Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Prevotella diversity, niches and interactions with the human host

Abstract

The genus Prevotella includes more than 50 characterized species that occur in varied natural habitats, although most Prevotella spp. are associated with humans. In the human microbiome, Prevotella spp. are highly abundant in various body sites, where they are key players in the balance between health and disease. Host factors related to diet, lifestyle and geography are fundamental in affecting the diversity and prevalence of Prevotella species and strains in the human microbiome. These factors, along with the ecological relationship of Prevotella with other members of the microbiome, likely determine the extent of the contribution of Prevotella to human metabolism and health. Here we review the diversity, prevalence and potential connection of Prevotella spp. in the human host, highlighting how genomic methods and analysis have improved and should further help in framing their ecological role. We also provide suggestions for future research to improve understanding of the possible functions of Prevotella spp. and the effects of the Western lifestyle and diet on the host–Prevotella symbiotic relationship in the context of maintaining human health.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Genomic overview of the genus Prevotella.
Fig. 2: Distribution and stratification of Prevotella spp. across human populations and body sites.
Fig. 3: Current diversity of Prevotella spp. in the human microbiome.
Fig. 4: Evidence for a role of Prevotella spp. in human infections and autoimmunity.

References

  1. 1.

    Shah, H. N. & Collins, D. M. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int. J. Syst. Bacteriol. 40, 205–208 (1990). This work describes the initial identification, naming and description of the genus Prevotella.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  2. 2.

    Oliver, W. W. & Wherry, W. B. Notes on some bacterial parasites of the human mucous membranes. J. Infect. Dis. 28, 341–344 (1921).

    Article  Google Scholar 

  3. 3.

    Shah, H. N., Chattaway, M. A., Rajakurana, L. & Gharbia, S. E. Prevotella. Bergey’s Manual of Systematics of Archaea and Bacteria 1–25 (Springer, 2015).

  4. 4.

    Fehlner-Peach, H. et al. distinct polysaccharide utilization profiles of human intestinal Prevotella copri isolates. Cell Host Microbe 26, 680–690.e5 (2019). This study highlights how different strains in the P. copri complex have different abilities to target different types of polysaccharides.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  5. 5.

    Gmür, R. & Thurnheer, T. Direct quantitative differentiation between Prevotella intermedia and Prevotella nigrescens in clinical specimens. Microbiology 148, 1379–1387 (2002).

    PubMed  Article  PubMed Central  Google Scholar 

  6. 6.

    Zambon, J. J., Reynolds, H. S. & Slots, J. Black-pigmented Bacteroides spp. in the human oral cavity. Infect. Immun. 32, 198–203 (1981).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  7. 7.

    Segata, N. et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 13, R42 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  8. 8.

    Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012). This is one of the first and most comprehensive reports on the higher abundance and prevalence of Prevotella spp. in non-Westernized populations by 16S rRNA gene sequencing.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  9. 9.

    Smits, S. A. et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357, 802–806 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. 10.

    Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11.

    Obregon-Tito, A. J. et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat. Commun. 6, 6505 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. 12.

    Hansen, M. E. B. et al. Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana. Genome Biol. 20, 16 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  13. 13.

    De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. USA 107, 14691–14696 (2010). This work reports one of the first pieces of evidence that Prevotella spp. dominate the gut microbiome in ‘non-Westernized’ populations.

    PubMed  Article  PubMed Central  Google Scholar 

  14. 14.

    Brewster, R. et al. Surveying gut microbiome research in Africans: toward improved diversity and representation. Trends Microbiol. 27, 824–835 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019). This study shows how microbial genomes can be reconstructed from metagenomic sequencing on a large scale, which is crucial to better understand the genetic basis and variability of human-associated Prevotella spp.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  16. 16.

    Tett, A. et al. The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations. Cell Host Microbe 26, 666–679.e7 (2019). This work reports the discovery that P. copri is not monotypic but comprises genetically distinct clades, and that this diversity should be considered in future studies.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  17. 17.

    Scher, J. U. et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2, e01202 (2013). This is the first report of a link between P. copri and rheumatoid arthritis, which has since been expanded to other cohorts and related diseases.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  18. 18.

    Zhao-Fleming, H. H. et al. Traditional culture methods fail to detect principle pathogens in necrotising soft tissue infection: a case report. J. Wound Care 27, S24–S28 (2018).

    PubMed  Article  PubMed Central  Google Scholar 

  19. 19.

