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Community ecology as a framework for human microbiome research


The field of human microbiome research has revealed the intimate co-association of humans with diverse communities of microbes in various habitats in the human body, and the necessity of these microbes for the maintenance of human health. Microbial heterogeneity between humans and across spatial and temporal gradients requires multidimensional datasets and a unifying set of theories and statistical tools to analyze the human microbiome and fully realize the potential of this field. Here we consider the utility of community ecology as a framework for the interrogation and interpretation of the human microbiome.

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Fig. 1: Microbial ecological concepts.


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The authors would like to thank a number of colleagues for suggestions on articles to include in this review. Specifically, L. P. Coelho; B. Prithiviraj; E. Jasarevic; J. Pickard; M. Yassour; and E. Weinstein‏. S.V.L. is supported by awards from the National Institutes of Health (AI089473, AI113916, AI133765, PO515267, DH082147, DA040532) and the Crohn’s and Colitis Foundation of America.

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Correspondence to Jack A. Gilbert or Susan V. Lynch.

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Competing interests

J.A.G. reports roles as Chief Scientific Advisor, 4inno; Scientific Advisory Board, Biome Makers, Inc.; Scientific Advisory Board, DayTwo Inc.; Scientific Advisory Board, Growcentia Inc.; Scientific Advisory Board, Holobiome Inc.; and Scientific Advisory Board, Valent BioSciences. S.V.L. reports research grants from the NIH/NIAID, NIH/NIDA, NIH/NICHD, NIH/Office of the Director and the Crohn’s and Colitis Foundation of America and the following patents and royalties: ‘Reductive prodrug cancer chemotherapy (Stan449-PRV)’; ‘Combination antibiotic and antibody therapy for the treatment of Pseudomonas aeruginosa infection (WO2010091189A1)’ licensed with royalties by KaloBios Inc.; ‘Therapeutic microbial consortium for induction of immune tolerance’ licensed with royalties by Siolta Therapeutics; ‘Systems and methods for detecting antibiotic resistance (WO2012027302A3)’ issued; ‘Nitroreductase enzymes (US7687474B2)’ issued; ‘Sinusitis diagnostics and treatments (WO2013155370A1)’ licensed by Reflourish, LLC; and ‘Methods and systems for phylogenetic analysis (US20120264637A1)’ issued. S.V.L. is a board member of and consultant for Siolta Therapeutics and reports personal fees for this consultancy outside the submitted work.

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Gilbert, J.A., Lynch, S.V. Community ecology as a framework for human microbiome research. Nat Med 25, 884–889 (2019).

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