more species, such as those shown in Table 1, could be introduced into the supply from an exogenous source. In the fecal material, the amount of bacterial species in the fecal material is increased (eg, to at least about 0.01%, 0.02%, 0.05%, 0.10%, 0.20%, 0.40%, 0.50%, 0.60% of the total bacteria in the fecal material .0.80%, 1.0%, 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 8.5%, 9.0% or 10%) and then processed for FMT for weight loss for the purpose of treating overweight or obese individuals.

Alternatively, beneficial species (one or more of those shown in Table 1) can be obtained from a sufficient amount of bacterial culture and then formulated into a suitable composition that does not contain of any fecal material for delivery into the gut of an overweight/obese patient. Similar to FMT, this composition can be introduced into a patient by oral, nasal or rectal administration.

Immediately after the step of introducing an effective amount of the desired species into the patient's gastrointestinal tract (eg, via an FMT procedure), the recipient can be further monitored by continuously testing the amount or relative abundance of the species in stool samples daily until 5 days after the procedure, the patient's weight as well as the patient's general health are also monitored in order to assess treatment outcomes and the corresponding amounts of relevant bacteria in the recipient's gastrointestinal tract: health benefits associated with weight loss (such as blood sugar, cholesterol, and triglycerides can be observed in combination). improvement in the amount of ester) to monitor the amount of species (one or more of those shown in Table 1). IV. Assessing Weight Loss Prospects and Corresponding Treatment

The inventors of the present application have also discovered that the amount of change in certain bacterial species can be indicative of an individual's prospects or likelihood of achieving success following weight loss treatment (eg, by FMT): they revealed certain Correlation between increased amounts of these species, such as those shown in Table 1, and FMT-induced weight loss in these patients. In addition, the amount or relative abundance of certain species (such as one or more of the species shown in Table 2) has been revealed to indicate, when correctly calculated using certain specific mathematical tools, the individual's subsequent FMT treatment regimen The prospect or likelihood of successful weight loss in

For example, when a stool sample is obtained from two or more individuals, the amount or relative abundance of the species in Table 1 or 2 in the sample can be determined, for example, by PCR, especially quantitative PCR. For the species listed in Table 1, lower amounts found in patient stool samples indicate that the patient is less likely to achieve FMT-induced weight loss; conversely, higher amounts are indicative of the likelihood of FMT-induced weight loss in the individual higher. Where the amounts of multiple species (eg, those listed in Tables 1 or 2) are measured and compared, a determination of the likelihood of weight loss success is made based on indications from the most relevant species measured.

Once a weight loss outlook has been assessed, eg, an overweight or obese individual is considered to have a reasonable expectation of successfully achieving weight loss by FMT treatment, appropriate therapeutic steps can be taken as measures to achieve this goal. For example, a composition comprising an effective amount of one or more of the species listed in Table 1 can be administered to a patient by FMT or by an alternative method of administration such that the distribution of bacteria in the patient's gastrointestinal tract is altered to favor weight loss outcomes bacterial distribution. V. KITS AND COMPOSITIONS FOR WEIGHT MANAGEMENT TREATMENT

The present invention also provides novel kits and compositions that can be used to promote weight loss in a patient, to treat or reduce the risk of obesity or T2D, or to assess a patient's successful weight loss by FMT therapy possibility. For example, a kit is provided comprising a first container containing a first composition comprising (i) an effective amount of one of the species shown in Table 1, and (ii) An effective amount of another different strain shown in Table 1. In some variations, the first composition and/or the second composition may contain both species of Table 1.

In some cases, the first composition comprises fecal material from a donor that has been processed, formulated, and packaged into a suitable form according to the delivery means in the FMT procedure, which can be deposited directly into the recipient's fecal material. Lower gastrointestinal tract (eg, wet or semi-moist form) or by oral ingestion (eg, frozen, dry/cold-dried, encapsulated). Alternatively, the first composition may not contain any donor fecal material, but an artificial mixture containing a suitable ratio and quantity of preferred bacterial species, such as one or more species shown in Table 1. The first composition is formulated and packaged according to its intended means of delivery to the patient, eg, by oral ingestion, nasal delivery, or rectal deposition.

Similarly, the second composition can be formulated from donor fecal material or other non-fecal derived material for oral, nasal or rectal delivery. Typically, the second composition contains a different species or combination of species from the species or combination of species contained in the first composition. The first composition and the second composition may or may not be formulated for the same method or route of delivery.