    Bein, T., Brem, J. & Schüsselbauer, T. Bacteremia and sepsis due to Prevotella oris from dentoalveolar abscesses. Intensive Care Med. 29, 856 (2003).

    PubMed  Article  PubMed Central  Google Scholar 

  20. 20.

    Teanpaisan, R., Douglas, C. W., Eley, A. R. & Walsh, T. F. Clonality of Porphyromonas gingivalis, Prevotella intermedia and Prevotella nigrescens isolated from periodontally diseased and healthy sites. J. Periodontal Res. 31, 423–432 (1996).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  21. 21.

    Baumgartner, J. C., Watkins, B. J., Bae, K. S. & Xia, T. Association of black-pigmented bacteria with endodontic infections. J. Endod. 25, 413–415 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  22. 22.

    Si, J., You, H. J., Yu, J., Sung, J. & Ko, G. Prevotella as a hub for vaginal microbiota under the influence of host genetics and their association with obesity. Cell Host Microbe 21, 97–105 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  23. 23.

    Larsen, J. M. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology 151, 363–374 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. 24.

    Teles, F. R. et al. Early microbial succession in redeveloping dental biofilms in periodontal health and disease. J. Periodontal Res. 47, 95–104 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  25. 25.

    Cani, P. D. Human gut microbiome: hopes, threats and promises. Gut 67, 1716–1725 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. 26.

    Ley, R. E. Gut microbiota in 2015: Prevotella in the gut: choose carefully. Nat. Rev. Gastroenterol. Hepatol. 13, 69–70 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  27. 27.

    Claus, S. P. The strange case of Prevotella copri: Dr. Jekyll or Mr. Hyde? Cell Host Microbe 26, 577–578 (2019). This commentary summarizes some of the conflicting evidence for a favourable or detrimental role of P. copri.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  28. 28.

    Henderson, G. et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5, 14567 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  29. 29.

    Deusch, S. et al. A structural and functional elucidation of the rumen microbiome influenced by various diets and microenvironments. Front. Microbiol. 8, 1605 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  30. 30.

    Accetto, T. & Avguštin, G. The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: a factor in their ubiquity? Syst. Appl. Microbiol. 42, 107–116 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  31. 31.

    Guevarra, R. B. et al. Piglet gut microbial shifts early in life: causes and effects. J. Anim. Sci. Biotechnol. 10, 1 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  32. 32.

    Wang, X. et al. Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria. Microbiome 7, 109 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  33. 33.

    Coil, D. A. et al. Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment. PLoS ONE 14, e0214354 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. 34.

    Kogawa, M., Hosokawa, M., Nishikawa, Y., Mori, K. & Takeyama, H. Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes. Sci. Rep. 8, 2059 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  35. 35.

    Ueki, A., Akasaka, H., Satoh, A., Suzuki, D. & Ueki, K. Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil. Int. J. Syst. Evol. Microbiol. 57, 1803–1809 (2007).

    PubMed  Article  PubMed Central  Google Scholar 

  36. 36.

    Sutton, T. D. S. & Hill, C. Gut bacteriophage: current understanding and challenges. Front. Endocrinol. 10, 784 (2019).

    Article  Google Scholar 

  37. 37.

    Gregg, K., Kennedy, B. G. & Klieve, A. V. Cloning and DNA sequence analysis of the region containing attP of the temperate phage ΦAR29 of Prevotella ruminicola AR29. Microbiology 140, 2109–2114 (1994).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  38. 38.

    Ambrozic, J., Ferme, D., Grabnar, M., Ravnikar, M. & Avgustin, G. The bacteriophages of ruminal prevotellas. Folia Microbiol. 46, 37–39 (2001).

    CAS  Article  Google Scholar 

  39. 39.

    Devoto, A. E. et al. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat. Microbiol. 4, 693–700 (2019). This study reports the discovery of large intestine megaphages associated with Prevotella and some initial characterization of their genetic features, such as the use of an alternative genetic code.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. 40.

    Crisci, M. A., Chen, L. X., Devoto, A. E., Borges, A. L. & Bordin, N. Wide distribution of alternatively coded Lak megaphages in animal microbiomes. bioRxiv https://doi.org/10.1101/2021.01.08.425732 (2021).

    Article  Google Scholar 

  41. 41.

    Donati, C. et al. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat. Microbiol. 1, 16070 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  42. 42.

