NDLI: Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

Content Provider	PubMed Central
Author	Patricio, Jeraldo Sipos, Maksim Chia, Nicholas Brulc, Jennifer M. Dhillon, A. Singh Konkel, Michael E. Larson, Charles L. Nelson, Karen E. Qu, Ani Schook, Lawrence B. Yang, Fang White, Bryan A. Nigel, Goldenfeld
Abstract	The theoretical description of the forces that shape ecological communities focuses around two classes of models. In niche theory, deterministic interactions between species, individuals, and the environment are considered the dominant factor, whereas in neutral theory, stochastic forces, such as demographic noise, speciation, and immigration, are dominant. Species abundance distributions predicted by the two classes of theory are difficult to distinguish empirically, making it problematic to deduce ecological dynamics from typical measures of diversity and community structure. Here, we show that the fusion of species abundance data with genome-derived measures of evolutionary distance can provide a clear indication of ecological dynamics, capable of quantifying the relative roles played by niche and neutral forces. We apply this technique to six gastrointestinal microbiomes drawn from three different domesticated vertebrates, using high-resolution surveys of microbial species abundance obtained from carefully curated deep 16S rRNA hypervariable tag sequencing data. Although the species abundance patterns are seemingly well fit by the neutral theory of metacommunity assembly, we show that this theory cannot account for the evolutionary patterns in the genomic data; moreover, our analyses strongly suggest that these microbiomes have, in fact, been assembled through processes that involve a significant nonneutral (niche) contribution. Our results demonstrate that high-resolution genomics can remove the ambiguities of process inference inherent in classic ecological measures and permits quantification of the forces shaping complex microbial communities.
Related Links	http://dx.doi.org/10.1073/pnas.1206721109
Ending Page	9698
Page Count	7
Starting Page	9692
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	25
Volume Number	109
Language	English
Publisher	National Academy of Sciences
Publisher Date	2012-06-19
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.

Relative roles of niche and neutral processes in structuring a soil microbial community

Relative roles of niche and neutral processes in structuring a soil microbial community

Community assembly and invasion: An experimental test of neutral versus niche processes

The importance of neutral over niche processes in structuring Ediacaran early animal communities

The transition between the niche and neutral regimes in ecology

Structure and Dynamics of the Breast Tissue Microbiomes Under Tumor Influences: An Approach With Neutral, Near-Neutral, and Niche-Neutral Hybrid Models

Combined niche and neutral effects in a microbial wastewater treatment community

Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

Similar Documents

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.

Relative roles of niche and neutral processes in structuring a soil microbial community

Relative roles of niche and neutral processes in structuring a soil microbial community

Community assembly and invasion: An experimental test of neutral versus niche processes

The importance of neutral over niche processes in structuring Ediacaran early animal communities

The transition between the niche and neutral regimes in ecology

Structure and Dynamics of the Breast Tissue Microbiomes Under Tumor Influences: An Approach With Neutral, Near-Neutral, and Niche-Neutral Hybrid Models

Combined niche and neutral effects in a microbial wastewater treatment community

Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes