Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 6 (3), 588-96

Co-habiting Amphibian Species Harbor Unique Skin Bacterial Communities in Wild Populations


Co-habiting Amphibian Species Harbor Unique Skin Bacterial Communities in Wild Populations

Valerie J McKenzie et al. ISME J.


Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens.


Figure 1
Figure 1
Phylotype richness per amphibian species. The number of unique phylotypes per individual amphibian, estimated from a sampling depth of 750 sequences per sample. Each symbol represents the estimate of unique phylotypes or operational taxonomic units (OTUs) per amphibian individuals at a given site. Different symbols correspond to different pond locations.
Figure 2
Figure 2
Ordination plot. β-Diversity patterns were visualized using a MDS ordination approach with skin-associated bacterial community differences represented as Bray–Curtis distances. The 2D stress (or measure of distortion) in the MDS configuration was relatively low (0.13), so the 2D distance between points in the ordination plot is a good representation of the degree of similarity between each sample's bacterial community. Each point represents the skin bacterial community of an individual amphibian; color indicates species and shape indicates pond location.
Figure 3
Figure 3
Heat map. A color-scale heat map demonstrates the relative abundance of the 19 most common bacterial phylotypes across species and ponds; red cells indicate higher proportional abundance and blue cells indicate lower proportional abundance. The relative abundance of each phylotype was converted to a proportion of the total number of classified sequences. The total number of unclassified sequences summed together for each amphibian sample comprised on average only 5.7% (±s.d.=0.06) of the sequences per sample and were removed from the table. In order to condense the bacterial groups and present the most common phylotypes in the heat map, we further removed all phylotypes that comprised ⩽5% of the total number of classified sequences across all samples. The proportion of sequences that are represented in the heat map for each species in each pond site varied between 55–98%. Nineteen unique phylotypes remained and the average proportion was calculated per amphibian species per pond.

Similar articles

See all similar articles

Cited by 96 PubMed Central articles

See all "Cited by" articles


    1. Annis SL, Dastoor FP, Ziel H, Daszak P, Longcore JE. A DNA-based assay identifies Batrachochytrium dendrobatidis in amphibians. J Wildl Dis. 2004;40:420–428. - PubMed
    1. Banning JL, Weddle AL, Wahl GW, Simon MA, Lauer A, Walters RL, et al. Antifungal skin bacteria, embryonic survival, and communal nesting in four-toed salamanders, Hemidactylium scutatum. Oecologia. 2008;156:423–429. - PubMed
    1. Belden LK, Harris RN. Infectious diseases in wildlife: the community ecology context. Front Ecol Environ. 2007;5:533–539.
    1. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–336. - PMC - PubMed
    1. Carey C, Cohen N, Rollins-Smith L. Amphibian declines: an immunological perspective. Dev Comp Immunol. 1999;23:459–472. - PubMed

Publication types