    Gupta, V. K., Chaudhari, N. M., Iskepalli, S. & Dutta, C. Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human. BMC Genomics 16, 153 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  43. 43.

    Mueller, S. et al. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl. Environ. Microbiol. 72, 1027–1033 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. 44.

    Santos-Marcos, J. A. et al. Sex differences in the gut microbiota as potential determinants of gender predisposition to disease. Mol. Nutr. Food Res. 63, 1800870 (2019).

    Article  CAS  Google Scholar 

  45. 45.

    Kornman, K. S. & Loesche, W. J. The subgingival microbial flora during pregnancy. J. Periodontal Res. 15, 111–122 (1980).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  46. 46.

    Kornman, K. S. & Loesche, W. J. Effects of estradiol and progesterone on Bacteroides melaninogenicus and Bacteroides gingivalis. Infect. Immun. 35, 256–263 (1982).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  47. 47.

    Akcalı, A. et al. Association between polycystic ovary syndrome, oral microbiota and systemic antibody responses. PLoS ONE 9, e108074 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  48. 48.

    Karcher, N. et al. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol. 21, 138 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. 49.

    Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. 50.

    Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  51. 51.

    Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  52. 52.

    Könönen, E. Pigmented Prevotella species in the periodontally healthy oral cavity. FEMS Immunol. Med. Microbiol. 6, 201–205 (1993).

    PubMed  Article  PubMed Central  Google Scholar 

  53. 53.

    Mättö, J. et al. Role of Porphyromonas gingivalis, Prevotella intermedia, and Prevotella nigrescens in extraoral and some odontogenic infections. Clin. Infect. Dis. 25, S194–S198 (1997).

    PubMed  Article  PubMed Central  Google Scholar 

  54. 54.

    Brook, I. Prevotella and Porphyromonas infections in children. J. Med. Microbiol. 42, 340–347 (1995).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  55. 55.

    Renson, A. et al. Sociodemographic variation in the oral microbiome. Ann. Epidemiol. 35, 73–80.e2 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  56. 56.

    Willis, J. R. et al. Citizen science charts two major ‘stomatotypes’ in the oral microbiome of adolescents and reveals links with habits and drinking water composition. Microbiome 6, 218 (2018).

    PubMed  PubMed Central  Article  Google Scholar 

  57. 57.

    Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435–439 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. 58.

    Lassalle, F. et al. Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet. Mol. Ecol. 27, 182–195 (2018).

    PubMed  Article  PubMed Central  Google Scholar 

  59. 59.

    Laiola, M., De Filippis, F., Vitaglione, P. & Ercolini, D. A Mediterranean diet intervention reduces the levels of salivary periodontopathogenic bacteria in overweight and obese subjects. Appl. Environ. Microbiol. 86, e00777–20 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. 60.

    Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J. & Segata, N. Shotgun metagenomics, from sampling to analysis. Nat. Biotechnol. 35, 833–844 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  61. 61.

    Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

    Article  CAS  Google Scholar 

  62. 62.

    Castro-Nallar, E. et al. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ 3, e1140 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  63. 63.

    Ferretti, P. et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe 24, 133–145.e5 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. 64.

    Olm, M. R. et al. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res. 27, 601–612 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. 65.

    Ghensi, P. et al. Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics. NPJ Biofilms Microbiomes 6, 47 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. 66.

    Eren, A. M., Borisy, G. G., Huse, S. M. & Mark Welch, J. L. Oligotyping analysis of the human oral microbiome. Proc. Natl Acad. Sci. USA 111, E2875–E2884 (2014).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  67. 67.

    Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626–638 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  68. 68.

    Van Rossum, T., Ferretti, P., Maistrenko, O. M. & Bork, P. Diversity within species: interpreting strains in microbiomes. Nat. Rev. Microbiol. 18, 491–506 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  69. 69.

    Yassour, M. et al. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Cell Host Microbe 24, 146–154.e4 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  70. 70.

    Korpela, K. et al. Selective maternal seeding and environment shape the human gut microbiome. Genome Res. 28, 561–568 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. 71.

    Schmidt, T. S. et al. Extensive transmission of microbes along the gastrointestinal tract. eLife 8, e42693 (2019). This work provides evidence that transmission to the large intestine by oral microorganisms is common and is particularly relevant for Prevotella spp.

    PubMed  PubMed Central  Article  Google Scholar 

  72. 72.

    Thomas, A. M. et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat. Med. 25, 667–678 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  73. 73.

    Wirbel, J. et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat. Med. 25, 679–689 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. 74.

