WO2022261365A1

WO2022261365A1 - Primers and methods for microbial detection and quantification of porphyromonas in a sample

Info

Publication number: WO2022261365A1
Application number: PCT/US2022/032893
Authority: WO
Inventors: Christopher Hale CORZETT; Benjamin John TULLY; Molly B. Schmid; Cesar Escobar BLANCO; Sapna Shah JAIN; Steven Eric FINKEL
Original assignee: Alfred E. Mann Institute For Biomedical Engineering At The University Of Southern California
Priority date: 2021-06-11
Filing date: 2022-06-09
Publication date: 2022-12-15

Abstract

This disclosure relates to systems, formulations and methods that may be used in determination of presence/absence, relative and/or absolute abundance of Porphyromonas in a microbiome sample. This disclosure relates to formulations or kits that include target specific primers. This disclosure further relates to formulations or that may include reference primers, and/or reference materials, which may be used in determination of relative and/or absolute abundance of Porphyromonas in a microbiome sample.

Description

SYSTEMS, FORMULATIONS AND METHODS FOR MICROBIAL DETECTION AND QUANTIFICATION OF PORPHYROMONAS IN A SAMPLE

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Patent Application No. 63/209,857, filed June 11 , 2021 , the entire contents of which is incorporated by reference herein.

REFERENCE TO SEQUENCE LISTING

[0002] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled AMISC021 WO- Correct_ST25.TXT, which was created and last modified on June 8, 2022, which is 14,262 bytes in size. The information in the electronic Sequence Listing is hereby incorporated by reference in its entirety.

BACKGROUND

TECHNICAL FIELD

[0003] This disclosure relates to systems, formulations and methods that may be used in determination of presence/absence, relative and/or absolute abundance of Porphyromonas in a microbiome sample. This disclosure relates to formulations or kits that include target specific primers. This disclosure further relates to formulations or that may include reference primers, and/or reference materials, which may be used in determination of relative and/or absolute abundance of Porphyromonas in a sample.

DESCRIPTION OF RELATED ART

[0004] Members of the genus Porphyromonas have been thought to reside primarily within the human oral microbiome community. However, recent next generation sequencing reports have correlated the abundance of Porphyromonas spp. in a wide variety of body locations with several disease progression outcomes, including in the gut microbiome of colorectal cancer [1], [2] and cervical cancer patients [3], as well as in the lung microbiome of cystic fibrosis patients [4]

RELATED ART REFERENCES

[0005] The following publications are related art for the background of this disclosure. One digit or two-digit numbers in the box brackets before each reference, correspond to the numbers in the box brackets used in the other parts of this disclosure.

[1] Thomas AM, Manghi P, Asnicar F, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat Med. 2019.

[2] Wirbel J, Pyl PT, Kartal E, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med. 2019.

[3] Sims, TT, El Alam, MB, Karpinets, TV, et al. Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation. Communications Biology. 2021.

[4] Keravec M, Mounier J, Guilloux C-A, et al. Porphyromonas, a potential predictive biomarker of Pseudomonas aeruginosa pulmonary infection in cystic fibrosis. BMJ Open Resp Res. 2019.

[0006] The entire contents of each of the above references, including its supplemental content, if available, are incorporated herein by reference.

SUMMARY

[0007] Examples described herein relate to systems, formulations and methods that may be used in determination of presence/absence, relative and/or absolute abundance of Porphyromonas in a microbiome sample. This disclosure relates to formulations or kits that include target specific primers. This disclosure further relates to formulations or that may include reference primers, and/or reference materials, which may be used in determination of relative and/or absolute abundance of Porphyromonas in a sample.

[0008] An exemplary method of this disclosure relates to the identification of a target microorganism in a microbiome sample. The method may include: obtaining the microbiome sample that potentially includes at least one DNA; processing the sample to have the at least one DNA accessible to react with a specific primer pair designed specifically for identification of the target microorganism present in the microbiome; mixing the accessible DNA with a primer mixture that includes the specific primer pair to form a microbiome reaction mixture; subjecting the microbiome reaction mixture to a reaction under which at least one section of the accessible DNA is amplified and produces a fluorescence signal; measuring amount of fluorescence signal produced; and identifying whether the target microorganism is present in the microbiome sample.

[0009] In this disclosure, the method may further include determining abundance of the target microorganism in the microbiome sample.

