Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography

Molecular Ecology

Volumn 21, Issue 11, 2012, Pages 2617-2627

  Phillips, Caleb D ^a   Phelan, Georgina ^a,b   Dowd, Scot E ^a,c   McDonough, Molly M ^a   Ferguson, Adam W ^a   Delton Hanson, J ^c   Siles, Lizette ^a   OrdO'Ñez Garza, Nicté ^a   San Francisco, Michael ^a   Baker, Robert J ^a  

^a TEXAS TECH UNIVERSITY   (United States)

^b MANCHESTER METROPOLITAN UNIVERSITY   (United Kingdom)

^c Research and Testing Laboratory   (United States)

Author keywords

dietary evolution; host phylogeny; host reproductive microbiota; phyllostomidae

Indexed keywords

ANIMAL; ARTICLE; BAT; CARNIVORY; FEMALE; GENETICS; GUATEMALA; HERBIVORY; MALE; METAGENOME; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY;

ANIMALS; CARNIVORY; CHIROPTERA; FEMALE; GUATEMALA; HERBIVORY; MALE; METAGENOME; PHYLOGENY;

CHIROPTERA; PHYLLOSTOMIDAE;

EID: 84861574806     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05568.x     Document Type: Article

References (25)

1. Abecia L, Fondevila M, Balcells J, McEwan NR, (2007) The effect of lactating rabbit does on the development of the caecal microbial community in the pups they nurture. Journal of Applied Microbiology, 103, 557-564.
2. Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M, (2010a) Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. Infection Immunology, 78, 1509-1519.
3. Bailey MT, Walton JC, Dowd SE, Weil ZM, Nelson RJ, (2010b) Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus). Brain Behavior Immunity, 24, 577-584.
4. Baker RJ, Bininda-Emonds ORP, Mantilla-Meluk H, Porter CA, Van Den Bussche RA, (forthcoming) Molecular timescale of diversification of feeding strategy and morphology in new world leaf-nosed bats (Phyllostomidae): a phylogenetic perspective. In: Evolutionary history of bats: fossils, molecules and morphology (eds, Gunell, and, Simmons,), pp. 385-409. Cambridge University Press, Cambridge.
5. Ballal SA, Gallini CA, Segata N, Huttenhower C, Garrett WS, (2011) Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Cellular Microbiology, 13, 508-517.
6. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R, (2010a) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics, 26, 266-267.
7. Caporaso JG, Kuczynski J, Stombaugh J, et al. (2010b) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
8. Collado MC, Isolauri E, Laitinen K, Salminen S, (2008) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. The American Journal of Clinical Nutrition, 88, 894-899.
9. Coolon JD, Jones KL, Narayanan S, Wisely SM, (2010) Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination. Molecular Ecology, 19, 67-80.
10. Datzmann T, von Helversen O, Mayer F, (2010) Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia). BMC Evolutionary Biology, 4, 165-179.
11. Dunning T, (1993) Accurate methods for the statistics of surprise and coincidence. Computational Lunguistics, 19, 61-74.
12. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
13. Faith DP, (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
14. Famularo G, De Simone C, Pandey V, Sahu AR, Minisola G, (2005) Probiotic lactobacilli: an innovative tool to correct the malabsorption syndrome of vegetarians? Medical Hypotheses, 65, 1132-1135.
15. Gontcharova V, Youn E, Wolcott RD, Hollister EB, Gentry TJ, Dowd SE, (2010) Black box chimera check (B2C2): a windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Microbiology Journal, 4, 6.
16. Ley RE, Hamaday M, Lozupone C, et al. (2008) Evolution of mammals and their gut microbes. Science, 320, 1647-1651.
17. Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71, 8228-8235.
18. Muegge BD, Kuczynski J, Knights D, et al. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, 332, 970-974.
19. Nemergut DR, Costello EK, Hamady M, et al. (2011) Global patterns in the biogeography of bacterial taxa. Environmental Microbiology, 13, 135-144.
20. Orchman H, Worobey M, Kuo CH, et al. (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biology, 8, e1000546.
21. Price MN, Dehal PS, Arkin AP, (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution, 26, 1641-1650.
22. Rojas D, Vale A, Ferrero V, Navarro L, (2011) When did plants become important to leaf-nosed bats? Diversification of feeding habits in the family Phyllostomidae. Molecular Ecology, 20, 2217-2228.
23. Teeling EC, Springer MS, Madsen O, Bates P, O'Brien SJ, Murphy WJ, (2005) A molecular phylogeny for bats illuminates biogeography and the fossil record. Science, 307, 580-584.
24. de Vienne DM, Giraud T, Martin OC, (2007) A congruence index for testing topological similarity between trees. Bioinformatics, 23, 3119-3124.
25. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naïve Bayesian classifier for rapid assignment of rDNA sequences into the new bacterial taxonomy. Applied Environmental Microbiology, 73, 5261-5267.