    Nagy, E. Anaerobic infections: update on treatment considerations. Drugs 70, 841–858 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  75. 75.

    Socransky, S. S., Haffajee, A. D., Cugini, M. A., Smith, C. & Kent, R. L. Jr. Microbial complexes in subgingival plaque. J. Clin. Periodontol. 25, 134–144 (1998). This is the seminal work in the presequencing era associating species in the dental plaque biofilm, including Prevotella spp., with oral diseases.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  76. 76.

    Schincaglia, G. P. et al. Clinical, immune, and microbiome traits of gingivitis and peri-implant mucositis. J. Dent. Res. 96, 47–55 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  77. 77.

    Valm, A. M. et al. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc. Natl Acad. Sci. USA 108, 4152–4157 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  78. 78.

    Mark Welch, J. L., Rossetti, B. J., Rieken, C. W., Dewhirst, F. E. & Borisy, G. G. Biogeography of a human oral microbiome at the micron scale. Proc. Natl Acad. Sci. USA 113, E791–E800 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  79. 79.

    Kolenbrander, P. E., Palmer, R. J., Periasamy, S. & Jakubovics, N. S. Oral multispecies biofilm development and the key role of cell–cell distance. Nat. Rev. Microbiol. 8, 471–480 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  80. 80.

    Kolenbrander, P. E. Oral microbial communities: biofilms, interactions, and genetic systems. Annu. Rev. Microbiol. 54, 413–437 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  81. 81.

    Ammann, T. W., Belibasakis, G. N. & Thurnheer, T. Impact of early colonizers on in vitro subgingival biofilm formation. PLoS ONE 8, e83090 (2013).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  82. 82.

    Fine, D. H. et al. Aggregatibacter actinomycetemcomitans and its relationship to initiation of localized aggressive periodontitis: longitudinal cohort study of initially healthy adolescents. J. Clin. Microbiol. 45, 3859–3869 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. 83.

    Bao, K., Bostanci, N., Selevsek, N., Thurnheer, T. & Belibasakis, G. N. Quantitative proteomics reveal distinct protein regulations caused by Aggregatibacter actinomycetemcomitans within subgingival biofilms. PLoS ONE 10, e0119222 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  84. 84.

    Hajishengallis, G., Darveau, R. P. & Curtis, M. A. The keystone-pathogen hypothesis. Nat. Rev. Microbiol. 10, 717–725 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  85. 85.

    Ibrahim, M., Subramanian, A. & Anishetty, S. Comparative pan genome analysis of oral Prevotella species implicated in periodontitis. Funct. Integr. Genomics 17, 513–536 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  86. 86.

    Könönen, E., Nyfors, S., Máttö, J., Asikainen, S. & Somer, H. J. β-lactamase production by oral pigmented Prevotella species isolated from young children. Clin. Infect. Dis. 25, S272–S274 (1997).

    PubMed  Article  PubMed Central  Google Scholar 

  87. 87.

    Falagas, M. E. & Siakavellas, E. Bacteroides, Prevotella, and Porphyromonas species: a review of antibiotic resistance and therapeutic options. Int. J. Antimicrob. Agents 15, 1–9 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  88. 88.

    Diop, K., Dufour, J.-C., Levasseur, A. & Fenollar, F. Exhaustive repertoire of human vaginal microbiota. Hum. Microbiome J. 11, 100051 (2019).

    Article  Google Scholar 

  89. 89.

    Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA 108, 4680–4687 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  90. 90.

    Gilbert, N. M. et al. Gardnerella vaginalis and Prevotella bivia trigger distinct and overlapping phenotypes in a mouse model of bacterial vaginosis. J. Infect. Dis. 220, 1099–1108 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  91. 91.

    Randis, T. M. & Ratner, A. J. Gardnerella and Prevotella: co-conspirators in the pathogenesis of bacterial vaginosis. J. Infect. Dis. 220, 1085–1088 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  92. 92.

    Aroutcheva, A., Ling, Z. & Faro, S. Prevotella bivia as a source of lipopolysaccharide in the vagina. Anaerobe 14, 256–260 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  93. 93.

    Muzny, C. A. et al. Identification of key bacteria involved in the induction of incident bacterial vaginosis: a prospective study. J. Infect. Dis. 218, 966–978 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94.

