Journal ArticleDOI
Microbial biogeography : putting microorganisms on the map
Jennifer B. H. Martiny,Brendan J. M. Bohannan,James H. Brown,Robert K. Colwell,Jed A. Fuhrman,Jessica L. Green,M. Claire Horner-Devine,Matthew D. Kane,Jennifer Adams Krumins,Cheryl R. Kuske,Peter J. Morin,Shahid Naeem,Lise Øvreås,Anna-Louise Reysenbach,Val H. Smith,James T. Staley +15 more
TLDR
Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity, but recent studies also dispute the idea that 'everything is everywhere'.Abstract:
We review the biogeography of microorganisms in light of the biogeography of macroorganisms A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity However, recent studies also dispute the idea that 'everything is everywhere' We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial worldread more
Citations
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Journal ArticleDOI
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale.
TL;DR: The results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
Journal ArticleDOI
Bacterial Community Variation in Human Body Habitats Across Space and Time
Elizabeth K. Costello,Christian L. Lauber,Micah Hamady,Noah Fierer,Noah Fierer,Jeffrey I. Gordon,Rob Knight,Rob Knight +7 more
TL;DR: The results indicate that the microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.
Journal ArticleDOI
MEGAN analysis of metagenomic data
TL;DR: MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets, is introduced and provides graphical and statistical output for comparing different data sets.
Journal ArticleDOI
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Donovan H. Parks,Maria Chuvochina,David W. Waite,Christian Rinke,Adam Skarshewski,Pierre-Alain Chaumeil,Philip Hugenholtz +6 more
TL;DR: This work used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence.
Journal ArticleDOI
Structure and function of the global ocean microbiome
Shinichi Sunagawa,Luis Pedro Coelho,Samuel Chaffron,Jens Roat Kultima,Karine Labadie,Guillem Salazar,Bardya Djahanschiri,Georg Zeller,Daniel R. Mende,Adriana Alberti,Francisco M. Cornejo-Castillo,Paul I. Costea,Corinne Cruaud,Francesco d'Ovidio,Stefan Engelen,Isabel Ferrera,Josep M. Gasol,Lionel Guidi,Falk Hildebrand,Florian Kokoszka,Cyrille Lepoivre,Gipsi Lima-Mendez,Julie Poulain,Bonnie T. Poulos,Marta Royo-Llonch,Hugo Sarmento,Sara Vieira-Silva,Céline Dimier,Marc Picheral,Sarah Searson,Stefanie Kandels-Lewis,Tara Oceans Coordinators,Chris Bowler,Colomban de Vargas,Gabriel Gorsky,Nigel Grimsley,Pascal Hingamp,Daniele Iudicone,Olivier Jaillon,Fabrice Not,Hiroyuki Ogata,Stephane Pesant,Sabrina Speich,Lars Stemmann,Matthew B. Sullivan,Jean Weissenbach,Patrick Wincker,Eric Karsenti,Jeroen Raes,Silvia G. Acinas,Peer Bork +50 more
TL;DR: This work identifies ocean microbial core functionality and reveals that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
References
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The Detection of Disease Clustering and a Generalized Regression Approach
TL;DR: The technic to be given below for imparting statistical validity to the procedures already in vogue can be viewed as a generalized form of regression with possible useful application to problems arising in quite different contexts.
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Ecological Diversity and its Measurement
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Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
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