Skip to main content

Thank you for visiting 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.

Diversity, stability and resilience of the human gut microbiota


Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time — especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Maintaining our gut microbial lawn.
Figure 2: Tools for evaluating microbiota diversity.
Figure 3: Diversity of the human microbiota at different phylogenetic scales.
Figure 4: Functional redundancy.
Figure 5: Human microbial diversity and enterotypes.
Figure 6: Compositional transitions in the human gut microbiota.


  1. 1

    Candela, M. et al. Interaction of probiotic Lactobacillus and Bifidobacterium strains with human intestinal epithelial cells: adhesion properties, competition against enteropathogens and modulation of IL-8 production. Int. J. Food Microbiol. 125, 286–292 (2008).

    CAS  Article  Google Scholar 

  2. 2

    Fukuda, S. et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543–547 (2011).

    ADS  CAS  Article  Google Scholar 

  3. 3

    Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959 (2005).

    ADS  CAS  Article  Google Scholar 

  4. 4

    Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).

    ADS  CAS  Article  Google Scholar 

  5. 5

    Olszak, T. et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336, 489–493 (2012).

    ADS  CAS  Article  Google Scholar 

  6. 6

    Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023 (2006).

    ADS  CAS  Article  Google Scholar 

  7. 7

    Turnbaugh, P. J., Backhed, F., Fulton, L. & Gordon, J. I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3, 213–223 (2008).

    CAS  Article  Google Scholar 

  8. 8

    Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L. & Gordon, J. I. Human nutrition, the gut microbiome and the immune system. Nature 474, 327–336 (2011).

    CAS  Article  Google Scholar 

  9. 9

    Dicksved, J. et al. Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J. 2, 716–727 (2008).

    CAS  Article  Google Scholar 

  10. 10

    Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104, 13780–13785 (2007).

    ADS  CAS  Article  Google Scholar 

  11. 11

    Gonzalez, A. et al. The mind–body–microbial continuum. Dialogues Clin. Neurosci. 13, 55–62 (2011).

    PubMed  PubMed Central  Google Scholar 

  12. 12

    Lupton, J. R. Microbial degradation products influence colon cancer risk: the butyrate controversy. J. Nutr. 134, 479–482 (2004).

    CAS  Article  Google Scholar 

  13. 13

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

    CAS  Article  Google Scholar 

  14. 14

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

  15. 15

    Borenstein, E., Kupiec, M., Feldman, M. W. & Ruppin, E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc. Natl Acad. Sci. USA 105, 14482–14487 (2008).

    ADS  CAS  Article  Google Scholar 

  16. 16

    Freilich, S. et al. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol. 10, R61 (2009).

    Article  Google Scholar 

  17. 17

    Claesson, M. J. et al. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4, e6669 (2009).

    ADS  Article  Google Scholar 

  18. 18

    Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005).

    ADS  Article  Google Scholar 

  19. 19

    Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334–338 (2010).

    ADS  CAS  Article  Google Scholar 

  20. 20

    Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009).

    ADS  CAS  Article  Google Scholar 

  21. 21

    Biagi, E. et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS ONE 5, e10667 (2010).

    ADS  Article  Google Scholar 

  22. 22

    Nelson, K. E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994–999 (2010).

    CAS  Article  Google Scholar 

  23. 23

    Verberkmoes, N. C. et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179–189 (2009).

    CAS  Article  Google Scholar 

  24. 24

    Jansson, J. et al. Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS ONE 4, e6386 (2009).

    ADS  Article  Google Scholar 

  25. 25

    Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011).

    ADS  CAS  Article  Google Scholar 

  26. 26

    Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108, 4578–4585 (2011).

    ADS  CAS  Article  Google Scholar 

  27. 27

    Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007).

    Article  Google Scholar 

  28. 28

    Dominguez-Bello, M. G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl Acad. Sci. USA 107, 11971–11975 (2010).

    ADS  Article  Google Scholar 

  29. 29

    Kozyrskyj, A. L., Bahreinian, S. & Azad, M. B. Early life exposures: impact on asthma and allergic disease. Curr. Opin. Allergy Clin. Immunol. 11, 400–406 (2011).

    CAS  Article  Google Scholar 

  30. 30

    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).

    ADS  Article  Google Scholar 

  31. 31

    Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011). This paper reports that there is an association between co-occurring microbial groups, and that high Prevotella versus Bacteroides genus level abundance estimates are associated with major patterns of differentiation in the microbiota across people.

    CAS  Article  Google Scholar 

  32. 32

    Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011). This study found a strong correlation between microbiota diversity and long-term diets as assessed using diet inventories.

    ADS  CAS  Article  Google Scholar 

  33. 33

    Loftus, E. V. Jr. Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences. Gastroenterology 126, 1504–1517 (2004).

    Article  Google Scholar 

  34. 34

    Cann, H. M. et al. A human genome diversity cell line panel. Science 296, 261–262 (2002).

    CAS  Article  Google Scholar 

  35. 35

    Bach, J. F. & Chatenoud, L. The hygiene hypothesis: an explanation for the increased frequency of insulin-dependent diabetes. Cold Spring Harb. Perspect. Med. 2, a007799 (2012).

    Article  Google Scholar 

  36. 36

    Clayton, T. A., Baker, D., Lindon, J. C., Everett, J. R. & Nicholson, J. K. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc. Natl Acad. Sci. USA 106, 14728–14733 (2009).

    ADS  CAS  Article  Google Scholar 

  37. 37

    Jackson, R. L., Greiwe, J. S. & Schwen, R. J. Emerging evidence of the health benefits of S-equol, an estrogen receptor beta agonist. Nutr. Rev. 69, 432–448 (2011).

    Article  Google Scholar 

  38. 38

    Setchell, K. D. & Clerici, C. Equol: history, chemistry, and formation. J. Nutr. 140, 1355S–1362S (2010).

    CAS  Article  Google Scholar 

  39. 39

    Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).

    Article  Google Scholar 

  40. 40

    Costello, E. K. et al. Bacterial community variation in human body habitats across space and time. Science 326, 1694–1697 (2009).

    ADS  CAS  Article  Google Scholar 

  41. 41

    Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108, 4554–4561 (2011). This paper gives insight into the resilience of the human microbiota in the face of repeated disturbances, and the degree of baseline variation.

    ADS  CAS  Article  Google Scholar 

  42. 42

    Jakobsson, H. E. et al. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE 5, e9836 (2010).

    ADS  Article  Google Scholar 

  43. 43

    Beisner, B. E., Haydon, D. T. & Cuddington, K. Alternative stable states in ecology. Front. Ecol. Environ. 1, 376–382 (2003).

    Article  Google Scholar 

  44. 44

    Walker, B., Hollin, C. S., Carpenter, S. R. & Kinzig, A. Resilience, adaptability and transformability in social-ecological systems. Ecol. Soc. 9, (16 September, 2004).

  45. 45

    Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).

    ADS  Article  Google Scholar 

  46. 46

    Sun, Y. et al. Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data. Nucleic Acids Res. 38, e205 (2010).

    ADS  Article  Google Scholar 

  47. 47

    Knights, D., Parfrey, L. W., Zaneveld, J., Lozupone, C. & Knight, R. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe 10, 292–296 (2011).

    CAS  Article  Google Scholar 

  48. 48

    Carroll, I. M. et al. Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome. Am. J. Physiol. Gastrointest. Liver Physiol. 301, G799–G807 (2011).

    CAS  Article  Google Scholar 

  49. 49

    Chang, J. Y. et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J. Infect. Dis. 197, 435–438 (2008).

    Article  Google Scholar 

  50. 50

    Young, V. B. & Schmidt, T. M. Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J. Clin. Microbiol. 42, 1203–1206 (2004).

    Article  Google Scholar 

  51. 51

    Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854 (2010).

    Article  Google Scholar 

  52. 52

    Swidsinski, A., Loening-Baucke, V. & Herber, A. Mucosal flora in Crohn's disease and ulcerative colitis — an overview. J. Physiol. Pharmacol. 60, 61–71 (2009).

    PubMed  Google Scholar 

  53. 53

    Lozupone, C. et al. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles in human gut symbionts. Genome Res. (4 June, 2012).

  54. 54

    Libby, J. M., Donta, S. T. & Wilkins, T. D. Clostridium difficile toxin A in infants. J. Infect. Dis. 148, 606 (1983).

    CAS  Article  Google Scholar 

  55. 55

    Yamamoto-Osaki, T., Kamiya, S., Sawamura, S., Kai, M. & Ozawa, A. Growth inhibition of Clostridium difficile by intestinal flora of infant faeces in continuous flow culture. J. Med. Microbiol. 40, 179–187 (1994).

    CAS  Article  Google Scholar 

  56. 56

    Folke, C. et al. Regime shifts, resilience, and biodiversity in ecosystem management. Annu. Rev. Ecol. Evol. Syst. 35, 557–581 (2004).