    Muzny, C. A., Łaniewski, P., Schwebke, J. R. & Herbst-Kralovetz, M. M. Host-vaginal microbiota interactions in the pathogenesis of bacterial vaginosis. Curr. Opin. Infect. Dis. 33, 59–65 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  95. 95.

    Fettweis, J. M. et al. The vaginal microbiome and preterm birth. Nat. Med. 25, 1012–1021 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  96. 96.

    Brown, R. G. et al. Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes. Transl. Res. 207, 30–43 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  97. 97.

    Callahan, B. J. et al. Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women. Proc. Natl Acad. Sci. USA 114, 9966–9971 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  98. 98.

    Filardo, S. et al. Selected immunological mediators and cervical microbial signatures in women with Chlamydia trachomatis infection. mSystems 4, e00094–19 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  99. 99.

    Abdool Karim, S. S., Baxter, C., Passmore, J.-A. S., McKinnon, L. R. & Williams, B. L. The genital tract and rectal microbiomes: their role in HIV susceptibility and prevention in women. J. Int. Aids Soc. 22, e25300 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  100. 100.

    Cohen, J. Vaginal microbiome affects HIV risk. Science 353, 331–331 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  101. 101.

    van Teijlingen, N. H. et al. Vaginal dysbiosis associated-bacteria Megasphaera elsdenii and Prevotella timonensis induce immune activation via dendritic cells. J. Reprod. Immunol. 138, 103085 (2020).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  102. 102.

    Mitra, A. et al. The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions. Nat. Commun. 11, 1999 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  103. 103.

    Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  104. 104.

    Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011). This study introduces the concept of enterotypes, including the Prevotella enterotype, which is one of the enterotypes with the strongest evidence in recent refinements of the concept.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  105. 105.

    Cheng, M. & Ning, K. Stereotypes about enterotype: the old and new ideas. Genomics Proteom. Bioinforma. 17, 4–12 (2019).

    Article  Google Scholar 

  106. 106.

    Costea, P. I. et al. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3, 8–16 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  107. 107.

    Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  108. 108.

    Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  109. 109.

    Pasolli, E. et al. Accessible, curated metagenomic data through ExperimentHub. Nat. Methods 14, 1023–1024 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  110. 110.

    Pianta, A. et al. Evidence of the immune relevance of Prevotella copri, a gut microbe, in patients with rheumatoid arthritis. Arthritis Rheumatol. 69, 964–975 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  111. 111.

    Alpizar-Rodriguez, D. et al. Prevotella copri in individuals at risk for rheumatoid arthritis. Ann. Rheum. Dis. 78, 590–593 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  112. 112.

    Dillon, S. M. et al. An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia. Mucosal Immunol. 7, 983–994 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  113. 113.

    Wen, C. et al. Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. Genome Biol. 18, 142 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  114. 114.

    Rolhion, N. et al. A Listeria monocytogenes bacteriocin can target the commensal Prevotella copri and modulate intestinal infection. Cell Host Microbe 26, 691–701.e5 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  115. 115.

    Iljazovic, A., Amend, L., Galvez, E. J. C., de Oliveira, R. & Strowig, T. Modulation of inflammatory responses by gastrointestinal Prevotella spp. – from associations to functional studies. Int. J. Med. Microbiol. 311, 151472 (2021).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  116. 116.

    Kishikawa, T. et al. Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population. Ann. Rheum. Dis. 79, 103–111 (2020).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  117. 117.

    Lee, J.-Y. et al. Comparative analysis of fecal microbiota composition between rheumatoid arthritis and osteoarthritis patients. Genes 10, 748 (2019).

    CAS  PubMed Central  Article  Google Scholar 

  118. 118.

    Zhao, Y. et al. Detection and characterization of bacterial nucleic acids in culture-negative synovial tissue and fluid samples from rheumatoid arthritis or osteoarthritis patients. Sci. Rep. 8, 14305 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  119. 119.

    Wells, P. M. et al. Associations between gut microbiota and genetic risk for rheumatoid arthritis in the absence of disease: a cross-sectional study. Lancet Rheumatol. 2, e418–e427 (2020).

    PubMed  PubMed Central  Article  Google Scholar 

  120. 120.

    Maeda, Y. et al. Dysbiosis contributes to arthritis development via activation of autoreactive T cells in the intestine. Arthritis Rheumatol. 68, 2646–2661 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  121. 121.

    Hayashi, H., Shibata, K., Sakamoto, M., Tomita, S. & Benno, Y. Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 57, 941–946 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  122. 122.