[0010] In this disclosure, the method may further include: forming a patient microorganism profile based on said identification and/or determination; comparing the patient microorganism profile with a microorganism profile of a healthy patient; determining whether the patient has a disease/clinical complication, has a risk of developing a disease/clinical complication, or responds to a treatment, or determining progression of a disease/clinical complication of the patient; and treating the patient if the patient has a disease/clinical complication.

[0011] In this disclosure, the target microorganism may include one or more specific target bacteria.

[0012] In this disclosure, the determining abundance of the target microorganism may include establishing or obtaining a standard curve.

[0013] In this disclosure, the determining abundance of target microorganism may include establishing or obtaining a standard curve by reacting a template microbiome reaction mixture with a known concentration of the target microorganism. [0014] In this disclosure, the determining abundance of the target microorganism may include mixing the microbiome reaction mixture with a known reference standard.

[0015] In this disclosure, the primer mixture may include a specific primer pair; and wherein each specific primer pair may include a forward primer and a reverse primer.

[0016] In this disclosure, the target microorganism may include at least one genus of bacteria, and wherein the genus of bacteria has at least one sub-clade, or at least two sub-clades.

[0017] In this disclosure, the primer mixture may include at least two specific primer pairs; wherein each specific primer pair may include a forward primer and a reverse primer; and wherein at least one first specific primer pair is capable of amplifying a first species belonging to a first sub-clade of the target bacteria and at least one second specific primer pair is capable of amplifying a second species belonging to a second sub-clade of the target bacteria.

[0018] In this disclosure, the primer mixture may include a specific primer pair; wherein the specific primer pair may include a forward primer and a reverse primer; wherein the forward primer is p0173 and the reverse primer is p0174.

[0019] In this disclosure, the primer mixture may include a specific primer pair; wherein the specific primer pair may include a forward primer and a reverse primer selected from the primer pairs of Table 1 , Primer IDs p0171 to p0344, or a combination thereof; wherein at least one first specific primer pair is capable of amplifying a first species belonging to a first sub-clade of the target microorganism and at least one second specific primer pair is capable of amplifying a second species belonging to a second sub-clade of the target microorganism.

[0020] In this disclosure, the target microorganism may be Porphyromonas.

[0021] In this disclosure, the microbiome sample may be obtained from a patient.

[0022] In this disclosure, the target microorganism may belong to at least one species of the Porphyromonas genus. [0023] In this disclosure, the target microorganism may belong to at least one species of Porphyromonas genus of Table 2, ID no. AMI_0025 to AMI_0032, or a combination thereof.

[0024] In this disclosure, the subjecting the microbiome reaction mixture may include subjecting the microbiome reaction mixture to a PCR or a qPCR reaction. [0025] In this disclosure, the disease/clinical complication may include (chronic) oral infections, cancers, neurodegenerative diseases, or a combination thereof. [0026] In this disclosure, the disease/clinical complication may include colorectal cancer, endometrial cancer, gastric adenocarcinomas, and cervical cancer, P. aeruginosa pulmonary infections in cystic fibrosis, oral pathological process, or a combination thereof.

[0027] In this disclosure, the disease/clinical complication may include an oral pathological process, and wherein the oral pathological process may include periodontitis, oral squamous cell carcinomas, or a combination thereof.

[0028] In this disclosure, the disease/clinical complication may include colorectal cancer.

[0029] In this disclosure, the microbiome sample may include stool, saliva, skin, nasal swab, vaginal swab, blood, urine, hair, or oral swab.

[0030] In this disclosure, the method further may include validating the specific primer pair to determine whether the specific primer pair reacts with the DNA to confirm that the specific primer pair is substantially unique to the target microorganism.

[0031] In this disclosure, wherein the method further may include validating the specific primer pair to determine whether the specific primer pair reacts with the DNA to confirm that the specific primer pair is substantially unique to the target microorganism, and to determine the specific primer pair sensitivity and/or specificity.

[0032] In this disclosure, the reaction product may be analyzed by a gel electrophoresis method. [0033] In this disclosure, the specific primer pair may be a pair of polymerase chain reaction (PCR) primers.

[0034] In this disclosure, the method further may include forming a microbiome profile for the microbiome sample.

[0035] In this disclosure, the amplifying the DNA may include amplifying the DNA with qPCR.

[0036] In this disclosure, the determining the presence and/or abundance may include measuring a fluorescence signal during the amplifying step.

[0037] In this disclosure, the microbiome sample may be from a human patient.

[0038] In this disclosure, the patient may be a human or an animal.

[0039] In this disclosure, the method further may include administering a therapeutic to the patient.

[0040] In this disclosure, the therapeutic may not be chemotherapy and/or radiation.

[0041] This disclosure also relates to a nucleic acid that may have at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to any one of the sequences of Table 1 , Primer IDs p0171 to p0344, or a combination thereof.

[0042] This disclosure also relates to a primer pair that may include a forward primer and a reverse primer, each having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the forward primers or reverse primers of Table 1 , Primer IDs p0171 to p0344, or a combination thereof; wherein the primer pair is specific for a target microorganism cluster.

[0043] This disclosure also relates to a primer pair that may include a forward primer and a reverse primer, each having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the forward primers or reverse primers of Table 1 , wherein the primer pair is specific for a target sub-clade of the microorganism genus. [0044] This disclosure also relates to a diagnostic kit that may include one or more specific primer pairs of any preceding examples or any following examples.

[0045] This disclosure also relates to a diagnostic kit of any preceding examples or any following that may further include a reference standard.

[0046] This disclosure also relates to a diagnostic kit, wherein the kit is suitable for the method of any preceding examples for identification of the target microorganism present in the microbiome sample and/or, if the target microorganism is present in the microbiome, for determination of abundance of the target microorganism present in the microbiome sample.

[0047] Any combination of above products and methods is within the scope of the instant disclosure.

[0048] These, as well as other components, steps, features, objects, benefits, and advantages, will now become clear from a review of the following detailed description of illustrative examples, the accompanying drawings, and the claims.

BRIEF DESCRIPTION OF DRAWINGS

[0049] The drawings are of illustrative examples. They do not illustrate all examples. Other examples may be used in addition or instead. Details that may be apparent or unnecessary may be omitted to save space or for more effective illustration. Some examples may be practiced with additional components or steps and/or without all the components or steps that are illustrated. When the same numeral appears in different drawings, it refers to the same or like components or steps.

[0050] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

[0051] FIG. 1. Exemplary Specific primer Design and Assessment Flowchart.

[0052] FIG. 2. Exemplary Porphyromonas Phylogeny and Taxon-Specific Amplification. Specific primer pairs designed to specifically amplify products only from intended target taxa were assessed against a panel of templates from a diverse set of representative organisms. This figure is a compilation of cropped gel images illustrating PCR reaction products using the specific primer pairs shown to the right. The template material in each reaction was about 1 :100 dilution of gDNA obtained from DSMZ. PCR reactions: about 95°C, about 1 min.; about 95°C, about 15 sec.; about 60°C, about 30 sec.; repeat previous 2 cycles 40 times. Gel conditions: about 2% agarose gel, about 100 V, ethidium bromide staining. Representative data illustrating differential PCR amplification of target taxa.

[0053] FIG. 3. Exemplary qPCR Standard Curves for MC3-specific Primers.

[0054] FIG. 4. Exemplary Specific Quantification of MC3 Target Strains.

[0055] FIG. 5. Exemplary Quantification within Stool Communities.

DETAILED DESCRIPTION OF ILLUSTRATIVE EXAMPLES

[0056] Illustrative examples are now described. Other examples may be used in addition or instead. Details that may be apparent or unnecessary may be omitted to save space or for a more effective presentation. Some examples may be practiced with additional components or steps and/or without all of the components or steps that are described.

[0057] This disclosure relates to systems, formulations and methods that may be used in determination of presence/absence, relative and/or absolute abundance of Porphyromonas in a microbiome sample. This disclosure relates to formulations or kits that include target specific primers. This disclosure further relates to formulations or that may include reference primers, and/or reference materials, which may be used in determination of relative and/or absolute abundance of Porphyromonas in a microbiome sample.

[0058] The specific primers of this disclosure may specifically amplify targeted bacterial clades at various levels of taxonomic resolution (e.g., genus, species, strain). These taxon-specific primers may be designed to target putative microbial biomarkers reflecting human disease states to help characterize and validate their clinical relevance. Eventually, panels of biomarker-specific primers may be used to develop rapid and cost-effective qPCR-based microbiome-based diagnostics. [0059] These specific primer pairs may distinguish target species from close relatives within the Porphyromonas genus. These specific primers may also allow rapid qPCR quantification of the species-level taxa within human stool samples. These specific primer sets may also enable rapid and efficient hypothesis testing involving Porphyromonas species to validate the clinical utility of specific Porphyromonas species as biomarkers of disease progression and to provide insights into mechanisms of action.

[0060] In one example, to better understand the specific Porphyromonas species contributing to these effects, we designed PCR specific primer pairs capable of specifically amplifying P. somerae, P. bennonis, gut-associated relatives of P. endodontalis, and sub-genus clades that include the related species P. catoniae, P. gulae, and P. gingivalis, and another clade including P. uenonis and P. asaccharolytica.

[0061] In another example, specific PCR primers were developed that may specifically amplify target regions found only in specific taxonomic groups of gut- associated Porphyromonas. We analyzed the Porphyromonas phylogenetic tree to identify distinct clades and sub-clades suitable for targeted amplification.

[0062] In another example, we identified and targeted five distinct clades for primer development that, when combined, may be capable of encompassing the entire Porphyromonas genus. We also targeted two species within one of these clades for primer design. We selected the species P. uenonis and P. assacharolytica because both have been implicated as putative bacterial biomarkers of clinical relevance.

[0063] In another example, after assessing each primer set against a panel of representative Porphyromonas genomes to ensure they amplified products on their intended targets, we assessed each primer using qPCR within complex human stool- derived communities to ensure the absence of non-specific amplification and determine the dynamic range of each primer set.

Example 1. Primer Design [0064] Primers used in this example were designed by following the methodology schematically shown in FIG. 1. First, clade-specific primer sets encompassing the breadth of Porphyromonas diversity, as well as species-specific primer sets targeting a subset of Porphyromonas species of clinical relevance were designed. Each primer set was then assessed against a representative panel of Porphyromonas strains. In this disclosure, each primer set comprises a forward primer and a reverse primer.

[0065] A single primer set capable of specifically targeting the entire Porphyromonas genus may be designed. Such single primer sets are within the scope of this disclosure.

[0066] The genomes of representative Porphyromonas were obtained from publicly available databases. We identified genus sub-clades through the use of a phylogenetic tree containing members of the genus. Phylogeny was determined using a set of 25 concatenated marker proteins, wherein these markers are universal for 95% of all known Bacteria and Archaea (Lee MD, Bioinformatics, Volume 35,

Issue 20, 15 October 2019, Pages 4162-4164. The entire content of this publication is incorporated herein by reference). These sub-clades may provide greater phylogenetic resolution which may facilitate more targeted mechanistic and clinical insights.

[0067] Putative primers were screened for non-specific targets against other members of Porphyromonas and close to 4,000 common members of the human gut microbiome. Five Porphyromonas sub-clades were identified and used to design primer pairs intended to detect all members within a designated sub-clade. Primers designed for each sub-clade were shown in Table 1. Primers optimized for downstream qPCR applications were ordered from Integrated DNA Technologies.

Table 1. Primer pairs (forward primer and reverse primer) designed for detection of Porphyromonas.

Example 2. Assessing primers.

[0068] In this example, Porphyromonas species shown in Table 2 were used as exemplary species representing the genus. We purchased genomic DNA for a variety of representative Porphyromonas isolates, shown in Table 2, from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). These representative isolates were selected based upon their genome availability, clinical relevance, and distribution across the phylogenetic tree. Genomic DNA was quantified using Qubit Fluorometric Quantitation (Thermo Fisher Scientific) and diluted in TE Buffer prior to PCR reactions. Table 2. Exemplary Porphyromonas species

[0069] The Porphyromonas species shown in Table 2 was targeted by using the primer sets shown in Table 3.

Table 3. Exemplary primers.

[0070] Amplification and detection reactions were conducted in 96-well optical plates on a Bio-Rad CFX Connect using 2x iTaq PCR Master Mix (Bio-Rad), about 0.25 mM of each primer, and a defined concentration of genomic DNA within reactions totaling about 20 mI_. Each qPCR reaction was initiated with about 1 -minute incubation at about 95°C, then cycled between about 15 seconds at 95°C and about 30 seconds at about 60°C for 40 cycles. Fluorescence intensity was detected following each cycle. Finally, a melt curve analysis of products over the range of about 60°C to about 95°C at about 0.5°C increments was conducted. Fluorescence intensity results were used to detect, monitor, and quantify amplicons from target sub-clades. Some reaction products were also analyzed using agarose gel electrophoresis with ethidium bromide staining.