The first composition and the second composition are typically kept separately in two different containers in the set. In some cases, the first composition and the second composition can be combined in a single composition such that they can be administered to a patient simultaneously, eg, by oral or topical delivery.

Finally, a kit for quantitative detection of one or more species, such as those shown in Tables 1 or 2, is provided. The kits include reagents for quantitative detection of each species, for example, such reagents may include a set of oligonucleotide primers for each of the species derived from the relevant species (as shown in Tables 1-2). Any one or more of the strains shown) and preferably each of the related strains (such as any one or more of the strains shown in Tables 1-2) unique to the amplification of polynucleotide sequences such as Polymerase chain reaction (PCR), especially quantitative PCR. Example

The following examples are provided by way of illustration only, and not by way of limitation. Those skilled in the art will readily recognize that various non-critical parameters can be changed or modified to produce substantially the same or similar results. background

The aim of this study was to determine how the human gut microbiome is associated with weight loss following fecal microbiome transplantation (FMT). Practical uses of the present invention include improving human health and combating obesity-related disease risk by modulating the human gut microbiome. These measures can include FMT with optimized protocols, supplementation of synthetic strains, countermeasures for scavenging microbes to modulate obesity-related diseases. These findings facilitate the development of microbial products and propose a set of criteria for establishing fecal banks and their derivatives in diagnostics and therapeutics. Example 1: Identification of a Potential Probiotic Approach in a Randomized Placebo-Controlled Trial of Fecal Microbiota Transplantation in Individuals with Obesity and Diabetes Study Design

A randomized placebo-controlled study of fecal microbiome transplantation (FMT) in obese individuals with type 2 diabetes (NCT03127696). Informed consenting individuals meeting eligibility criteria at Prince of Wales Hospital were recruited. Inclusion criteria included age 18-70 years, BMI ≥ 28kg/m2 and <45 kg/m2; and a diagnosis of type 2 diabetes for ≥3 months. Exclusion criteria included current pregnancy, use of any weight loss medication in the past 1 year, known medical history or concomitant significant gastrointestinal conditions (including inflammatory bowel disease, current colorectal cancer, current GI infection), known medical history or concomitant significant GI infection Food allergies, immunosuppressed individuals, known history of severe organ failure (including decompensated cirrhosis), inflammatory bowel disease, renal failure, epilepsy, acquired immunodeficiency syndrome, current active sepsis, recent Active malignant disease for 2 years, known contraindications for esophago-gastric-duodenoscopy (OGD), probiotics or antibiotics in the last 3 months, randomized sodium-glucose cotransporter-2 inhibitor or pancreatic hyperglycemia Glucagon-like peptide-1 receptor agonists, or randomized proton-pump inhibitors. Individuals were randomized 1:1:1 into 3 groups (Group 1: FMT and lifestyle intervention, Group 2: FMT alone, Group 3: sham and lifestyle intervention) (Figure 1 ). Banned drugs

Antibiotics, probiotic or prebiotic preparations, sodium-glucose co-transporter-2 (SGLT2) inhibitors, glucagon-like peptide-1 (GLP-1) receptor agonists, or proton pump inhibition were not permitted during the study agent (PPI).

Individuals who ingested prohibited drugs during the study were allowed to remain in the study and evaluate the results. Reported intake of prohibited drugs is recorded and documented. Fecal microbiota transplantation (FMT)/ sham infusion

Subjects received 4 FMT/sham infusions at Weeks 0, 4, 8, and 12 and were followed until Week 52. Each time, 100-200 ml of FMT/sham solution was infused via OGD into the distal duodenum or jejunum over 2-3 minutes. The FMT and sham solutions were prepared as follows.

FMT: Frozen feces from donors from a fecal bank are used. For each FMT, the FMT solution was infused using feces from a single donor or a mixture of feces from multiple donors. The FMT solution was prepared by diluting feces with sterile saline (0.9%). The solution was mixed and filtered using a screening procedure. The resulting supernatant was then stored as a frozen FMT solution for later use.

