Review Article | Published:

Role of priority effects in the early-life assembly of the gut microbiota

Nature Reviews Gastroenterology & Hepatology volume 15, pages 197205 (2018) | Download Citation

Abstract

Understanding how microbial communities develop is essential for predicting and directing their future states. Ecological theory suggests that community development is often influenced by priority effects, in which the order and timing of species arrival determine how species affect one another. Priority effects can have long-lasting consequences, particularly if species arrival history varies during the early stage of community development, but their importance to the human gut microbiota and host health remains largely unknown. Here, we explore how priority effects might influence microbial communities in the gastrointestinal tract during early childhood and how the strength of priority effects can be estimated from the composition of the microbial species pool. We also discuss factors that alter microbial transmission, such as delivery mode, diet and parenting behaviours such as breastfeeding, which can influence the likelihood of priority effects. An improved knowledge of priority effects has the potential to inform microorganism-based therapies, such as prebiotics and probiotics, which are aimed at guiding the microbiota towards a healthy state.

Key points

  • Infant gut microbiota assembly is driven by four ecological processes — dispersal, diversification, drift and selection — and can be understood by resolving their relative contributions, mechanisms and interactive effects

  • Priority effects, whereby the order and timing of dispersal alters how diversification, drift and selection affect infant gut microbiota assembly, could have long-lasting consequences for host health

  • Priority effects in the infant gut are influenced by the regional species pool, which is made up of numerous local communities, some of which are host-associated, while others are not

  • To understand the role of priority effects in the infant gut, future studies in model systems should intentionally vary dispersal order and timing

  • In future studies, when intentional variation in dispersal order is not feasible, dispersal order should be carefully recorded along with relevant environmental variables

  • An understanding of the processes that govern priority effects can be used to inform microorganism-based therapies and manage strategies aimed at guiding the microbiota towards a healthy state

  • Subscribe to Nature Reviews Gastroenterology & Hepatology for full access:

    $199

    Subscribe

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    , & How glycan metabolism shapes the human gut microbiota. Nat. Rev. Microbiol. 10, 323–335 (2012).

  2. 2.

    , , & How colonization by microbiota in early life shapes the immune system. Science 352, 539–544 (2016).

  3. 3.

    & Microbiota-mediated colonization resistance against intestinal pathogens. Nat. Rev. Immunol. 13, 790–801 (2013).

  4. 4.

    et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15, 382–392 (2014).

  5. 5.

    et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS ONE 7, e49138 (2012).

  6. 6.

    et al. Unstable composition of the fecal microbiota in ulcerative colitis during clinical remission. Am. J. Gastroenterol. 103, 643–648 (2008).

  7. 7.

    et al. Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers. Gut 64, 1553–1561 (2015).

  8. 8.

    , & Primary sclerosing cholangitis and the microbiota: current knowledge and perspectives on etiopathogenesis and emerging therapies. Scand. J. Gastroenterol. 49, 901–908 (2014).

  9. 9.

    et al. Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease. Sci. Rep. 5, 8096 (2015).

  10. 10.

    et al. Small intestine bacterial overgrowth and environmental enteropathy in Bangladeshi children. mBio 7, e02102–02115 (2016).

  11. 11.

    et al. Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model. Nat. Commun. 6, 7806 (2015).

  12. 12.

    et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).

  13. 13.

    et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2008).

  14. 14.

    et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1131 (2006).

  15. 15.

    et al. Dysbiosis and alterations in predicted functions of the subgingival microbiome in chronic periodontitis. Appl. Environ. Microbiol. 81, 783–793 (2015).

  16. 16.

    et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 7, 1016–1025 (2013).

  17. 17.

    et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19, 576–585 (2013).

  18. 18.

    Community Ecology (Wiley-Blackwell, 2011).

  19. 19.

    Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).This review lays out a conceptual framework for understanding and studying the role of historical contingency in community assembly.

  20. 20.

    , , , & The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255–1262 (2012).

  21. 21.

    Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183–206 (2010).

  22. 22.

    The Theory of Ecological Communities (Princeton Univ. Press, 2016).This book provides a theoretical foundation for understanding how ecological communities arise and change though time.

  23. 23.

    , , , & Microbiome assembly across multiple body sites in low-birthweight infants. mBio 4, e00782–e00713 (2013).

  24. 24.

    et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314–326 (2017).

  25. 25.

    , , , & Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007).

  26. 26.

    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).This paper provides early evidence that birth mode affects early infant colonization.

  27. 27.

    et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section. Gut 63, 559–566 (2014).

  28. 28.

    et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690–703 (2015).

  29. 29.

    et al. Mode of delivery affects the bacterial community in the newborn gut. Early Hum. Dev. 86 (Suppl. 1), 13–15 (2010).

  30. 30.

    et al. Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants. Clin. Exp. Allergy 43, 198–211 (2013).

  31. 31.

    et al. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc. Natl Acad. Sci. USA 110, 13880–13885 (2013).

  32. 32.

    , , & Horizontal versus familial transmission of Helicobacter pylori. PLoS Pathog. 4, e1000180 (2008).

  33. 33.

    et al. Diversity, transmission and persistence of Escherichia coli in a cohort of mothers and their infants. Environ. Microbiol. Rep. 3, 352–359 (2011).

  34. 34.

    , , & An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 26, 1612–1625 (2016).This paper shows that strain-level sharing between mothers and children changes over time.

  35. 35.

    et al. Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota. PLoS ONE 8, e78331 (2013).

  36. 36.

    et al. Exploring vertical transmission of bifidobacteria from mother to child. Appl. Environ. Microbiol. 81, 7078–7087 (2015).

  37. 37.

    & Is a foetus developing in a sterile environment? Lett. Appl. Microbiol. 59, 572–579 (2014).

  38. 38.

    & Does a prenatal bacterial microbiota exist? Mucosal Immunol. 10, 598–601 (2017).

  39. 39.

    et al. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 4, 29 (2016).

  40. 40.

    et al. The placenta harbors a unique microbiome. Sci. Transl Med. 6, 237ra65 (2014).

  41. 41.

    , , , & Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci. Rep. 6, 23129 (2016).

  42. 42.

    Diversity of microbes in amniotic fluid. Semin. Fetal Neonatal Med. 17, 2–11 (2012).

  43. 43.

    et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS ONE 9, e90784 (2014).

  44. 44.

    et al. Is meconium from healthy newborns actually sterile? Res. Microbiol. 159, 187–193 (2008).

  45. 45.

    et al. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS ONE 8, e66986 (2013).

  46. 46.

    The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth. BJOG 122, 213–218 (2015).

  47. 47.

    , , , & Transmission of diverse oral bacteria to murine placenta: evidence for the oral microbiome as a potential source of intrauterine infection. Infect. Immun. 78, 1789–1796 (2010).

  48. 48.

    & Mom knows best: the universality of maternal microbial transmission. PLoS Biol. 11, e1001631 (2013).This review gives a comparative view of maternal microbial transmission across the animal kingdom.

  49. 49.

    , & Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat. Commun. 6, 8945 (2015).

  50. 50.

    et al. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J. 10, 655–664 (2016).This paper assesses the role of neutral processes in community assembly by fitting observations in a powerful experimental model to a mathematical model.

  51. 51.

    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).

  52. 52.

    The Unified Neutral Theory of Biodiversity and Biogeography. (Princeton Univ. Press, 2001).

  53. 53.

    et al. Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PLoS Comput. Biol. 13, e1005706 (2017).

  54. 54.

    & Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108 (Suppl. 1), 4554–4561 (2011).

  55. 55.

    , , & Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nat. Genet. 47, 57–64 (2015).

  56. 56.

    et al. Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat. Rev. Microbiol. 10, 841–851 (2012).