    Vangay, P. et al. US Immigration westernizes the human gut microbiome. Cell 175, 962–972.e10 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  123. 123.

    De Filippis, F. et al. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host Microbe 25, 444–453.e3 (2019). This work reports important recent evidence of the effect of diet in shaping the subspecies pangenomic diversity of P. copri.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  124. 124.

    Goris, J. et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  125. 125.

    Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  126. 126.

    Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl Acad. Sci. USA 102, 2567–2572 (2005).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  127. 127.

    Gálvez, E. J. C. et al. Distinct polysaccharide utilization determines interspecies competition between intestinal Prevotella spp. Cell Host Microbe 28, 838–852.e6 (2020). This work describes how distinct Prevotella spp. compete in vivo for similar plant-derived polysaccharides.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  128. 128.

    Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  129. 129.

    Ou, J. et al. Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am. J. Clin. Nutr. 98, 111–120 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  130. 130.

    De Filippis, F. et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut 65, 1812–1821 (2016).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  131. 131.

    Haro, C. et al. Consumption of two healthy dietary patterns restored microbiota dysbiosis in obese patients with metabolic dysfunction. Mol. Nutr. Food Res. 61, 1700300 (2017).

    Article  CAS  Google Scholar 

  132. 132.

    Precup, G. & Vodnar, D.-C. Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles: a comprehensive literature review. Br. J. Nutr. 122, 131–140 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  133. 133.

    Gomez, A. et al. Gut microbiome of coexisting BaAka pygmies and bantu reflects gradients of traditional subsistence patterns. Cell Rep. 14, 2142–2153 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  134. 134.

    Benítez-Páez, A. et al. A multi-omics approach to unraveling the microbiome-mediated effects of arabinoxylan oligosaccharides in overweight humans. mSystems 4, e00209–19 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  135. 135.

    Roager, H. M. et al. Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial. Gut 68, 83–93 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  136. 136.

    Marungruang, N., Tovar, J., Björck, I. & Hållenius, F. F. Improvement in cardiometabolic risk markers following a multifunctional diet is associated with gut microbial taxa in healthy overweight and obese subjects. Eur. J. Nutr. 57, 2927–2936 (2018).

    PubMed  Article  PubMed Central  Google Scholar 

  137. 137.

    Ghosh, T. S. et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut 69, 1218–1228 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  138. 138.

    Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  139. 139.

    Christensen, L., Roager, H. M., Astrup, A. & Hjorth, M. F. Microbial enterotypes in personalized nutrition and obesity management. Am. J. Clin. Nutr. 108, 645–651 (2018).

    PubMed  Article  PubMed Central  Google Scholar 

  140. 140.

    Hjorth, M. F. et al. Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. Int. J. Obes. 42, 284 (2018).

    CAS  Article  Google Scholar 

  141. 141.

    Hjorth, M. F. et al. Prevotella-to-Bacteroides ratio predicts body weight and fat loss success on 24-week diets varying in macronutrient composition and dietary fiber: results from a post-hoc analysis. Int. J. Obes. 43, 149–157 (2019).

    CAS  Article  Google Scholar 

  142. 142.

    Ortega-Santos, C. P. & Whisner, C. M. The key to successful weight loss on a high-fiber diet may be in gut microbiome Prevotella abundance. J. Nutr. 149, 2083–2084 (2019).

    PubMed  Article  PubMed Central  Google Scholar 

  143. 143.

    Eriksen, A. K. et al. Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial. Am. J. Clin. Nutr. 111, 864–876 (2020).

    PubMed  Article  PubMed Central  Google Scholar 

  144. 144.

    Chung, W. S. F. et al. Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides. BMC Microbiol. 20, 283 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  145. 145.

    Kovatcheva-Datchary, P. et al. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 22, 971–982 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  146. 146.

    De Vadder, F. et al. Microbiota-produced succinate improves glucose homeostasis via intestinal gluconeogenesis. Cell Metab. 24, 151–157 (2016).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  147. 147.

    Asnicar, F. et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat. Med. 27, 321–332 (2021).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  148. 148.

    Pedersen, H. K. et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 535, 376–381 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  149. 149.

    Meslier, V. et al. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut 69, 1258–1268 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  150. 150.

    Kaoutari, A. E. et al. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat. Rev. Microbiol. 11, 497–504 (2013).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  151. 151.

    Chen, T. et al. Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota. Sci. Rep. 7, 2594 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  152. 152.

