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Worlds within worlds: evolution of the vertebrate gut microbiota.

Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI.

Nat Rev Microbiol. 2008 Oct;6(10):776-88. doi: 10.1038/nrmicro1978. Review.


Evolution of mammals and their gut microbes.

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI.

Science. 2008 Jun 20;320(5883):1647-51. doi: 10.1126/science.1155725. Epub 2008 May 22. Erratum in: Science. 2008 Nov 21;322(5905):1188.


Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.

Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI.

Science. 2011 May 20;332(6032):970-4. doi: 10.1126/science.1198719.


Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities.

Yildirim S, Yeoman CJ, Sipos M, Torralba M, Wilson BA, Goldberg TL, Stumpf RM, Leigh SR, White BA, Nelson KE.

PLoS One. 2010 Nov 12;5(11):e13963. doi: 10.1371/journal.pone.0013963.


A core gut microbiome in obese and lean twins.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI.

Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540. Epub 2008 Nov 30.


Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing.

Nam YD, Jung MJ, Roh SW, Kim MS, Bae JW.

PLoS One. 2011;6(7):e22109. doi: 10.1371/journal.pone.0022109. Epub 2011 Jul 29.


Sympatric chimpanzees and gorillas harbor convergent gut microbial communities.

Moeller AH, Peeters M, Ndjango JB, Li Y, Hahn BH, Ochman H.

Genome Res. 2013 Oct;23(10):1715-20. doi: 10.1101/gr.154773.113. Epub 2013 Jun 26.


Evidence for a core gut microbiota in the zebrafish.

Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF.

ISME J. 2011 Oct;5(10):1595-608. doi: 10.1038/ismej.2011.38. Epub 2011 Apr 7.


Bacterial microbiome of Coptotermes curvignathus (Isoptera: Rhinotermitidae) reflects the coevolution of species and dietary pattern.

King JH, Mahadi NM, Bong CF, Ong KH, Hassan O.

Insect Sci. 2014 Oct;21(5):584-96. doi: 10.1111/1744-7917.12061. Epub 2013 Dec 17.


Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut.

Wong S, Stephens WZ, Burns AR, Stagaman K, David LA, Bohannan BJ, Guillemin K, Rawls JF.

MBio. 2015 Sep 29;6(5):e00687-15. doi: 10.1128/mBio.00687-15.


Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

Sullam KE, Essinger SD, Lozupone CA, O'Connor MP, Rosen GL, Knight R, Kilham SS, Russell JA.

Mol Ecol. 2012 Jul;21(13):3363-78. doi: 10.1111/j.1365-294X.2012.05552.x. Epub 2012 Apr 4.


Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.

Jones BV, Sun F, Marchesi JR.

BMC Genomics. 2010 Jan 19;11:46. doi: 10.1186/1471-2164-11-46.


The gut bacterial community of mammals from marine and terrestrial habitats.

Nelson TM, Rogers TL, Brown MV.

PLoS One. 2013 Dec 30;8(12):e83655. doi: 10.1371/journal.pone.0083655. eCollection 2013. Erratum in: PLoS One. 2014;9(5):e99562.


The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities.

Brucker RM, Bordenstein SR.

Evolution. 2012 Feb;66(2):349-62. doi: 10.1111/j.1558-5646.2011.01454.x. Epub 2011 Oct 5.


Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm.

Walter J, Britton RA, Roos S.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4645-52. doi: 10.1073/pnas.1000099107. Epub 2010 Jun 25. Review.


Do diet and taxonomy influence insect gut bacterial communities?

Colman DR, Toolson EC, Takacs-Vesbach CD.

Mol Ecol. 2012 Oct;21(20):5124-37. doi: 10.1111/j.1365-294X.2012.05752.x. Epub 2012 Sep 14.


Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.

De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6. doi: 10.1073/pnas.1005963107. Epub 2010 Aug 2.


The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments.

Zhao W, Wang Y, Liu S, Huang J, Zhai Z, He C, Ding J, Wang J, Wang H, Fan W, Zhao J, Meng H.

PLoS One. 2015 Feb 17;10(2):e0117441. doi: 10.1371/journal.pone.0117441. eCollection 2015.


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