    Article  Google Scholar 

  57. 57

    Scheffer, M. et al. Floating plant dominance as a stable state. Proc. Natl Acad. Sci. USA 100, 4040–4045 (2003).

    ADS  CAS  Article  Google Scholar 

  58. 58

    Hazen, T. C. et al. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330, 204–208 (2010).

    ADS  CAS  Article  Google Scholar 

  59. 59

    Valentine, D. L. et al. Dynamic autoinoculation and the microbial ecology of a deep water hydrocarbon irruption. Proc. Natl Acad. Sci. USA (10 January, 2012).

  60. 60

    Jernberg, C., Lofmark, S., Edlund, C. & Jansson, J. K. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1, 56–66 (2007).

    CAS  Article  Google Scholar 

  61. 61

    van der Waaij, D., Berghuis, J. M. & Lekkerkerk, J. E. Colonization resistance of the digestive tract of mice during systemic antibiotic treatment. J. Hyg. (Lond.) 70, 605–610 (1972).

    CAS  Article  Google Scholar 

  62. 62

    McNulty, N. P. et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 3, 106ra106 (2011).

    Article  Google Scholar 

  63. 63

    Manichanh, C. et al. Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res. 20, 1411–1419 (2010). This study indicates that the indigenous microbiota may be more plastic than previously thought. The observation that antibiotic pretreatment interfered with, rather than promoted, establishment of the donor community indicates that low species abundance or diversity alone cannot predict low colonization resistance.

    CAS  Article  Google Scholar 

  64. 64

    Levine, J. M. & D'antonio, C. M. Elton revisited: a review of evidence linking diversity and invasibility. Oikos 87, 15–26 (1999).

    Article  Google Scholar 

  65. 65

    Khoruts, A., Dicksved, J., Jansson, J. K. & Sadowsky, M. J. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J. Clin. Gastroenterol. 44, 354–360 (2010).

    PubMed  Google Scholar 

  66. 66

    Gough, E., Shaikh, H. & Manges, A. R. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin. Infect. Dis. 53, 994–1002 (2011).

    Article  Google Scholar 

  67. 67

    Hautier, Y., Niklaus, P. A. & Hector, A. Competition for light causes plant biodiversity loss after eutrophication. Science 324, 636–638 (2009).

    ADS  CAS  Article  Google Scholar 

  68. 68

    Elmqvist, T. et al. Response diversity, ecosystem change, and resilience. Front. Ecol. Environ. 1, 488–494 (2003).

    Article  Google Scholar 

  69. 69

    Hansen, E. E. et al. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc. Natl Acad. Sci. USA 108, 4599–4606 (2011).

    ADS  CAS  Article  Google Scholar 

  70. 70

    Flint, H. J., Duncan, S. H., Scott, K. P. & Louis, P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ. Microbiol. 9, 1101–1111 (2007).

    CAS  Article  Google Scholar 

  71. 71

    Louis, P. et al. Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J. Bacteriol. 186, 2099–2106 (2004).

    CAS  Article  Google Scholar 

  72. 72

    Chaffron, S., Rehrauer, H., Pernthaler, J. & von Mering, C. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20, 947–959 (2010).

    CAS  Article  Google Scholar 

  73. 73

    Stecher, B. et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathogens 6, e1000711 (2010).

    Article  Google Scholar 

  74. 74

    Bever, J. D., Westover, K. M. & Antonovics, J. Incorporating the soil community into plant population dynamics: the utility of the feedback approach. J. Ecol. 85, 561–573 (1997).

    Article  Google Scholar 

  75. 75

    Stark, P. L. & Lee, A. The microbial ecology of the large bowel of breast-fed and formula-fed infants during the 1st year of life. J. Med. Microbiol. 15, 189–203 (1982).

    CAS  Article  Google Scholar 

  76. 76

    Glover, L. E. & Colgan, S. P. Hypoxia and metabolic factors that influence inflammatory bowel disease pathogenesis. Gastroenterology 140, 1748–1755 (2011).

    CAS  Article  Google Scholar 

  77. 77

    Goodman, A. L. et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108, 6252–6257 (2011).

    ADS  CAS  Article  Google Scholar 

  78. 78

    Dupont, H. L. Gastrointestinal infections and the development of irritable bowel syndrome. Curr. Opin. Infect. Dis. 24, 503–508 (2011).

    Article  Google Scholar 

Download references


We would like to thank L. Parfrey, J. Knight and A. Knight for their comments on this manuscript.

Author information



Corresponding author

Correspondence to Rob Knight.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reprints and permissions information is available at

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lozupone, C., Stombaugh, J., Gordon, J. et al. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links