    Wright, D. P., Rosendale, D. I. & Robertson, A. M. Prevotella enzymes involved in mucin oligosaccharide degradation and evidence for a small operon of genes expressed during growth on mucin. FEMS Microbiol. Lett. 190, 73–79 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  153. 153.

    Shanahan, F., Ghosh, T. S. & O’Toole, P. W. The healthy microbiome — what is the definition of a healthy gut microbiome? Gastroenterology 160, 483–494 (2021).

    PubMed  Article  PubMed Central  Google Scholar 

  154. 154.

    De Filippis, F., Pellegrini, N., Laghi, L., Gobbetti, M. & Ercolini, D. Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns. Microbiome 4, 57 (2016).

    PubMed  PubMed Central  Article  Google Scholar 

  155. 155.

    Metwaly, A. & Haller, D. Strain-level diversity in the gut: the P. copri case. Cell Host Microbe 25, 349–350 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  156. 156.

    Li, X., Kolltveit, K. M., Tronstad, L. & Olsen, I. Systemic diseases caused by oral infection. Clin. Microbiol. Rev. 13, 547–558 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  157. 157.

    Rajasuo, A., Perkki, K., Nyfors, S., Jousimies-Somer, H. & Meurman, J. H. Bacteremia following surgical dental extraction with an emphasis on anaerobic strains. J. Dent. Res. 83, 170–174 (2004).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  158. 158.

    Daly, C., Mitchell, D., Grossberg, D., Highfield, J. & Stewart, D. Bacteraemia caused by periodontal probing. Aust. Dent. J. 42, 77–80 (1997).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  159. 159.

    Lei, W.-Y., Chang, W.-H., Shih, S.-C., Liu, C.-J. & Shih, C.-H. Pyogenic liver abscess with Prevotella species and Fusobacterium necrophorum as causative pathogens in an immunocompetent patient. J. Formos. Med. Assoc. 108, 253–257 (2009).

    PubMed  Article  PubMed Central  Google Scholar 

  160. 160.

    Kholy, K. E., Genco, R. J. & Van Dyke, T. E. Oral infections and cardiovascular disease. Trends Endocrinol. Metab. 26, 315–321 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  161. 161.

    Posteraro, P. et al. First bloodstream infection caused by Prevotella copri in a heart failure elderly patient with Prevotella-dominated gut microbiota: a case report. Gut Pathog. 11, 44 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  162. 162.

    Teanpaisan, R., Douglas, C. W. & Nittayananta, W. Isolation and genotyping of black-pigmented anaerobes from periodontal sites of HIV-positive and non-infected subjects in Thailand. J. Clin. Periodontol. 28, 311–318 (2001).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  163. 163.

    Steingruber, I., Bach, C. M., Czermak, B., Nogler, M. & Wimmer, C. Infection of a total hip arthroplasty with Prevotella loeschii. Clin. Orthop. Relat. Res. 418, 222–224 (2004).

    Article  Google Scholar 

  164. 164.

    Myers, C. et al. Postoperative gram-negative anaerobic bacterial endocarditis. Pediatr. Infect. Dis. J. 26, 369 (2007).

    PubMed  Article  PubMed Central  Google Scholar 

  165. 165.

    Mehmood, M., Jaffar, N. A., Nazim, M. & Khasawneh, F. A. Bacteremic skin and soft tissue infection caused by Prevotella loescheii. BMC Infect. Dis. 14, 162 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  166. 166.

    Thomaidis, P. C. et al. Sonication assisted microbiological diagnosis of implant-related infection caused by Prevotella disiens and Staphylococcus epidermidis in a patient with cranioplasty. BMC Res. Notes 8, 307 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

  167. 167.

    Krüger, W., Vielreicher, S., Kapitan, M., Jacobsen, I. D. & Niemiec, M. J. Fungal-bacterial interactions in health and disease. Pathogens 8, 70 (2019).

    PubMed Central  Article  CAS  Google Scholar 

  168. 168.

    Contreras, A. & Slots, J. Herpesviruses in human periodontal disease. J. Periodontal Res. 35, 3–16 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  169. 169.

    Bancescu, G., Didilescu, A., Bancescu, A. & Bari, M. Antibiotic susceptibility of 33 Prevotella strains isolated from Romanian patients with abscesses in head and neck spaces. Anaerobe 35, 41–44 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  170. 170.

    Mory, F. et al. Bacteremia caused by a metronidazole-resistant Prevotella sp. strain. J. Clin. Microbiol. 43, 5380 (2005).