  57. 57.

    et al. Sharing of bacterial strains between breast milk and infant feces. J. Hum. Lact. 28, 36–44 (2012).

  58. 58.

    et al. Maternal breast-milk and intestinal bifidobacteria guide the compositional development of the Bifidobacterium microbiota in infants at risk of allergic disease. Clin. Exp. Allergy 37, 1764–1772 (2007).

  59. 59.

    , , & Impact of lactation stage, gestational age and mode of delivery on breast milk microbiota. J. Perinatol. 34, 599–605 (2014).

  60. 60.

    , , , & Establishment and development of lactic acid bacteria and bifidobacteria microbiota in breast-milk and the infant gut. Anaerobe 16, 307–310 (2010).

  61. 61.

    , , , & Diversity of the Lactobacillus group in breast milk and vagina of healthy women and potential role in the colonization of the infant gut. J. Appl. Microbiol. 103, 2638–2644 (2007).

  62. 62.

    et al. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE 6, e21313 (2011).

  63. 63.

    Human milk oligosaccharides: every baby needs a sugar mama. Glycobiology 22, 1147–1162 (2012).

  64. 64.

    et al. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe 10, 507–514 (2011).

  65. 65.

    et al. Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression. Proc. Natl Acad. Sci. USA 111, 3074–3079 (2014).

  66. 66.

    et al. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature 534, 263–266 (2016).

  67. 67.

    , , & Assessing the relative importance of neutral stochasticity in ecological communities. Oikos 123, 1420–1430 (2014).

  68. 68.

    et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci. Transl Med. 8, 343ra81 (2016).This longitudinal study examines the role of environmental factors in early-life colonization patterns.

  69. 69.

    et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci. Transl Med. 8, 343ra82 (2016).

  70. 70.

    et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc. Natl Acad. Sci. USA 105, 18964–18969 (2008).

  71. 71.

    et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108 (Suppl. 1), 4578–4585 (2011).

  72. 72.

    & Human milk oligosaccharide consumption by intestinal microbiota. Clin. Microbiol. Infect. 18 (Suppl. 4), 12–15 (2012).

  73. 73.

    et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96–99 (2013).

  74. 74.

    & Historical contingency in species interactions: towards niche-based predictions. Ecol. Lett. 17, 115–124 (2014).

  75. 75.

    & Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection. PLoS Pathog. 10, e1004527 (2014).

  76. 76.

    , & First arrived takes all: inhibitory priority effects dominate competition between co-infecting Borrelia burgdorferi strains. BMC Microbiol. 15, 61 (2015).

  77. 77.

    et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426–429 (2013).This paper identifies the ccf locus as a possible basis of priority effects for B. fragilis.

  78. 78.

    et al. Strain competition restricts colonization of an enteric pathogen and prevents colitis. EMBO Rep. 17, 1281–1291 (2016).

  79. 79.

    et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842–853 (2016).

  80. 80.

    et al. Stool microbiota and vaccine responses of infants. Pediatrics 134, e362–372 (2014).

  81. 81.

    et al. Production of immune response mediators by HT-29 intestinal cell-lines in the presence of Bifidobacterium-treated infant microbiota. Benef. Microbes 6, 543–552 (2015).

  82. 82.

    et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).

  83. 83.

    et al. Temporal and spatial variation of the human microbiota during pregnancy. Proc. Natl Acad. Sci. USA 112, 11060–11065 (2015).

  84. 84.

    & Antibiotic prophylaxis versus no prophylaxis for preventing infection after cesarean section. Cochrane Database Syst. Rev. 10, CD007482 (2014).

  85. 85.

    et al. Elective cesarean delivery: does it have a negative effect on breastfeeding? Birth 37, 275–279 (2010).

  86. 86.

    et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat. Med. 22, 250–253 (2016).

  87. 87.

    et al. Transmission of the major skin microbiota, Malassezia, from mother to neonate. Pediatr. Int. 54, 350–355 (2012).

  88. 88.

    et al. Cohabiting family members share microbiota with one another and with their dogs. eLife 2, e00458 (2013).

  89. 89.

    & Kangaroo mother care to reduce morbidity and mortality in low birthweight infants. Cochrane Database Syst. Rev. 4, CD002771 (2014).

  90. 90.

    et al. Skin-to-skin care and the development of the preterm infant oral microbiome. Am. J. Perinatol. 32, 1205–1216 (2015).

  91. 91.

    et al. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am. J. Clin. Nutr. 96, 544–551 (2012).

  92. 92.

    , , , & Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front. Cell. Infect. Microbiol. 5, 3 (2015).

  93. 93.

    et al. The early infant gut microbiome varies in association with a maternal high-fat diet. Genome Med. 8, 77 (2016).

  94. 94.

    et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510, 417–421 (2014).

  95. 95.

    et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511–521 (2006).

  96. 96.

    et al. Having older siblings is associated with gut microbiota development during early childhood. BMC Microbiol. 15, 154 (2015).

  97. 97.

    , , , & Furry pets modulate gut microbiota composition in infants at risk for allergic disease. J. Allergy Clin. Immunol. 136, 1688–1690.e1 (2015).

  98. 98.

    et al. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159, 253–266 (2014).

  99. 99.

    et al. Intestinal microbiota of preterm infants differ over time and between hospitals. Microbiome 2, 36 (2014).

  100. 100.

    et al. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome 2, 1 (2014).

  101. 101.

    et al. Shaping the oral microbiota through intimate kissing. Microbiome 2, 41 (2014).

  102. 102.

    et al. Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication. PeerJ 4, e2660 (2016).

  103. 103.

    & Pacifier cleaning practices and risk of allergy development. Pediatrics 134, S136–S137 (2014).

  104. 104.

    et al. Effect of topical emollient treatment of preterm neonates in Bangladesh on invasion of pathogens into the bloodstream. Pediatr. Res. 61, 588–593 (2007).

  105. 105.

    Traditional practices of women from India: pregnancy, childbirth, and newborn care. J. Obstet. Gynecol. Neonatal Nurs. 26, 533–539 (1997).

  106. 106.

    & The practice of prelacteal feeding to newborns among Hindu and Muslim families. J. Midwifery Womens Health 54, 78–81 (2009).

  107. 107.

    Can establishment of human microbiome be customized after birth with local traditions of first feed and intimate kissing? J. Lab. Physicians 7, 73–74 (2015).

  108. 108.

    & Assessment, behavioral treatment, and prevention of pica: clinical guidelines and recommendations for practitioners. Res. Dev. Disabil. 33, 2050–2057 (2012).

  109. 109.

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

  110. 110.

    et al. Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype. ISME J. 10, 145–157 (2015).

  111. 111.

    & Cyclic assembly trajectories and scale-dependent productivity-diversity relationships. Ecology 85, 107–113 (2004).

  112. 112.

    et al. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 23, 111–120 (2013).

  113. 113.

    Antibiotic use and its consequences for the normal microbiome. Science 352, 544–545 (2016).

  114. 114.

    & Life at the beginning: perturbation of the microbiota by antibiotics in early life and its role in health and disease. Nat. Immunol. 15, 307–310 (2014).

  115. 115.

    et al. The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice. Nat. Med. 20, 524–530 (2014).

  116. 116.

    et al. Intestinal commensal bacteria mediate lung mucosal immunity and promote resistance of newborn mice to infection. Sci. Transl Med. 9, eaaf9412 (2017).

  117. 117.

    et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 488, 621–626 (2012).

  118. 118.

    et al. Exploring the contribution of maternal antibiotics and breastfeeding to development of the infant microbiome and pediatric obesity. Semin. Fetal Neonatal Med. 21, 406–409 (2016).

  119. 119.

    et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell 158, 705–721 (2014).

  120. 120.

    , & Mapping the assembly of protist communities in microcosms. Ecology 84, 1001–1011 (2003).

  121. 121.

    , , , & Bifidobacterium breve BBG-001 in very preterm infants: a randomised controlled phase 3 trial. Lancet 387, 649–660 (2016).

  122. 122.

    et al. A randomized synbiotic trial to prevent sepsis among infants in rural India. Nature 548, 407–412 (2017).

  123. 123.

    & Probiotics for prevention of necrotizing enterocolitis in preterm infants. Cochrane Database Syst. Rev. 4, CD005496 (2014).

  124. 124.

    et al. Rectal swabs for analysis of the intestinal microbiota. PLoS ONE 9, e101344 (2014).

  125. 125.

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

  126. 126.

    et al. Species associations during the succession of wood-inhabiting fungal communities. Fungal Ecol. 11, 17–28 (2014).

  127. 127.

    ., , . & Within-host competition among the honey bees pathogens Nosema ceranae and deformed wing virus is asymmetric and to the disadvantage of the virus. J. Invertebr. Path. 124, 31–34 (2015).

  128. 128.

    ., , , & Within-host interactions of lymantria dispar (Lepidoptera: Lymantriidae) nucleopolyhedrosis virus and Entomophaga maimaiga (Zygomycetes: Entomophthorales). J. Invertebr. Path. 73, 91–100 (1999).

  129. 129.

    & . Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes. Proc. R. Soc. B. Biol. Sci. 281, 20132637 (2014).

  130. 130.

    et al. Inhibition of tissue inflammation and bacterial translocation as one of the protective mechanisms of Saccharomyces boulardii against Salmonella infection in mice. Microbes Infect. 15, 270–279 (2013).

  131. 131.

    , & Infant fungal communities: current knowledge and research opportunities. BMC Med. 15, 30 (2017).

Download references

Acknowledgements

The authors' work is supported by the US National Science Foundation (NSF) Graduate Research Fellowship award number DGE-114747 (D.S.), the National Institute of General Medical Sciences of the NIH under award number T32GM007276 (D.S.), the Thomas C. and Joan M. Merigan Endowment at Stanford University (D.A.R.), The Leona and Harry B. Helmsley Foundation grant number 2014PG-IBD014 (D.A.R.), US NSF award numbers DEB-1555786 and DEB-1737758 (T.F.) and the Terman Fellowship of Stanford University (T.F.). Any opinion, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the US NSF or the NIH. The authors especially thank E. Costello for her helpful feedback.

Author information

Affiliations

  1. Department of Microbiology and Immunology, Stanford University School of Medicine, 291 Campus Drive, Stanford, California 94305, USA.

    • Daniel Sprockett
    •  & David A. Relman
  2. Department of Biology, Stanford University, 371 Serra Mall, Stanford, California 94305, USA.

    • Tadashi Fukami
  3. Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, California 94305, USA.

    • David A. Relman
  4. Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304, USA.

    • David A. Relman

Authors

  1. Search for Daniel Sprockett in:

  2. Search for Tadashi Fukami in:

  3. Search for David A. Relman in:

Contributions

All authors researched data for the article and provided substantial contributions to discussion of the content. D.S. wrote the article. All authors contributed equally to reviewing and/or editing of the manuscript before submission.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David A. Relman.

Glossary

Community assembly

The construction and maintenance of local communities through sequential, repeated immigration of species from a regional species pool.

Regional species pool

The set of species that could potentially colonize and establish within a community.

Niche pre-emption

Occurs when the first species to arrive in a given habitat uses or otherwise sequesters resources and, as a consequence, inhibits the colonization of later species.

Community state types

(CSTs). Categories of stereotypical microbial communities that are typically defined by their dominant taxa and found at a given body site.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nrgastro.2017.173

Rights and permissions

To obtain permission to re-use content from this article visit RightsLink.