Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: Lessons from time-series analyses using next-generation sequencing for application in field studies

Methods in Ecology and Evolution

Volumn 6, Issue 9, 2015, Pages 1080-1087

  Menke, Sebastian ^a,b   Meier, Matthias ^a   Sommer, Simone ^a,b  

^a LEIBNIZ INSTITUTE FOR ZOO AND WILDLIFE RESEARCH   (Germany)

^b UNIVERSITY OF ULM   (Germany)

Author keywords

Bacteria; Giraffe; Gut microbiome; Mammals; Namibia; Non invasive sampling; Springbok; Time series

Indexed keywords

EID: 84941805672     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12394     Document Type: Article

References (37)

1. Amato, K.R., Yeoman, C.J., Kent, A., Righini, N., Carbonero, F., Estrada, A. et al. (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal, 7, 1344-1353.
2. Arrieta, J.M., Weinbauer, M.G. & Herndl, G.J. (2000) Interspecific variability in sensitivity to UV radiation and subsequent recovery in selected isolates of marine bacteria. Applied and Environmental Microbiology, 66, 1468-1473.
3. Becker, M.H., Richards-Zawacki, C.L., Gratwicke, B. & Belden, L.K. (2014) The effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki). Biological Conservation, 176, 199-206.
4. Brusa, T., Canzi, E., Pacini, N., Zanchi, R. & Ferrari, P.A. (1989) Oxygen tolerance of anaerobic bacteria isolated from human feces. Current Microbiology, 19, 39-43.
5. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K. et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
6. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Frierer, N. et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal, 6, 1621-1624.
7. Cardona, S., Eck, A., Cassellas, M., Gallart, M., Alastrue, C., Dore, J. et al. (2012) Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiology, 12, 158.
8. Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
9. Fox, J. & Weisberg, S. (2011) An R companion to applied regression. Sage, Thousand Oaks, CA.
10. Fuhrmann, J.J. & Zuberer, D.A. (2004) Principles and applications of soil microbiology. Prentice Hall, Upper Saddle River, NJ.
11. Fujioka, R.S., Hashimoto, H.H., Siwak, E.B. & Young, R.H. (1981) Effect of sunlight on survival of indicator bacteria in seawater. Applied and Environmental Microbiology, 41, 690-696.
12. Hijnen, W.A.M., Beerendonk, E.F. & Medema, G.J. (2006) Inactivation credit of UV radiation for viruses, bacteria and protozoan (oo)cysts in water: a review. Water Research, 40, 3-22.
13. Khan, A.A., Shrivastava, A. & Khurshid, M. (2012) Normal to cancer microbiome transformation and its implication in cancer diagnosis. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, 1826, 331-337.
14. Kinross, J.M., Darzi, A.W. & Nicholson, J.K. (2011) Gut microbiome-host interactions in health and disease. Genome Medicine, 3, 1-12.
15. Knights, D., Kuczynski, J., Charlson, E.S., Zaneveld, J., Mozer, M.C., Collman, R.G., Bushman, F.D., Knight, R. & Kelley, S.T. (2011) Bayesian community-wide culture-independent microbial source tracking. Nature Methods, 8, 761-763.
16. Kohl, K.D., Skopec, M.M. & Dearing, M.D. (2014) Captivity results in disparate loss of gut microbial diversity in closely related hosts. Conservation Physiology, 2, 1-11.
17. Kuczynski, J., Lauber, C.L., Walters, W.A., Parfrey, L.W., Clemente, J.C., Gevers, D. & Knight, R. (2012) Experimental and analytical tools for studying the human microbiome. Nature Reviews Genetics, 13, 47-58.
18. Lauber, C.L., Zhou, N., Gordon, J.I., Knight, R. & Fierer, N. (2010) Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples: influence of short-term storage conditions on microbiota. FEMS Microbiology Letters, 307, 80-86.
19. Magoč, T. & Salzberg, S.L. (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27, 2957-2963.
20. Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal, 17, 10-12.
21. McCambridge, J. & McMeekin, T.A. (1981) Effect of solar radiation and predacious microorganisms on survival of fecal and other bacteria. Applied and Environmental Microbiology, 41, 1083-1087.
22. McKenna, P., Hoffmann, C., Minkah, N., Aye, P.P., Lackner, A., Liu, Z. et al. (2008) The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathogens, 4, e20.
23. Menke, S., Wasimuddin, Meier, M., Melzheimer, J., Mfune, J.K.E., Heinrich, S., Thalwitzer, S., Wachter, B. & Sommer, S. (2014) Oligotyping reveals differences between gut-microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level. Systems Microbiology, 5, 526.
24. Muegge, B.D., Kuczynski, J., Knights, D., Clemente, J.C., Gonzales, A., Fontana, L., Henrissat, B., Knight, R. & Gordon, J.I. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, 332, 970-974.
25. Phillips, C.D., Phelan, G., Dowd, S.E., McDonough, M.M., Ferguson, A.W., Delton Hanson, J. et al. (2012) Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography. Molecular ecology, 21, 2617-2627.
26. R Core Team (2013) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. Retrieved from http://www.R-project.org.
27. Roesch, L.F., Casella, G., Simell, O., Krischer, J., Wasserfall, C.H., Schatz, D., Atkinson, M.A., Neu, J. & Triplett, E.W. (2009) Influence of fecal sample storage on bacterial community diversity. The Open Microbiology Journal, 3, 40-46.
28. Rudi, K., Moen, B., Sekelja, M., Frisli, T. & Lee, M.R.F. (2012) An eight-year investigation of bovine livestock fecal microbiota. Veterinary Microbiology, 160, 369-377.
29. Shannon, C.E. & Weaver, W. (1949) The mathematical theory of communication. The University of Illinois Press, Urbana.
30. Spellerberg, I.F. & Fedor, P.J. (2003) A tribute to Claude Shannon (1916-2001) and a plea for more rigorous use of species richness, species diversity and the "Shannon-Wiener" Index. Global ecology and biogeography, 12, 177-179.
31. Taberlet, P., Waits, L.P. & Luikart, G. (1999) Noninvasive genetic sampling: look before you leap. Trends in Ecology & Evolution, 14, 323-327.
32. Tzeneva, V.A., Salles, J.F., Naumova, N., de Vos, W.M., Kuikman, P.J., Dolfing, J. & Smidt, H. (2009) Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity. Research in Microbiology, 160, 89-98.
33. Waits, L.P. & Paetkau, D. (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. Journal of Wildlife Management, 69, 1419-1433.
34. Wickham, H. (2009) ggplot2: elegant graphics for data analysis. Springer, New York.
35. Wood, S. (2006) Generalized additive models: an introduction with R. CRC Press, London, England.
36. Wood, S.N. (2011) Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 73, 3-36.
37. Zuur, A., Ieno, E.N., Walker, N., Saveliev, A.A. & Smith, G.M. (2009) Mixed effects models and extensions in ecology with R. Springer, Berlin, Germany.