[0071] Primer sets yielding products within appropriate clades or species were next assessed against non-target Porphyromonas strains to ensure the absence of non-specific amplification among near neighbors.

[0072] For each of the targeted taxons at least three probes were designed and assessed. Representative data is shown in FIG. 2. As summarized in Table 4, we were able to successfully design primers capable of specifically amplifying distinct regions within each targeted Porphyromonas clade. Furthermore, we went on to successfully design species-specific primers targeting distinct regions in the clinically relevant species P. uenonis and P. assacharolytica.

Table 4. Results Summary

[0073] Each primer pair was assessed against genomic DNA from a diverse panel of representative Porphyromonas isolates. Plus signs in Table 3 denote the presence of amplified products whereas zeros indicate no PCR product was observed. Primer sets targeted either distinct Porphyromonas clades or species, as indicated by the designated Target Taxon. Cells highlighted in green in Table 3 emphasize expected products were observed exclusively on all appropriate isolates assessed for primers targeting MC1 , MC2, MC3, MC5, P. uenonis, and P. asaccharolytica. There are no readily available gut-associated MC4 isolates; accordingly, the absence of a product on P. endodontalis is highlighted in green for MC4 primers to denote the expected absence of product on the most closely related near neighbor not targeted by the primer set.

[0074] While most primer sets proved successful, failed primer pairs either did not amplify the intended target in all targeted strains or amplified unintended targets when tested against the other Porphyromonas sub-clades. Primer sets falling within the first category may still prove useful as probes targeting higher resolution Porphyromonas sub-clades. For this reason, all primer sets shown in Table 1 are within the scope of this disclosure.

Example 3. Quantitative PCR: Determining Target Abundance.

[0075] While traditional end-point PCR reactions may determine the presence or absence of target templates within a complex matrix, determining the absolute or relative abundance of putative bacterial biomarkers may be necessary to infer clinical insights. Accordingly, in this Example, primer sets were designed to be suitable for quantitative PCR (qPCR) applications.

[0076] During qPCR, fluorescent dyes bound to amplicon products may be used to monitor product formation following each round of amplification. The cycle number when florescence crosses a threshold above background defines the quantification cycle (Cq), which is determined by the initial template concentration and its geometric increase following each round of amplification. By comparing Cq values of reactions with known template concentrations, the abundance of template initially present in unknown samples may be determined.

[0077] Primer sets with validated target-specific Porphyromonas amplification may be used to determine the presence and quantify the abundance of target taxon or species within unknown samples using quantitative PCR. By comparing Cq values of reactions with known template concentrations, the abundance of template initially present in unknown samples may be determined.

[0078] Standard curves were established with Cq values obtained from reactions with known template concentration, initiated as a series of 10-fold dilutions (FIG. 3). Dilutions were quantified in triplicate. Templates were purified amplicon products obtained from prior reactions on purified genomic DNA from a representative target strain and quantified using a QuBit Fluorometric quantification (Thermo Fisher Scientific).

[0079] Representative data shown here were used to establish a standard curve from one set of Porphyromonas primers specific for members within Clade 3 obtained by quantifying a dilution series with known concentrations of P. gingivalis (AMI_0029) amplicon template across eight orders of magnitude. The 10¹⁰-dilution yielded the last reliable set of products, establishing a limit of detection representing 71 copies of template within the reaction.

[0080] Next, in the same plate, primers were assessed against the same panel of representative Porphyromonas strains (Table 2) in triplicate. Again, we observed primer specificity for Porphyromonas Clade 3 strains. Here, only members of Clade 3 (P. catoniae, P. gulae, and P. gingivalis) yielded product (FIG. 4). Template genomic DNA from all other strains assessed either failed to produce any product or fell below the established limit of detection.

[0081] Finally, primers suitable for research and potential diagnostic purposes need to specifically and sensitively amplify PCR products exclusively from target taxa within diverse communities in complex samples. To begin assessing the specificity and sensitivity of our Porphyromonas primers within increasingly complex samples, we selected primer pairs that passed our initial quality controls and assessed their performance against diverse stool-derived microbial communities.

[0082] The complex microbial communities shown in FIG. 5 originate from human stool samples obtained from OpenBiome, a non-profit stool bank that provides stool preparations to clinicians for fecal microbiota transplants and clinical scientists to support research on the human microbiome. Here, a Fecal Microbiota Preparation for Research (FMP-R) was obtained from OpenBiome. This sample comprises of a mixture of fecal-derived material from numerous pre-screened, healthy human donors and intended to reflect a representative complex and healthy gut microbiome community.

