Categorization of microbial communities

Abstract

The present disclosure provides embodiments of a method for characterizing microbial populations. Exemplified by methods for characterizing microbiota in vaginal samples, the methods provided herein are widely applicable to the characterization of microbial communities. Also provided are probiotic regimens and methods for selecting appropriate probiotic regimens based on the normal vaginal microbiota of a subject. Reagents and kits for detecting normal vaginal microbiota and diagnosing pathogenic microorganisms in the vagina are also provided.

1 . A set of nucleic acid probes that detect one or more phylogenetically informative genes of vaginal microorganisms comprising a plurality of oligonucleotide probes which hybridize to at least one phylogenetically informative gene for a plurality of vaginal microorganisms, wherein the plurality of vaginal microorganisms comprises  Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri, Lactobacillus coleohominis, Staphylococcus  sp.,  Streptococcus  sp.,  Atopobium vaginae , Lachnospiraceae sp.,  Megasphaera  sp.,  Enterococcus faecalis, Peptoniphilus  sp.,  Anaerococcus  sp.,  Micromonas  sp.,  Gemella palaticanis , Dialister  sp.,  Aerococcus  sp.,  Veillonella  sp.,  Finegoldia magna, Granulicatella elegans, Clostridium perfringens, Gardinerella vaginalis, Pseudomonas  sp.,  Mycoplasma  sp.,  Mobiluncus muleiri, Peptostreptococcus anaerobis, Escherichia coli, Shigella  sp. and Clostridiales sp. 
     
     
         2 . The set of nucleic acid probes of  claim 1 , wherein the nucleic acid probes are 19 to 26 oligonucleotides in length. 
     
     
         3 . The set of nucleic acid probes of  claim 1  attached to a solid support. 
     
     
         4 . The set of nucleic acid probes of  claim 1 , wherein the one or more phylogenetically informative gene is selected from the group consisting of: 16S rRNA; rpoB; gyrB; gyrA; tmRNA; recA; EF-Tu (tuf); groEL (cnp60, hsp60); atpD; ompA gene; gapA; pgi; fusA; ileS; lepA; leuS; pyrG; recG; rplB; pmoA/amoA genes; mmoX; nifH; nirS; nirK; norB; mcrA; and rbcL. 
     
     
         5 . A set of nucleic acid tags probes comprising a plurality of nucleic acid sequences selected from the group consisting of SEQ ID NOs: 6-23. 
     
     
         6 . The set of nucleic acid probes of  claim 5  attached to a solid support. 
     
     
         7 . A set of nucleic acid probes that detect one or more phylogenetically informative genes of vaginal microorganisms comprising a plurality of oligonucleotide probes which hybridize to at least one phylogenetically informative gene for a plurality of vaginal microorganisms, wherein the plurality of vaginal microorganisms comprises two or more microorganisms selected from the group consisting of  Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri, Lactobacillus coleohominis, Staphylococcus  sp.,  Streptococcus  sp.,  Atopobium vaginae , Lachnospiraceae sp.,  Megasphaera  sp.,  Enterococcus faecalis, Peptoniphilus  sp.,  Anaerococcus  sp.,  Micromonas  sp.,  Gemella palaticanis, Dialister  sp.,  Aerococcus  sp.,  Veillonella  sp.,  Finegoldia magna, Granulicatella elegans, Clostridium perfringens, Gardinerella vaginalis, Pseudomonas  sp.,  Mycoplasma  sp.,  Mobiluncus muleiri, Peptostreptococcus anaerobis, Escherichia coli, Shigella  sp., and Clostridiales sp., and wherein the one or more phylogenetically informative gene is selected from the group consisting of: 16S rRNA; rpoB; gyrB; gyrA; tmRNA; recA; EF-Tu (tuf); groEL (cnp60, hsp60); atpD; ompA gene; gapA; pgi; fusA; ileS; lepA; leuS; pyrG; recG; rplB; pmoA/amoA genes; mmoX; nifH; nirS; nirK; norB; mcrA; and rbcL. 
     
     
         8 . The set of nucleic acid probes of  claim 7 , wherein the nucleic acid probes are 19 to 26 oligonucleotides in length. 
     
     
         9 . The set of nucleic acid probes of  claim 7  attached to a solid support. 
     
     
         10 . A set of nucleic acid tags probes comprising a plurality of nucleic acid sequences selected from the group consisting of SEQ ID NOs: 6-23. 
     
     
         11 . The set of nucleic acid probes of  claim 10  attached to a solid support. 
     
     
         12 . A kit for detecting more than one species of vaginal microbiota, the kit comprising: a plurality of species specific probes, each of which species specific probes identifies a species of vaginal microbiota, wherein the specific probes specifically identify a gene selected from the group consisting of: 16S rRNA; rpoB; gyrB; gyrA; tmRNA; recA; EF-Tu (tuf); groEL (cnp60, hsp60); atpD; ompA gene; gapA; pgi; fusA; ileS; lepA; leuS; pyrG; recG; rplB; pmoA/amoA genes; mmoX; nifH; nirS; nirK; norB; mcrA; and rbcL 
     
     
         13 . The kit of  claim 12 , wherein the wherein the more than one species of vaginal microbiota is selected from the group consisting of  Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri, Lactobacillus coleohominis, Staphylococcus  sp.,  Streptococcus  sp.,  Atopobium vaginae , Lachnospiraceae sp.,  Megasphaera  sp.,  Enterococcus faecalis, Peptoniphilus  sp.,  Anaerococcus  sp.,  Micromonas  sp.,  Gemella palaticanis, Dialister  sp.,  Aerococcus  sp.,  Veillonella  sp.,  Finegoldia magna, Granulicatella elegans, Gardinerella vaginalis, Pseudomonas  sp.,  Mycoplasma  sp.,  Mobiluncus muleiri, Peptostreptococcus anaerobis, Escherichia coli, Shigella  sp., and Clostridiales sp. 
     
     
         14 . The kit of  claim 12 , wherein the plurality of species specific probes are arrayed on a solid matrix. 
     
     
         15 . A set of nucleic acid probes that detect one or more phylogenetically informative genes of vaginal microorganisms comprising a plurality of oligonucleotide probes which hybridize to at least one phylogenetically informative gene for a plurality of vaginal microorganisms, wherein the plurality of vaginal microorganisms comprises  Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri , and  Lactobacillus coleohominis.    
     
     
         16 . The set of nucleic acid probes of  claim 15 , further comprising a plurality of oligonucleotide probes which hybridize to at least one phylogenetically informative gene for a plurality of vaginal microorganisms comprising  Atopobium vaginae , Clostridiales sp. and  Megasphaera  sp. 
     
     
         17 . The set of nucleic acid probes of  claim 16 , further comprising a plurality of oligonucleotide probes which hybridize to at least one phylogenetically informative gene for a plurality of vaginal microorganisms comprising  Staphylococcus  sp.,  Streptococcus  sp., Lachnospiraceae sp.,  Enterococcus faecalis, Peptoniphilus  sp.,  Anaerococcus  sp.,  Micromonas  sp.,  Gemella palaticanis, Dialister  sp.,  Aerococcus  sp.,  Veillonella  sp.,  Finegoldia magna, Granulicatella elegans, Clostridium perfringens, Gardinerella vaginalis, Pseudomonas  sp.,  Mycoplasma  sp.,  Mobiluncus muleiri, Peptostreptococcus anaerobis, Escherichia coli , and  Shigella  sp.