Sham: Sterile saline (0.9%) was used as a sham. Fecal donors in the Fecal Bank of the Chinese University of Hong Kong

Donors (BMI < 23kg/m ² ) are volunteers from the general population, including spouses or partners, first-degree relatives, other relatives, friends, and other known or unknown potential individuals who meet eligibility criteria, and will be invited for screening experiments room test. A series of laboratory tests and interviews for infectious diseases were conducted. Feces from qualified donors were used in this study. An individual may receive stool from a single or multiple donors, who may not be able to obtain the identity of the donor. lifestyle intervention

Individuals were randomized to a lifestyle intervention (LSI) or a combined FMT and lifestyle intervention group and received seven individual dietitian-led counseling sessions over a 12-week treatment period. At baseline, weeks 1, 2, 4, 6, 8, and 12, they were scheduled for a consultation at the Prince of Wales Hospital.

Lifestyle interventions are primarily aimed at weight loss by reducing calorie intake while enhancing energy expenditure. In addition to diet, it also emphasizes lifestyle and behavioral changes that promote sustainable weight loss. During the first consultation at baseline, a comprehensive assessment of medical history, dietary and lifestyle habits and behaviors, knowledge of diet-disease relationships, and motivation for lifestyle changes was performed by the dietitian for approximately 1 hour, and then the dietitian and Individuals discuss weight goals for the treatment period together and give personalized advice on diet and lifestyle to achieve goals. During the subsequent 20-minute follow-up consultation, the dietitian commented on adherence to previously negotiated dietary and lifestyle recommendations and provided further advice accordingly.

Based on the recommendations of the American Dietetic Association [1], each individual was given an individualized dietary plan at the first consultation. A nutritionally balanced diet plan focuses on appropriate fruits and vegetables, moderate carbohydrates, low fat and glycemic index (GI) food choices. A set of 2 booklets containing meal planning, food portion exchanges, general tips for eating out was given to each individual for reference.

In addition to actual dietary and lifestyle recommendations, a variety of approaches were employed during the intervention to promote sustainable healthier behavioral changes. Individuals are advised to record their diet and physical activity daily before each review session to develop self-monitoring behaviors, while negotiating strategies for coping with "at-risk" situations such as stressful states, travel, festivals, and party eating. Where appropriate, individuals were also given recipes with simple instructions to encourage healthy cooking.

Adherence to the lifestyle intervention was revealed by the percentage of attendance at dietitian consultations during the 12-week treatment period and weekly diet and lifestyle records at each follow-up consultation. Fecal DNA extraction and DNA sequencing

Fecal DNA was extracted by using the Maxwell® RSC ^PureFood GMO and Authentication Kit (Promega) modified to increase fungal DNA production. Approximately 100 mg of each stool sample was pre-washed with 1 ml of ddH2O and pelleted by centrifugation at 13,000 xg for 1 min. The pellet was resuspended in 800 μL of TE buffer (pH 7.5) supplemented with 1.6 μl of 2-mercaptoethanol and 500 U of lyase (Sigma) and incubated at 37° C. for 60 minutes. The samples were then centrifuged at 13,000 xg for 2 minutes and the supernatant was discarded. Following this pretreatment, DNA was subsequently extracted from the pellet using the Maxwell® RSC PureFood GMO and Authentication Kit (Promega) according to the manufacturer's instructions. Briefly, 1 ml of CTAB buffer was added to the pellet and vortexed for 30 seconds, then the solution was heated at 95 °C for 5 minutes. Afterwards, the samples were vortexed thoroughly with beads (Biospec, 0.5 mm for fungi, 0.1 mm for bacteria, 1 : 1 ) at maximum speed for 15 minutes. Then, 40 μl of proteinase K and 20 μl of RNase A were added, and the mixture was incubated at 70° C. for 10 minutes. The supernatant was then obtained by centrifugation at 13,000 xg for 5 minutes and placed in a Maxwell® RSC instrument for DNA extraction. Extracted fecal DNA was used for ultra-deep polygenic genome sequencing via an Ilumina Novoseq 6000 (Novogen, Beijing, China). An average of 52 million ± 6.3 million reads per sample (12G clean data) were obtained. Quality trimming of the original sequence

Raw sequence reads were filtered and quality trimmed using Trimmomatic v0.36 [2] as follows: 1) trim low quality bases (quality score <20); 2) remove reads shorter than 50 bp; 3) remove length Sequences less than 50 bp; 3) Tracking and cutting out sequencing adaptors. Contaminating human reads were filtered using Kneaddata (Repository: GRCh38 p12 ) with preset parameters. Analysis of the bacterial microbiome