[0083] To determine the abundance of Porphyromonas within increasingly complex microbial communities, we performed qPCR on OpenBiome samples derived from human stool and compared to an established standard curve. Based upon the community composition provided by OpenBiome, these samples did not contain any Porphyromonas species. Accordingly, we assessed our primer pairs against OpenBiome samples as well as the same community spike with known concentrations of target template DNA from P. gingivalis.

[0084] While the results presented here are limited to Porphyromonas, the methods of this disclosure may be applicable to a wide variety of bacterial targets.

[0085] All articles, patents, patent applications, and other publications that have been cited in this disclosure are incorporated herein by reference.

[0086] In this disclosure, the indefinite article “a” and phrases “one or more” and “at least one” are synonymous and mean “at least one”.

[0087] Relational terms such as “first” and “second” and the like may be used solely to distinguish one entity or action from another, without necessarily requiring or implying any actual relationship or order between them. The terms “comprises,” “comprising,” and any other variation thereof when used in connection with a list of elements in the specification or claims are intended to indicate that the list is not exclusive and that other elements may be included. Similarly, an element preceded by an “a” or an “an” does not, without further constraints, preclude the existence of additional elements of the identical type.

[0088] The abstract is provided to help the reader quickly ascertain the nature of the technical disclosure. It is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the claims. In addition, various features in the foregoing detailed description are grouped together in various examples to streamline the disclosure. This method of disclosure should not be interpreted as requiring claimed examples to require more features than are expressly recited in each claim. Rather, as the following claims reflect, inventive subject matter lies in less than all features of a single disclosed example. Thus, the following claims are hereby incorporated into the detailed description, with each claim standing on its own as separately claimed subject matter.

Claims

WHAT IS CLAIMED IS:

1. A method of identification of a target microorganism in a microbiome sample, comprising: obtaining the microbiome sample that potentially comprises at least one DNA; processing the sample to have the at least one DNA accessible to react with a specific primer pair designed specifically for identification of the target microorganism present in the microbiome; mixing the accessible DNA with a primer mixture comprising the specific primer pair to form a microbiome reaction mixture; subjecting the microbiome reaction mixture to a reaction under which at least one section of the accessible DNA is amplified and produces a fluorescence signal; measuring amount of fluorescence signal produced; and identifying whether the target microorganism is present in the microbiome sample.

2. The method of Claim 1 , wherein the method further comprises determining abundance of the target microorganism in the microbiome sample

3. The method of Claims 1 or 2, further comprising: forming a patient microorganism profile based on said identification and/or determination; comparing the patient microorganism profile with a microorganism profile of a healthy patient; determining whether the patient has a disease/clinical complication, has a risk of developing a disease/clinical complication, or responds to a treatment, or determining progression of a disease/clinical complication of the patient; and treating the patient if the patient has a disease/clinical complication.

4. The method of Claims 1 to 2, wherein the target microorganism comprises one or more specific target bacteria.

5. The method of Claim 2, wherein the determining abundance of the target microorganism comprises establishing or obtaining a standard curve.

6. The method of Claim 2, wherein the determining abundance of target microorganism comprises establishing or obtaining a standard curve by reacting a template microbiome reaction mixture with a known concentration of the target microorganism.

7. The method of Claim 2, wherein the determining abundance of the target microorganism comprises mixing the microbiome reaction mixture with a known reference standard.

8. The method of Claims 1 to 2, wherein the primer mixture comprises a specific primer pair; and wherein each specific primer pair comprises a forward primer and a reverse primer.

9. The method of Claims 1 to 2, wherein the target microorganism comprises at least one genus of bacteria, and wherein the genus of bacteria has at least one sub- clade, or at least two sub-clades.

10. The method of Claim 9, wherein the primer mixture comprises at least two specific primer pairs; wherein each specific primer pair comprises a forward primer and a reverse primer; and wherein at least one first specific primer pair is capable of amplifying a first species belonging to a first sub-clade of the target bacteria and at least one second specific primer pair is capable of amplifying a second species belonging to a second sub-clade of the target bacteria.

11.The method of Claims 1 to 2, wherein the primer mixture comprises a specific primer pair; wherein the specific primer pair comprises a forward primer and a reverse primer; wherein the forward primer is p0173 and the reverse primer is p0174.

12. The method of any one of Claims 1 to 10, wherein the primer mixture comprises a specific primer pair; wherein the specific primer pair comprises a forward primer and a reverse primer selected from the primer pairs of Table 1 , Primer IDs p0171 to p0344, or a combination thereof; wherein at least one first specific primer pair is capable of amplifying a first species belonging to a first sub-clade of the target microorganism and at least one second specific primer pair is capable of amplifying a second species belonging to a second sub-clade of the target microorganism.

13. The method of any one of Claims 1 to 12, wherein the target microorganism is Porphyromonas.

14. The method of any one of the preceding claims or the following claims, wherein the microbiome sample is obtained from a patient.

15. The method of any one of the preceding claims, wherein the target microorganism belong to at least one species of the Porphyromonas genus.

16. The method of any one of the preceding claims, wherein the target microorganism belong to at least one species of Porphyromonas genus of Table 2, ID no. AMI_0025 to AMI_0032, or a combination thereof.

17. The method of any one of the preceding claims, wherein the subjecting the microbiome reaction mixture comprises subjecting the microbiome reaction mixture to a PCR or a qPCR reaction.

18. The method of any one of Claims 3 to 17, the disease/clinical complication comprises (chronic) oral infections, cancers, neurodegenerative diseases, or a combination thereof.

19. The method of any one of the Claims 3 to 18, wherein the disease/clinical complication comprises colorectal cancer, endometrial cancer, gastric adenocarcinomas, and cervical cancer, P. aeruginosa pulmonary infections in cystic fibrosis, oral pathological process, or a combination thereof.

20. The method of any one of the preceding Claims 3 to 19, wherein the disease/clinical complication comprises an oral pathological process, and wherein the oral pathological process comprises periodontitis, oral squamous cell carcinomas, or a combination thereof.

21. The method of any one of the preceding Claims 3 to 18, wherein the disease/clinical complication comprises colorectal cancer.

22. The method of any one of the preceding claims, wherein the microbiome sample comprises stool, saliva, skin, nasal swab, vaginal swab, blood, urine, hair, or oral swab.

23. The method of any one of the preceding claims, wherein the method further comprises validating the specific primer pair to determine whether the specific primer pair reacts with the DNA to confirm that the specific primer pair is substantially unique to the target microorganism.

24. The method of any one of the preceding claims, wherein the method further comprises validating the specific primer pair to determine whether the specific primer pair reacts with the DNA to confirm that the specific primer pair is substantially unique to the target microorganism, and to determine the specific primer pair sensitivity and/or specificity.

25. The method of any one of the preceding claims, wherein the reaction product may be analyzed by a gel electrophoresis method.

26. The method of any one of the preceding claims, wherein the specific primer pair is a pair of polymerase chain reaction (PCR) primers.

27. The method of any one of the preceding claims, wherein the method further comprises forming a microbiome profile for the microbiome sample.

28. The method of any one of the preceding claims, wherein the amplifying the DNA comprises amplifying the DNA with qPCR.

29. The method of any one of the preceding claims, wherein the determining the presence and/or abundance comprises measuring a fluorescence signal during the amplifying step.

30. The method of any one of the preceding claims, wherein the microbiome sample is from a human patient.

31.The method of any one of the preceding claims, wherein the patient is a human or an animal.

32. The method of any one of the preceding claims, wherein the method further comprises administering a therapeutic to the patient.

33. The method of Claim 32, wherein the therapeutic is not chemotherapy and/or radiation.

34. A nucleic acid having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to any one of the sequences of Table 1 , Primer IDs p0171 to p0344, or a combination thereof.

35. A primer pair comprising a forward primer and a reverse primer, each having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the forward primers or reverse primers of Table 1 , Primer IDs p0171 to p0344, or a combination thereof; wherein the primer pair is specific for a target microorganism cluster.

36. A primer pair comprising a forward primer and a reverse primer, each having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the forward primers or reverse primers of Table 1 , wherein the primer pair is specific for a target sub-clade of the microorganism genus.

37. A diagnostic kit comprising one or more primer pairs of any one of Claims 11 to 12, or 34 to 36.

38. The diagnostic kit of Claim 37, further comprising a reference standard.

39. The diagnostic kit of Claim 37 or 38, wherein the kit is suitable for the method of any preceding claims for identification of the target microorganism present in the microbiome sample and/or, if the target microorganism is present in the microbiome, for determination of abundance of the target microorganism present in the microbiome sample.