AiM> Vol.4 No.7, May 2014

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The Skin Microbiome of Gambusia affinis Is Defined and Selective ()

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DOI: 10.4236/aim.2014.47040 5,314 Downloads 7,062 Views Citations

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Annie B. Leonard, Jeanette M. Carlson, Dayna E. Bishoff, Sarah I. Sendelbach, Sonja B. Yung, Sonya Ramzanali, Ananda B. W. Manage, Embriette R. Hyde, Joseph F. Petrosino, Todd P. Primm

Affiliation(s)

Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA.
Department of Biological Sciences, Sam Houston State University, Huntsville, USA.
Department of Mathematics and Statistics, Sam Houston State University, Huntsville, USA.

ABSTRACT

Metagenomics and bacterial culture were used to determine the normal skin microbiome of the Western mosquitofish (Gambusia affinis). This is the first study of G. affinis, and the most in-depth study of any fish skin, utilizing a combination of 16S profile pyrosequencing and culture analysis. Over 1800 sequences obtained from three individuals reveal that over half of all sequences come from five invariant genera, Acinetobacter, Sphingomonas, Acidovorax, Enhydrobacter, and Aquabacterium. The microbiome is diverse but has low equitability, with a total of 81 genera detected. Challenge studies suggest that non-native bacteria cannot colonize the skin. This definition of the normal skin microbiome lays the foundation for future studies with this model system.

KEYWORDS

Fish, Microbiome, Acinetobacter, Sphingomonas, Metagenomics, Mucosal

Cite this paper

Leonard, A. , Carlson, J. , Bishoff, D. , Sendelbach, S. , Yung, S. , Ramzanali, S. , Manage, A. , Hyde, E. , Petrosino, J. and Primm, T. (2014) The Skin Microbiome of Gambusia affinis Is Defined and Selective. Advances in Microbiology, 4, 335-343. doi: 10.4236/aim.2014.47040.

Conflicts of Interest

The authors declare no conflicts of interest.

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[16] Kembel, S.W., Wu, M., Eisen, J.A. and Green, J.L. (2012) Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. PLoS Computational Biology, 8, Article ID: e1002743.
http://dx.doi.org/10.1371/journal.pcbi.1002743

[17] Lee, Z.M., Bussema 3rd, C. and Schmidt, T.M. (2009) rrnDB: Documenting the Number of rRNA and tRNA Genes in Bacteria and Archaea. Nucleic Acids Research, 37, 489-493.
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[18] Wiesner, J. and Vilcinskas, A (2010) Antimicrobial Peptides: The Ancient Arm of the Human Immune System. Virulence, 5, 440-464.
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[19] Garrity, G., Brenner, D.J., Krieg, N.R. and Staley, J.R. (2005) Bergey’s Manual of Systematic Bacteriology. 2nd Edition, Springer, Berlin.

[20] Fryer, J.L. and Mauel, M.J. (1997) The Rickettsia: An Emerging Group of Pathogens in Fish. Emerging Infectious Diseases, 3, 137-144.
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[1]	Human Microbiome Project Consortium (2012) Structure, Function and Diversity of the Healthy Human Microbiome. Nature, 486, 207-214. http://dx.doi.org/10.1038/nature11234

[2]	Sullam, K.E., Essinger, S.D., Lozupone, C.A., O’Conner, M.P., Rosen, G.L., Knight, R., Kilham, S.S. and Russell, J.A. (2012) Environmental and Ecological Factors That Shape the Gut Bacterial Communities of Fish: A Meta-Analysis. Molecular Ecology, 21, 3363-3378. http://dx.doi.org/10.1111/j.1365-294X.2012.05552.x

[3]	Landeira-Dabarca, A., Siero, C. and Alvarez, M. (2013) Change in Food Ingestion Induces Rapid Shifts in the Diversity of Microbiota Associated with Cutaneous Mucus of Atlantic Salmon Salmosalar. Journal of Fish Biology, 82, 893-906. http://dx.doi.org/10.1111/jfb.12025

[4]	Svanevik, C.S. and Lunestad, B.T. (2011) Characterization of the Microbiota of Atlantic Mackerel (Scomberscombrus). International Journal of Food Microbiology, 151, 164-170.

[5]	Wang, W., Zhou, Z., He, S., Liu, Y., Cao, Y., Shi, P., Yao, B. and Ringo, E. (2010) Identification of the Adherent Microbiota on the Gills and Skin of Poly-Cultured Gibel Carp (Carassiusauratusgibelio) and Bluntnose Black Bream (Megalobramaamblycephala Yih). Aquaculture Research, 41, e72-e83. http://dx.doi.org/10.1111/j.1365-2109.2009.02459.x

[6]	Larsen, A., Tao, Z., Bullard, S.A. and Arias, C.R. (2013) Diversity of the Skin Microbiota of Fishes: Evidence for Host Species Specificity. FEMS Microbial Ecology, 85, 1-12.

[7]	Rakers, S., Gebert, M., Uppalapati, S., Meyer, W., Maderson, P., Sell, A.F., Kruse, C. and Paus, R. (2010) Fish Matters: The Relevance of Fish Skin Biology to Investigative Dermatology. Experimental Dermatology, 19, 313-324. http://dx.doi.org/10.1111/j.1600-0625.2009.01059.x

[8]	Pawlitz, R.J. and Kayla, D.D. (2012) The National Nonindigenous Aquatic Species Program. US Geological Survey, Reston. http://nas.er.usgs.gov

[9]	Cureton II, J.C., Martin, M.E. and Deaton, R. (2010) Short Term Changes in Sex Ratio and Density Alter Coercive Male Mating Tactics. Behavior, 11, 1431-1442. http://dx.doi.org/10.1163/000579510X519495

[10]	Deaton, R. (2008) Factors Influencing Male Mating Behavior in Gambusia affinis (Baird & Girard) with a Coercive Mating System. Journal of Fish Biology, 72, 1607-1622. http://dx.doi.org/10.1111/j.1095-8649.2008.01827.x

[11]	Schloss, P.D., Westcott, S.L, Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A, Oakley, B.B., Parks, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G, Van Horn, D.J. and Weber, C.F. (2009) Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology, 75, 7537-7541. http://dx.doi.org/10.1128/AEM.01541-09

[12]	Angiuoli, S.V., Matalka, M., Gussman, G., Galens, K., Vangala, M., Riley, D.R., Arze, C., White, J.R., White, O. and Fricke, W.F. (2011) CloVR: A Virtual Machine for Automated and Portable Sequence Analysis from the Desktop Using Cloud Computing. BMC Bioinformatics, 12, 356. http://dx.doi.org/10.1186/1471-2105-12-356

[13]	Blodgett, R. (2010) Bacteriological Analytical Manual. Food and Drug Administration USA, Appendix 2.

[14]	Whittaker, R.H. (1972) Evolution and Measurement of Species Diversity. Taxon, 21, 213-251. http://dx.doi.org/10.2307/1218190

[15]	Beals, M., Gross, L. and Harrell, S. (1999) Diversity Indices: Simpson’s D and E. http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html

[16]	Kembel, S.W., Wu, M., Eisen, J.A. and Green, J.L. (2012) Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. PLoS Computational Biology, 8, Article ID: e1002743. http://dx.doi.org/10.1371/journal.pcbi.1002743

[17]	Lee, Z.M., Bussema 3rd, C. and Schmidt, T.M. (2009) rrnDB: Documenting the Number of rRNA and tRNA Genes in Bacteria and Archaea. Nucleic Acids Research, 37, 489-493. http://dx.doi.org/10.1093/nar/gkn689

[18]	Wiesner, J. and Vilcinskas, A (2010) Antimicrobial Peptides: The Ancient Arm of the Human Immune System. Virulence, 5, 440-464. http://dx.doi.org/10.4161/viru.1.5.12983

[19]	Garrity, G., Brenner, D.J., Krieg, N.R. and Staley, J.R. (2005) Bergey’s Manual of Systematic Bacteriology. 2nd Edition, Springer, Berlin.

[20]	Fryer, J.L. and Mauel, M.J. (1997) The Rickettsia: An Emerging Group of Pathogens in Fish. Emerging Infectious Diseases, 3, 137-144. http://dx.doi.org/10.3201/eid0302.970206