Analysis of the bacterial microbiome (bacteria) was performed via MetaPhlAn2 by mapping reads to clade-specific markers [3] and species pangenomes by Bowtie2 [4]. The resulting strain abundance table was used to correlate with blood parameters. Pearson correlation and Spearman correlation and P values were calculated using cor and cor.test functions in R and visualized using ggplot2 . clinical laboratory tests

Fasting blood samples were collected before FMT and at weeks 4, 12, 16, 20, and 24 for testing complete blood count (CBC), renal function test (RFT), liver function test (LFT) ), C-reactive protein (CRP), magnesium, glucose, insulin (before FMT and week 24 only), total cholesterol, low density lipoprotein (LDL) cholesterol, high density lipoprotein (HDL) cholesterol, triglycerides and Heme A1c (HbA1C). statistical methods

Statistical analysis was performed using SPSS. Repeated measures ANOVA was used to determine the difference between baseline, Week 12, Week 16, Week 20, and Week 24 follow-ups in the three treatment groups. Calculate the difference between the baseline and each time point. Post hoc analysis was performed using the Bonferroni test. p-values &lt; 0.05 were considered significant. Results Species associated with FMT -induced weight loss

Sixty-one individuals were recruited and randomly assigned to FMT+lifestyle intervention (FMT+LSI; n=21), FMT alone (n=20), and sham and lifestyle intervention (LSI; n=20). Four subjects withdrew from the study.

Although bacterial diversity did not change significantly between treatment groups, bacterial richness increased significantly in the FMT+LSI group at weeks 4 and 16 post-intervention (p<0.01 and p=0.039, Wilcoxon). signed rank test). Virus diversity and richness increased in both the FMT alone group and the FMT+LSI group after treatment (p<0.05, Wilcoxon signed-rank test). No significant changes in bacterial and viral richness were observed in the sham+LSI group. Bacterial and viral richness in the FMT group was significantly higher than in the sham+LSI group after treatment (p<0.0001, repeated measures ANOVA). For the bacterial and viral groups, the Euclidean distance between the baseline samples and the post-treatment samples in the FMT alone and FMT+LSI groups was significantly higher than that in the sham+LSI group (p<0.001, respectively). and p < 0.05, Wilcoxon signed-rank test), indicating that the effect of FMT on the microbiota was greater than that of the lifestyle intervention. Meanwhile, the relative abundances of 27, 26 and 6 bacterial species were significantly changed in the post-intervention FMT+LSI group, FMT alone and sham+LSI alone group, respectively (LDA>2, adjusted p<0.05). ). Individuals in both FMT groups had significant increases in several butyrate-producing bacteria, including Faecalibacterium prausnitzii, R. hominis, Collins tanaka, and Prevotella copri , as well as Flavonifractor plautii , Clostridium Bacteria 1_7_47FAA ( Clostridiales bacterium 1_7_47FAA), Clostridium clostridioforme and Fusobacterium ulcerans were decreased, which were not seen in the sham + LSI group. After treatment, the distribution of butyrate-producing bacterial groups in the FMT group was similar to that of the donor, whereas the sham+LSI group showed no significant bacterial changes. The relative abundance of several microbiota functional pathways increased after FMT compared to their respective baseline samples. Fecal microbiota in the FMT alone and FMT+LSI groups showed reduced amounts of amino acid degradation, secondary metabolite degradation, and increased amounts of secondary metabolite biosynthesis, non-carbon, compared to their baseline fecal samples Nutrient degradation, L-ornithine biosynthesis; increased amounts of carbohydrate degradation, vitamin biosynthesis, nucleotide degradation and amino acid biosynthesis (LDA>2, adjusted p<0.05). In the sham group + LSI group, no significant changes in microbiota functional pathways were observed.

Although 20% (4/20) of individuals who received the placebo infusion and lifestyle intervention lost more than 5% of their body weight at week 24, they all regained weight after the intervention was discontinued. None of them had more than 10% weight loss over the 52-week study period, while 13.5% (5/37) of recipients achieved more than 10% weight loss (Figure 2). This suggests that the effects of FMT-induced weight loss are more durable than lifestyle interventions. Therefore, changes in the gut microbiome play a role in FMT-induced weight loss. Shotgun polygenic genome sequencing reveals that in FMT responders, this post-FMT compositional change is dominated by the expansion of butyrate-producing bacteria (BPB), which contain the thick Corynebacterium oxydans, Collins tanaka, R. hominis, but no significant changes in the LSI group (Figure 3), suggesting that these species play a role in FMT-induced weight loss. Table 1: Species associated with FMT-induced weight loss (regardless of calorie intake) strain NCBI: txid Corynebacterium anaerobes 649756 Collins tanaka 626935 R. hominis 301301

Thus, the species listed in Table 1 can be administered to an individual to reduce body weight. Example 2: A Machine Learning Model Method for Predicting the Success Rate of FMT on Weight Loss Machine Learning Model

觀察結果。在無窮大的N的情況下，有36.8%的資料未出現在稱為袋外(OOB)觀察結果的訓練樣品中，這些資料將不會用於構造樹。另外，當每個決策樹基於從總體特徵中選擇的特徵的隨機子集分割節點時，將額外的隨機性引入到隨機森林。將具有最小基尼(基尼用於評價節點的純度)的特徵用於在每次反覆運算中分割節點以生成樹。對於不同的資料和特徵子集，該演算法能夠訓練不同的樹並藉由對來自樹模型的結果進行平均來獲得最終分類。除了預測模型之外，隨機森林還具有評估變數重要性的能力[6]。OOB觀察結果用於估計森林中每個樹的分類誤差。為了測量給定變數的重要性，隨機改變OOB資料中變數的值，然後改變的OOB資料被用於生成新的預測。將改變的與原始的OOB觀察之間的誤差率之差除以標準誤差計算為變數的重要性。為了對新樣品進行分類，將樣品的特徵向下傳遞到每個樹以估計分類的概率。隨機森林使用所有樹的平均概率來判定分類的最終結果。 Using fecal microbes (due to their superior performance for classification using binary features), random forests (RF) were chosen to build a successful FMT predictive model for weight loss. Random forest [5] is one of the most popular methods in macrogenomic data analysis to identify distinguishing features and build predictive models. As a widely used ensemble learning algorithm, random forest consists of a series of classification and regression trees (CART) to form a strong classifier. A subset of data randomly sampled from the original data set with replacement is called bootstrap sampling and is used to build the tree. When the training dataset for the current tree is drawn by the bootstrap method, omitted from the overall dataset

Observation results. In the case of infinite N, 36.8% of the data did not appear in training samples called out-of-bag (OOB) observations that would not be used to construct the tree. Additionally, additional randomness is introduced into random forests when each decision tree splits nodes based on a random subset of features selected from the population of features. The feature with the smallest Gini (Gini is used to evaluate the purity of the node) is used to split the node in each iteration to generate the tree. For different subsets of data and features, the algorithm can train different trees and obtain the final classification by averaging the results from the tree model. In addition to predictive models, random forests also have the ability to assess the importance of variables [6]. The OOB observations were used to estimate the classification error for each tree in the forest. To measure the importance of a given variable, the values of the variables in the OOB data were randomly changed, and the changed OOB data were then used to generate new predictions. The difference in the error rate between the altered and original OOB observations divided by the standard error was calculated as the importance of the variable. To classify a new sample, the features of the sample are passed down each tree to estimate the probability of classification. Random Forest uses the average probability of all trees to determine the final outcome of the classification.

The model was constructed from a group without weight loss (n=18) and a group with weight loss (n=19) between baseline and week 24. The importance of each species to the classification model was evaluated by recursive feature elimination. If its Pearson correlation value with any probe already present in the model is < 0.7, the selected species are added to the random forest model one by one according to the decreasing importance value. Each time a new feature is added to the model, the performance of the model is re-evaluated using 10-fold cross-validation. These models were compared in terms of the area under the curve (AUC) in the binary classifier and receiver operating characteristic (ROC) curves. The final model is chosen when the best accuracy and kappa are achieved. These analyses were performed using the R packages randomForest v4.6-14 [5] and pROC v1.15.3 [7]. result

Compared to baseline, microbiome composition at baseline was assessed between individuals with weight loss (FMT responders; n=19) and those without weight loss (FMT non-responders, n=18) at Week 24. All more abundant in FMT responders based on 5 species ( Desulfovibrio desulfuricans , candidate branch TM single cell isolate TM7b, Bacteroides faecalis, Weisseria aninus and Bacteroides donovani (Fig. 4a)) The random forest model of baseline relative abundance achieved good prediction in predicting response to lean donor FMT with a receiver operating characteristic [ROC]AUC of 0.912 (Fig. 4b). Notably, all 5 individuals who lost more than 10% of their body weight over the 52-week study period were classified as "responders" by the predictive model. Table 2: Species included in the machine learning model used to predict the success rate of FMT for weight loss strain NCBI: txid Candidate branch TM7 single cell isolate TM7b 447455 Bacteroides faecalis 46506 Bacteroides donovani 357276

Therefore, to determine the success rate of FMT for weight loss in an individual, the following steps will be performed: 1. By determining the relative abundance of the species selected from Table 2 (e.g., any 2 or 3 species) in the cohort of FMT recipients without weight loss at baseline and with weight loss prior to receiving FMT to obtain a set of training data; 2. Determine the relative abundance of these bacterial species in the individuals whose FMT success rate is to be determined; 3. Use a random forest model to compare the relative abundance of these species in individuals to the training data; and 4. The decision tree will be generated by random forest from the training data. Relative abundance will run down the decision tree and generate a risk score. If more than 50% of the trees in the model believe that the individual will have weight loss after FMT, the result will be "The tested individual is considered to have a high success rate of weight loss after receiving FMT". If less than 50% of the trees in the model consider the individual to have no weight loss after FMT, the result will be "the individual tested is considered to have a low success rate of weight loss after receiving FMT".

The bacterial species selected from Table 2 can be any 2 or 3 bacterial species, such as: 1. Candidate clade TM7 single-cell isolate TM7b + Bacteroides doveri + Bacteroides faecalis (AUC: 93%, light blue; Figure 4) 2. Bacteroides donovani + Bacteroides faecalis (AUC: 73.7%, red; Figure 4) 3. Candidate clade TM7 single cell isolate TM7b + Bacteroides faecalis (AUC: 78.4%, green; Figure 4) 4. Candidate clade TM7 single-cell isolate TM7b+Bacteroides donovani (AUC: 81.3%, dark blue; Figure 4) Research I

Listed in Table 2 from FMT recipients without (n=18) and with weight loss (n=19) were determined by polygenome sequencing and assigned taxonomy as described in Methods The relative abundances of the 3 species (relative abundances listed in Table 3). The decision tree is generated by random forest from the data in Table 3, and the parameters are: tree=801, mtry=2.

To determine the likelihood of another obese individual with T2DM. The relative abundance of the five species listed in Table 3 in the individual's fecal samples was determined by polygenome sequencing and the assigned taxonomy as described in Methods (Table 4). Relative abundance is run down a decision tree and a risk score is generated. The individual's score was 0.57 (Fig. 5a), so the individual was considered likely to lose weight after FMT. Research II

Listed in Table 2 from FMT recipients without (n=18) and with weight loss (n=19) were determined by polygenome sequencing and assigned taxonomy as described in Methods The relative abundances of the 3 species (relative abundances listed in Table 3). The decision tree is generated by random forest from the data in Table 3, and the parameters are: tree=801, mtry=2.

To determine the likelihood of another obese individual with T2DM. The relative abundance of the five species listed in Table 3 in the individual's fecal samples was determined by polygenome sequencing and the assigned taxonomy as described in Methods (Table 4). Relative abundance is run down a decision tree and a risk score is generated. The individual's score was 0.11 (Figure 5b), so the individual was considered unlikely to lose weight after FMT. Table 3: Relative abundance of the species listed in Table 2 in FMT recipients without (n=18) and with weight loss (n=19) group Candidate branch TM7 single cell isolate TM7b Bacteroides faecalis Bacteroides donovani responder 0 0.2151 1.71892 responder 0 0.44262 0.00157 non-responder 0 0 0 responder 0 0.63074 2.92262 non-responder 0 0.19493 0.02882 responder 0 0.14545 0.05869 responder 0 1.03775 0 non-responder 0 0.12171 0 non-responder 0 0.32889 0.02335 responder 0.00122 0.02669 0.00795 non-responder 0 0.26171 0.0928 responder 0.00356 0 1.62989 responder 0.00171 0.014 0.1802 non-responder 0 0.24599 0 responder 0.00157 2.15287 9.15962 non-responder 0 0 0.00246 non-responder 0 0.0277 0 non-responder 0 0.05174 0.13443 non-responder 0 0.12214 0.00608 responder 0 0.67459 1.42752 responder 0 0.15941 0.29319 non-responder 0 0.00224 0.00041 responder 0.00305 0.01253 0 non-responder 0 0 0.13803 responder 0 0.43893 0.02083 non-responder 0 0.00491 0 non-responder 0 0.04157 6.15639 responder 0 0 0.95711 non-responder 0 0.01345 0.06015 responder 0.00508 0.91856 0 responder 0.00737 0.1094 0.28737 responder 0 2.35214 0.02574 non-responder 0 0.32019 0 responder 0.00541 0 0.00112 non-responder 0 0.17835 0 responder 0 0.01597 0.3372 non-responder 0 0.13342 0.00379 Table 4: Relative abundance of the species listed in Table 2 in FMT recipients without (n=18) and with weight loss (n=19) group Candidate branch TM7 single cell isolate TM7b Bacteroides faecalis Bacteroides donovani Research I 0 0 0.406 Research II 0 0.00161 0.00597

All patents, patent applications, and other publications (including GenBank accession numbers, etc.) cited in this application are incorporated herein by reference in their entirety for all purposes. Reference 1. Wheeler ML, Franz M, Barrier P, Holler H, CRONMILLER N, Delahanty LM. Macronutrient and energy database for the 1995 exchange lists for meal planning: a rationale for clinical practice decisions. Journal of the American Dietetic Association 1996; 96:1167-71. 2. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114-20. 3. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS , et al. Metagenomic biomarker discovery and explanation. Genome biology 2011;12: R60. 4. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods 2012; 9:357. 5. Breiman L. Random Forests. Machine Learning 2001; 45:5-32. 6. Cutler DR, Edwards Jr TC, Beard KH, Cutler A, Hess KT, Gibson J , et al. Random forests for classification in ecology. Ecology 2007; 88:2783-92. 7. Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC , et al. pROC: an open-source package for R and S+ t o analyze and compare ROC curves. BMC Bioinformatics 2011;12:77.

[Figure 1]: Study protocol.

[Figure 2]: Changes in body weight of FMT responders and lifestyle responders after the intervention. FMT responders continued to lose weight until week 52 (40 weeks after the last intervention), while lifestyle responders regained weight after the intervention was discontinued.

[Figure 3]: After the intervention, the relative abundances of (a) C. pachyrhizi, (b) Collinsella tanaka, and (c) R. hominis were significantly increased in FMT responders, while in FMT responders There was no significant increase among lifestyle responders. Relative abundances are shown as percentages after log transformation.

[Fig. 4] a: Relative abundance of 3 species used to predict FMT response (weight loss 24 weeks after the first FMT compared to baseline) in FMT responders vs non-responders. b. Depicts the ROC of the model trained on the candidate clade TM7 single cell isolate TM7b + Bacteroides donovani + Bacteroides faecalis (light blue) at baseline fecal microbiota composition, Pseudomonas donovani Relative abundance of Bacillus faecalis + Bacteroides faecalis (red), candidate clade TM7 single cell isolate TM7b + Bacteroides faecalis (green), candidate clade TM7 single cell isolate TM7b + Bacteroides donovani (dark blue) predicted FMT response.

[Figure 5] a: Risk score for an obese individual with T2DM using the following 3 markers compared to FMT recipients without (n=18) and with weight loss (n=19): Candidate clade TM7 single cell isolates TM7b, Bacteroides donovani and Bacteroides faecalis. It is believed that the individual may lose weight after FMT. b. Risk scoring of an obese individual with T2DM using the following 3 markers compared to FMT recipients without (n=18) and with weight loss (n=19): candidate branch TM7 single Cell isolates TM7b, Bacteroides donovani and Bacteroides faecalis. Individuals were considered less likely to lose weight after FMT.

Claims (34)

A method for reducing body weight in an individual, comprising adding an effective amount of one or more of Corynebacterium thick anaerobic ( Anaerostipes hadrus ), Collinsella tanakaei ( Collinsella tanakaei ) and Roseburia hominis ( Roseburia hominis ) in an effective amount The species is introduced into the individual's gastrointestinal tract. The method of claim 1, wherein the introducing step comprises orally administering to the individual a composition comprising an effective amount of the one or more species. The method of claim 1, wherein the introducing step comprises delivering a composition comprising an effective amount of the one or more species to the small intestine, ileum or large intestine of the individual. The method of claim 1, wherein the introducing step comprises fecal microbiological transplantation (FMT). The method of claim 4, wherein the FMT comprises administering to the individual a composition comprising the treated donor fecal material. The method of claim 5, wherein the composition is administered orally. The method of claim 2, wherein the composition is deposited directly into the gastrointestinal tract of the individual. The method of claim 1, wherein the amount or relative abundance of the one or more species is in a first stool sample obtained from the individual before the introducing step and in a second stool sample obtained from the individual after the introducing step to determine in the sample. The method of claim 8, wherein the amount of the one or more species is determined by quantitative polymerase chain reaction (PCR). A kind of set for reducing body weight, it comprises first container and second container, this first container contains first composition, and this first composition comprises the bacterial strain Corynebacterium thick anaerobes, Tanaka Collins' One of the bacteria or the human Rosbyella, the second container contains a second composition, the second composition comprising an effective amount of Corynebacterium thick great, Collins tanaka or human Rosbyella of another. The kit of claim 10, wherein the first composition comprises processed donor fecal material for FMT. The kit of claim 10 or 11, wherein the first composition is formulated for oral administration. The kit of claim 10, wherein the second composition is formulated for oral administration. The kit of claim 11, wherein the first composition and the second composition are both formulated for oral ingestion. A method for determining the likelihood of weight loss by FMT in an individual, comprising: (1) determine the amount or relative abundance of one or more bacterial species shown in Table 2 in the stool sample from the individual; (2) determine the amount or relative abundance of the same species in fecal samples from a reference cohort comprising individuals who lost weight after FMT and individuals who did not lose weight after FMT; (3) generating a decision tree by using the random forest model of the data obtained from step (2), and running the amount or relative abundance of the one or more species from step (1) along the decision tree to generate rating; and (4) The individual with a score greater than 0.5 is judged as likely to achieve weight loss by FMT, and the individual with a score of not greater than 0.5 is judged as unlikely to achieve weight loss by FMT. The method of claim 15, wherein the one or more species comprises any two or three species shown in Table 2. A kit for assessing the likelihood of weight loss by FMT in an individual comprising reagents for detecting one or more of the species shown in Table 2. The kit of claim 17, wherein the reagent comprises a set of oligonucleotide primers for amplifying polynucleotide sequences from any of the species shown in Table 2. The kit of claim 18, wherein the amplification is PCR. The kit of claim 19, wherein the PCR is quantitative PCR. A method for reducing the risk of obesity and type 2 diabetes (T2D) in an individual or treating obesity and T2D in an individual comprising introducing into the gastrointestinal tract of the individual an effective amount of C. Bayerella. 21. The method of claim 21, wherein the introducing step comprises orally administering to the individual a composition comprising an effective amount of C. pachyrhizi or R. hominis. 21. The method of claim 21, wherein the introducing step comprises delivering a composition comprising an effective amount of C. pyogenes or R. hominis to the small intestine, ileum, or large intestine of the individual. The method of claim 21, wherein the introducing step comprises fecal microbiological transplantation (FMT). The method of claim 24, wherein the FMT comprises administering to the individual a composition comprising the treated donor fecal material. The method of claim 21, wherein the composition is administered orally. The method of claim 22, wherein the composition is deposited directly into the gastrointestinal tract of the individual. 21. The method of claim 21, wherein C. pyogenes or Rose hominis is determined in a first stool sample obtained from the individual before the introducing step and in a second stool sample obtained from the individual after the introducing step The amount or relative abundance of Bairostrea. The method of claim 28, wherein the amount of C. thaliana or R. hominis is determined by polymerase chain reaction (PCR), preferably quantitative polymerase chain reaction (qPCR) determination. A kit for assessing the risk of obesity and type 2 diabetes (T2D) in an individual or for assessing whether an individual suffers from microbiome-dependent obesity and T2D, comprising a thick anaerobic rod for detection of bacterial species Reagents for one or more of Bacillus and R. hominis. The kit of claim 30, wherein the reagent comprises a set of oligonucleotide primers for amplifying a polynucleoside from any of the species Corynebacterium thaliana and R. hominis acid sequence. The kit of claim 31, wherein the amplification is PCR. The kit of claim 32, wherein the PCR is quantitative PCR. The kit of claim 30, wherein the species is R. hominis.

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