Worlds within worlds: evolution of the vertebrate gut microbiota.
In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.
Ley
Ruth E
RE
Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA.
Lozupone
Catherine A
CA
Hamady
Micah
M
Knight
Rob
R
Gordon
Jeffrey I
JI
D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D018407:Bacterial Physiological Phenomena; D005075:Biological Evolution; D041981:Gastrointestinal Tract / Q000378:metabolism / Q000382:microbiology*; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D014714:Vertebrates / Q000033:anatomy & histology*
D012336:RNA, Ribosomal, 16S
Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2117-22
18252821
PLoS Biol. 2007 Jul;5(7):e177
17594176
Science. 2005 Jul 22;309(5734):603-7
16040704
Appl Environ Microbiol. 2003 Nov;69(11):6659-68
14602626
FEMS Microbiol Ecol. 2007 Nov;62(2):171-80
17937674
Exp Biol Med (Maywood). 2004 Oct;229(9):902-13
15388885
Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11436-40
17592124
Trends Ecol Evol. 2011 Jul;26(7):340-8
21561679
Science. 2000 Apr 14;288(5464):287-93
10777411
Philos Trans R Soc Lond B Biol Sci. 1991 Aug 29;333(1267):197-207, disscussion 207-8
1682959
Nature. 2007 Oct 18;449(7164):811-8
17943117
J Bacteriol. 2004 May;186(9):2629-35
15090503
Nature. 2007 Jan 11;445(7124):153
17215830
Science. 2003 Mar 7;299(5612):1582-5
12624269
Nature. 2006 Dec 21;444(7122):1027-31
17183312
Nature. 2008 May 15;453(7193):396-400
18425110
Trends Ecol Evol. 2006 Sep;21(9):517-23
16820245
Mol Cell Biol. 1990 Jun;10(6):2513-20
1692956
Science. 2008 Jun 20;320(5883):1647-51
18497261
Proc Natl Acad Sci U S A. 2008 Aug 12;105 Suppl 1:11512-9
18695234
Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
14985472
Nat Genet. 2007 Oct;39(10):1256-60
17828263
Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13506-11
11095758
Appl Environ Microbiol. 1999 Nov;65(11):4799-807
10543789
Pediatrics. 2007 Mar;119(3):e724-32
17332189
Nature. 2008 Mar 20;452(7185):340-3
18311127
Chem Res Toxicol. 2007 Oct;20(10):1388-92
17900170
Hum Mutat. 2007 Feb;28(2):99-130
17024666
Am J Hum Genet. 2001 Jan;68(1):160-172
11095994
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
16820507
Ecology. 2006 Jun;87(6):1387-98
16869413
Proc Natl Acad Sci U S A. 1994 Jun 7;91(12):5441-5
8202505
Nature. 2006 Dec 21;444(7122):1022-3
17183309
Nature. 1999 Jul 15;400(6741):219-20
10421357
Appl Environ Microbiol. 1998 Aug;64(8):3110-3
9687486
Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4596-601
15070763
Nat Rev Microbiol. 2006 Feb;4(2):102-12
16415926
Nat Rev Microbiol. 2005 May;3(5):431-8
15821725
Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1981-6
14766966
Proc Biol Sci. 2007 Jul 22;274(1619):1723-30
17472915
Appl Environ Microbiol. 1999 Nov;65(11):5050-8
10543822
Nature. 2006 Jun 8;441(7094):714-8
16760969
Science. 2005 Mar 25;307(5717):1915-20
15790844
Integr Comp Biol. 2002 Apr;42(2):319-26
21708724
Science. 2001 May 11;292(5519):1119-22
11352069
Appl Environ Microbiol. 2000 Apr;66(4):1328-33
10742207
Science. 1990 Oct 5;250:104-7
11538072
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5
16033867
Appl Environ Microbiol. 2005 Aug;71(8):4556-66
16085849
Nature. 2007 Oct 18;449(7164):804-10
17943116
Cell Host Microbe. 2007 Nov 15;2(5):328-39
18005754
Toxicol Sci. 2005 Sep;87(1):277-84
15933226
J Hum Evol. 1999 May;36(5):461-85
10222165
Appl Environ Microbiol. 2005 Dec;71(12):8228-35
16332807
Perspect Biol Med. 2002 Fall;45(4):475-98
12388882
J Med Microbiol. 2005 Dec;54(Pt 12):1239-1242
16278440
Curr Biol. 2006 Oct 24;16(20):R866-71
17055966
EMBO Rep. 2006 Oct;7(10):956-60
17016449
Cell. 2006 Feb 24;124(4):837-48
16497592
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W394-9
16845035
FEMS Microbiol Ecol. 2007 Mar;59(3):576-83
17381516
Appl Environ Microbiol. 2007 Mar;73(5):1576-85
17220268
Science. 2002 Nov 15;298(5597):1424-7
12434060
Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8742-7
12077305
Curr Opin Biotechnol. 1997 Jun;8(3):340-5
9206017
Science. 2000 Nov 24;290(5496):1503
11185503
Environ Microbiol. 2006 Apr;8(4):732-40
16584484
Genome Biol. 2007;8(8):R171
17708774
Nat Genet. 2003 Dec;35(4):311-3
14634648
J Nutr. 1982 Apr;112(4):636-41
6279804
Science. 2005 Jun 10;308(5728):1635-8
15831718
Evolution. 1996 Apr;50(2):559-572
28568959