    PubMed  PubMed Central  Article  Google Scholar 

  171. 171.

    Cobo, F., Rodríguez-Granger, J., Sampedro, A. & Navarro-Marí, J. M. Infected breast cyst due to Prevotella buccae resistant to metronidazole. Anaerobe 48, 177–178 (2017).

    PubMed  Article  PubMed Central  Google Scholar 

  172. 172.

    Veloo, A. C. M., Chlebowicz, M., Winter, H. L. J., Bathoorn, D. & Rossen, J. W. A. Three metronidazole-resistant Prevotella bivia strains harbour a mobile element, encoding a novel nim gene, nimK, and an efflux small MDR transporter. J. Antimicrob. Chemother. 73, 2687–2690 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  173. 173.

    Sherrard, L. J. et al. Antibiotic resistance in Prevotella species isolated from patients with cystic fibrosis. J. Antimicrob. Chemother. 68, 2369–2374 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  174. 174.

    Sherrard, L. J. et al. Mechanisms of reduced susceptibility and genotypic prediction of antibiotic resistance in Prevotella isolated from cystic fibrosis (CF) and non-CF patients. J. Antimicrob. Chemother. 69, 2690–2698 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  175. 175.

    Sherrard, L. J. et al. Production of extended-spectrum β-lactamases and the potential indirect pathogenic role of Prevotella isolates from the cystic fibrosis respiratory microbiota. Int. J. Antimicrob. Agents 47, 140–145 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  176. 176.

    Tunney, M. M. et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 66, 579–584 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  177. 177.

    Zhao, J. et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc. Natl Acad. Sci. USA 109, 5809–5814 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  178. 178.

    Iljazovic, A. et al. Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Mucosal. Immunol. 14, 113–124 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  179. 179.

    Depommier, C. et al. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat. Med. 25, 1096–1103 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  180. 180.

    Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902–903 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  181. 181.

    Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  182. 182.

    Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  183. 183.

    Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  184. 184.

    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  185. 185.

    Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 11, 2500 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  186. 186.

    Bromham, L. & Penny, D. The modern molecular clock. Nat. Rev. Genet. 4, 216–224 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  187. 187.

    Bos, K. I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506–510 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  188. 188.

    Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet. 45, 1176–1182 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  189. 189.

    Spyrou, M. A., Bos, K. I., Herbig, A. & Krause, J. Ancient pathogen genomics as an emerging tool for infectious disease research. Nat. Rev. Genet. 20, 323–340 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  190. 190.

    Spindler, K. The Man in the Ice (Weidenfeld and Nicolson, 1994).

  191. 191.

    Maixner, F. et al. The 5300-year-old Helicobacter pylori genome of the Iceman. Science 351, 162–165 (2016). This is one of the first studies showing that reconstruction of genomes from ancient samples is possible, which is particularly relevant to study the evolutionary history of Prevotella spp.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

Download references

Acknowledgements

The authors thank F. Cumbo, A. Blanco-Miguez, P. Manghi and F. Asnicar for support in retrieving and organizing the metagenome-assembled genomes. The work was supported by the European Research Council (ERC-STG project MetaPG), MIUR ‘Futuro in Ricerca’ (grant no. RBFR13EWWI_001), the National Cancer Institute of the US National Institutes of Health (1U01CA230551), the Premio Internazionale Lombardia e Ricerca 2019 and the European Union Horizon 2020 project ONCOBIOME-825410 to N.S, by the MASTER-818368 project to D.E. and N.S., and by the JPI HDHL-INTIMIC - Knowledge Platform of Food, Diet, Intestinal Microbiomics and Human Health (ID 790) and PRIN2017 (20174FHBWR_005) granted by the Italian Ministry of University and Research to D.E.

Author information

Affiliations

Authors

Contributions

D.E. and N.S. conceived the article. All authors researched data for the article. N.S., D.E. and A.T. contributed substantially to discussion of the content. E.P. performed the analyses. N.S., D.E. and A.T. wrote the article. All authors reviewed and/or edited the manuscript before submission.

Corresponding authors

Correspondence to Danilo Ercolini or Nicola Segata.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Microbiology thanks T. Strowig, H. Flint, G. Belibasakis, who co-reviewed with D. Manoil, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Tett, A., Pasolli, E., Masetti, G. et al. Prevotella diversity, niches and interactions with the human host. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00559-y

Download citation

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing