publication . Article . 2016

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

Li, Lianwei; Ma, Zhanshan (Sam);
Open Access English
  • Published: 01 Aug 2016 Journal: Scientific Reports, volume 6 (issn: 2045-2322, eissn: 2045-2322, Copyright policy)
  • Publisher: Nature Publishing Group
Abstract
The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health—the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 posit...
Subjects
free text keywords: Article
71 references, page 1 of 5

Hubbell S. P.The Unified Neutral Theory of Biodiversity and Biogeography. (Princeton University Press, 2001).

Fisher R. A., Corbet A. S. & Williams C. B. The Relation Between the Number of Species and the Number of Individuals. Journal of Animal Ecology 12, 42–58 (1943).

Preston F. W.The Commonness, And Rarity, of Species. ResearchGate 29, 254–283 (1948).

McGill B. J., Etienne R. S., Gray J. S., Alonso D. & Anderson M. J. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters 10, 995–1015 (2007).17845298 [OpenAIRE] [PubMed]

Ma Z., Geng J., Abdo Z. & Forney L. In Microbial Ecological Theory: Current Perspectives (Caister Academic Press, 2012).

White E. P., Thibault K. M. & Xiao X. Characterizing species abundance distributions across taxa and ecosystems using a simple maximum entropy model. Ecology 93, 1772–1778 (2012).22928405 [PubMed]

Locey K. J. & White E. P. How species richness and total abundance constrain the distribution of abundance. Ecol Lett 16, 1177–1185 (2013).23848604 [PubMed]

Matthews T. J., Borges P. A. V. & Whittaker R. J. Multimodal species abundance distributions: a deconstruction approach reveals the processes behind the pattern. Oikos 123, 533–544 (2014).

Grinnell J. & Grinnell J. The niche-relationships of the California thrasher. Auk. The Auk 34, 427–433 (1916).

Elton C. S.Animal Ecology. (eds Sidwich & Jackson, London: 1927).

Hutchinson G.Concluding Remarks. Cold Spring Harbor Symp. Quant. Bio.22, 415–427 (1957).

MacArthur R. H.On the relative abundance of bird species. Proc Natl Acad Sci USA 43, 293–295 (1957).16590018 [OpenAIRE] [PubMed]

Carroll I. T., Cardinale B. J. & Nisbet R. M. Niche and fitness differences relate the maintenance of diversity to ecosystem function. Ecology 92, 1157–1165 (2011).21661576 [PubMed]

Matthews B.. Under niche construction: an operational bridge between ecology, evolution, and ecosystem science. Ecological Monographs 84, 245–263 (2013).

Chave J.Neutral theory and community ecology. Ecology Letters 7, 241–253 (2004). [OpenAIRE]

71 references, page 1 of 5
Abstract
The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health—the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 posit...
Subjects
free text keywords: Article
71 references, page 1 of 5

Hubbell S. P.The Unified Neutral Theory of Biodiversity and Biogeography. (Princeton University Press, 2001).

Fisher R. A., Corbet A. S. & Williams C. B. The Relation Between the Number of Species and the Number of Individuals. Journal of Animal Ecology 12, 42–58 (1943).

Preston F. W.The Commonness, And Rarity, of Species. ResearchGate 29, 254–283 (1948).

McGill B. J., Etienne R. S., Gray J. S., Alonso D. & Anderson M. J. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters 10, 995–1015 (2007).17845298 [OpenAIRE] [PubMed]

Ma Z., Geng J., Abdo Z. & Forney L. In Microbial Ecological Theory: Current Perspectives (Caister Academic Press, 2012).

White E. P., Thibault K. M. & Xiao X. Characterizing species abundance distributions across taxa and ecosystems using a simple maximum entropy model. Ecology 93, 1772–1778 (2012).22928405 [PubMed]

Locey K. J. & White E. P. How species richness and total abundance constrain the distribution of abundance. Ecol Lett 16, 1177–1185 (2013).23848604 [PubMed]

Matthews T. J., Borges P. A. V. & Whittaker R. J. Multimodal species abundance distributions: a deconstruction approach reveals the processes behind the pattern. Oikos 123, 533–544 (2014).

Grinnell J. & Grinnell J. The niche-relationships of the California thrasher. Auk. The Auk 34, 427–433 (1916).

Elton C. S.Animal Ecology. (eds Sidwich & Jackson, London: 1927).

Hutchinson G.Concluding Remarks. Cold Spring Harbor Symp. Quant. Bio.22, 415–427 (1957).

MacArthur R. H.On the relative abundance of bird species. Proc Natl Acad Sci USA 43, 293–295 (1957).16590018 [OpenAIRE] [PubMed]

Carroll I. T., Cardinale B. J. & Nisbet R. M. Niche and fitness differences relate the maintenance of diversity to ecosystem function. Ecology 92, 1157–1165 (2011).21661576 [PubMed]

Matthews B.. Under niche construction: an operational bridge between ecology, evolution, and ecosystem science. Ecological Monographs 84, 245–263 (2013).

Chave J.Neutral theory and community ecology. Ecology Letters 7, 241–253 (2004). [OpenAIRE]

71 references, page 1 of 5
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publication . Article . 2016

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

Li, Lianwei; Ma, Zhanshan (Sam);