Evolutionary relationships of wild hominids recapitulated by gut microbial communities

PLoS Biology

Volumn 8, Issue 11, 2010, Pages

  Ochman, Howard ^a,h   Worobey, Michael ^a   Kuo, Chih Horng ^a,b   Ndjango, Jean Bosco N ^c   Peeters, Martine ^d   Hahn, Beatrice H ^e,f   Hugenholtz, Philip ^g,i  

^a University of Arizona   (United States)

^b INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

^c UNIVERSITY OF KISANGANI   (Congo)

^d INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^e University of Alabama at Birmingham   (United States)

^f University of Alabama at Birmingham   (United States)

^g DOE JOINT GENOME INSTITUTE   (United States)

^h YALE UNIVERSITY   (United States)

ⁱ UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; MITOCHONDRIAL DNA;

APE; ARTICLE; BACTEROIDES; FECES ANALYSIS; FIRMICUTES; GENETIC VARIABILITY; HOMINID; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; MICROFLORA; NONHUMAN; PARSIMONY ANALYSIS; PHYLOGENY; PHYLUM; PROTEOBACTERIA; TAXONOMIC RANK; Y CHROMOSOME; ANIMAL; CLASSIFICATION; GENETICS; INTESTINE; MICROBIOLOGY; MOLECULAR EVOLUTION; PRIMATE;

HOMINIDAE; PRIMATES;

ANIMALS; EVOLUTION, MOLECULAR; HOMINIDAE; INTESTINES; PHYLOGENY; PRIMATES;

EID: 78649978358     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1000546     Document Type: Article

References (41)

1. Tannock GW, Fuller R, Smith SL, Hall MA (1990) Plasmid profiling of members of the family Enterobacteriaceae, lactobacilli, and bifidobacteria to study the transmission of bacteria from mother to infant. J Clin Microbiol 28: 1225-1228.
2. Inoue R, Ushida K (2003) Vertical and horizontal transmission of intestinal commensal bacteria in the rat model. FEMS Microbiol Ecol 46: 213-219.
3. Favier CF, De Vos WM, Akkermans AD (2003) Development of bacterial and bifidobacterial communities in feces of newborn babies. Anaerobe 9: 219-229.
4. Linz B, Balloux F, Moodley Y, Manica A, Liu H, et al. (2007) An African origin for the intimate association between humans and Helicobacter pylori. Nature 445: 915-918.
5. Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837-848.
6. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6: 776-788.
7. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, et al. (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102: 11070-11075.
8. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915-1920.
9. Rawls JF, Mahowald MA, Ley RE, Gordon JI (2006) Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433.
10. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, et al. (2008) Evolution of mammals and their gut microbes. Science 320: 1647-1651.
11. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, et al. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255. doi:10.1371/journal.pgen.1000255.
12. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35: e120.
13. Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280. doi/10.1371/journal.pbio.0060280.
14. Keele BF, Jones JH, Terio KA, Estes JD, Rudicell RS, et al. (2009) Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz. Nature 460: 515-519.
15. Liu W, Worobey M, Li Y, Keele BF, Bibollete-Ruche F, et al. (2008) Molecular ecology and natural history of simian foamy virus infection in wild-living chimpanzees. PLoS Pathog 4: e1000097. doi/10.1371/journal.ppat.1000097.
16. Van Heuverswyn F, Li Y, Neel C, Bailes E, Keele BF, et al. (2006) Human immunodeficiency viruses: SIV infection in wild gorillas. Nature 444: 164.
17. Keele BF, Van Heuverswyn F, Li Y, Bailes E, Takehisa J, et al. (2006) Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science 313: 523-526.
18. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
19. Hamp TJ, Jones WJ, Fodor AA (2009) Effects of experimental choices and analysis noise on surveys of the ''rare biosphere''. Appl Environ Microbiol 75: 3263-3270.
20. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: Pyrosequencing errors lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
21. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, et al. (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3: 733-739.
22. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6: 431-440.
23. Frey JC, Rothman JM, Pell AN, Nizeyi JB, Cranfield MR, et al. (2006) Fecal bacterial diversity in a wild gorilla. Appl Environ Microbiol 72: 3788-3792.
24. Uenishi G (2007) Molecular analyses of the intestinal microbiota of chimpanzees in the wild and in captivity. Am J Primatol 69: 367-376.
25. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
26. Turnbaugh PJ, Hamady M, Yatsunkenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
27. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
28. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, et al. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11: 2574-2584.
29. Lozupone CA, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 731.
30. Lozupone CA, Hamady M, Kelley ST, Knight R (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-1585.
31. Fierer N, Hamady M, Lauber CL, Knight R (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 105: 17994-17999.
32. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
33. Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4: 182-190.
34. Liu Z, DeSantis TZ, Andersen GL, Knight R (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrose-quencers. Nucleic Acids Res 36: e120.
35. Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch DB (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: r143.
36. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
37. Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
38. Li L, Stoeckert CJ, Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
39. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650.
40. Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490. doi/10.1371/ journal.pone.0009490.
41. Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.