COREMIC: a web-tool to search for a niche associated CORE MICrobiome

PeerJ
Richard R RodriguesMark A Williams

Abstract

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool "COREMIC" meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the "core microbiome" associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of so...Continue Reading

References

Feb 24, 2001·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·T KanekoS Tabata
Sep 26, 2001·Applied and Environmental Microbiology·J B HughesB J Bohannan
Sep 4, 2004·Environmental Microbiology·Nabla KennedyNicholas Clipson
Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Jan 26, 2008·International Journal of Systematic and Evolutionary Microbiology·Joo Hwang ParkYoung Ryun Chung
Jul 17, 2009·International Journal of Systematic and Evolutionary Microbiology·Kemanthi G NandasenaJohn G Howieson
Mar 3, 2010·Annual Review of Plant Biology·Yunde Zhao
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Jul 17, 2010·Biotechnology Letters·Olubukola Oluranti Babalola
Aug 17, 2010·Bioinformatics·Robert C Edgar
Oct 19, 2011·Environmental Microbiology·Ashley Shade, Jo Handelsman
Oct 29, 2011·Trends in Microbiology·Jay D Evans, Ryan S Schwarz
May 9, 2012·Trends in Plant Science·Roeland L BerendsenPeter A H M Bakker
Aug 16, 2012·Environmental Microbiology·Yuejian MaoRoderick I Mackie
Aug 30, 2012·Ecology·Jay T LennonDonald R Schoolmaster
May 16, 2013·Antonie van Leeuwenhoek·Kamal GuerroujMustapha Missbah El Idrissi
May 31, 2013·The ISME Journal·Vanessa L BaileyLee Ann McCue
Aug 21, 2013·BioMed Research International·Darine Trabelsi, Ridha Mhamdi
Oct 8, 2013·Microbiological Research·Bernard R Glick
Jan 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ben P WerlingDouglas A Landis
Jul 9, 2014·Applied and Environmental Microbiology·Rahul A BahulikarMichael K Udvardi
Nov 19, 2014·International Journal of Systematic and Evolutionary Microbiology·Munusamy MadhaiyanKeun-Chul Lee
Nov 27, 2014·Frontiers in Plant Science·Bram Van de Poel, Dominique Van Der Straeten
Nov 6, 2015·Genetics and Molecular Biology·Rocheli de SouzaLuciane M P Passaglia

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Methods Mentioned

BETA
ISA
environmental stress
genetic modification

Software Mentioned

ANOSIM
ssl
jinja2
COREMIC
QIIME
MetaCoMET
requests
matplotlib
numpy
ete3

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