Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California
1.Fisher MC, Garner TWJ. Chytrid fungi and global amphibian declines. Nat Rev Microbiol. 2020;18:332–43.CAS
PubMed
Article
Google Scholar
2.Skerratt LF, Berger L, Speare R, Cashins S, McDonald KR, Phillott AD, et al. Spread of chytridiomycosis has caused the rapid global decline and extinction of frogs. Ecohealth. 2007;4:125–34.Article
Google Scholar
3.Voyles J, Vredenburg VT, Tunstall TS, Parker JM, Briggs CJ, Rosenblum EB. Pathophysiology in Mountain Yellow-Legged Frogs (Rana muscosa) during a Chytridiomycosis Outbreak. PLoS ONE. 2012;7:e35374.CAS
PubMed
PubMed Central
Article
Google Scholar
4.Voyles J, Young S, Berger L, Campbell C, Voyles WF, Dinudom A, et al. Pathogenesis of Chytridiomycosis, a cause of catastrophic amphibian declines. Science (80-). 2009;326:582–5.CAS
Article
Google Scholar
5.Antwis RE, Harrison XA. Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates. Mol Ecol. 2018;27:577–89.CAS
PubMed
Article
Google Scholar
6.Muletz-wolz CR, Almario JG, Barnett SE, DiRenzo GV, Martel A, Pasmans F, et al. Inhibition of fungal pathogens across genotypes and temperatures by amphibian skin bacteria. Front Microbiol. 2017;8:1551.7.Kueneman JG, Woodhams DC, Harris R, Archer HM, Knight R, McKenzie VJ, et al. Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity. Proc R Soc London B Biol Sci. 2016;283:20161553.8.Harris RN, Brucker RM, Walke JB, Becker MH, Schwantes CR, Flaherty DC, et al. Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus. ISME J. 2009;3:818–24.CAS
PubMed
Article
Google Scholar
9.Bletz MC, Loudon AH, Becker MH, Bell SC, Woodhams DC, Minbiole KP, et al. Mitigating amphibian chytridiomycosis with bioaugmentation: characteristics of effective probiotics and strategies for their selection and use. Ecol Lett. 2013;16:817–20.Article
Google Scholar
10.Becker MH, Harris RN, Minbiole KP, Schwantes CR, Rollins-Smith LA, Reinert LK, et al. Towards a better understanding of the use of probiotics for preventing chytridiomycosis in Panamanian golden frogs. Ecohealth. 2011;8:501–6.PubMed
Article
Google Scholar
11.Woodhams DC, Geiger CC, Reinert LK, Rollins-Smith LA, Lam B, Harris RN, et al. Treatment of amphibians infected with chytrid fungus: learning from failed trials with itraconazole, antimicrobial peptides, bacteria, and heat therapy. Dis Aquat Organ. 2012;98:11–25.CAS
PubMed
Article
Google Scholar
12.Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: networks, competition, and stability. Science. 2015;350:663–6.CAS
PubMed
Article
Google Scholar
13.Oh J, Byrd AL, Park M, Kong HH, Segre JA. Temporal stability of the human skin microbiome. Cell. 2016;165:854–66.CAS
PubMed
PubMed Central
Article
Google Scholar
14.Harrison XA, Price SJ, Hopkins K, Leung W, Sergeant C, Garner T. Diversity-stability dynamics of the amphibian skin microbiome and susceptibility to a lethal viral pathogen. Front Microbiol. 2019;10:1–13.CAS
Article
Google Scholar
15.Walke JB, Becker MH, Krinos A, Chang E, Santiago C, Umile TP, et al. Seasonal changes and the unexpected impact of environmental disturbance on skin bacteria of individual amphibians in a natural habitat. FEMS Microbiol Ecol. 2021;97:1–14.Article
Google Scholar
16.Bletz MC, Perl R, Bobowski BT, Japke LM, Tebbe CC, Dohrmann AB, et al. Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function. ISME J. 2017;11:1521–34.PubMed
PubMed Central
Article
Google Scholar
17.Familiar López M, Rebollar EA, Harris RN, Vredenburg VT, Hero J. Temporal variation of the skin bacterial community and Batrachochytrium dendrobatidis infection in the terrestrial cryptic frog Philoria loveridgei. Front Microbiol. 2017;8:1–12.Article
Google Scholar
18.Longo AV, Savage AE, Hewson I, Zamudio KR. Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians. R Soc Open Sci. 2015;2:140377.PubMed
PubMed Central
Article
CAS
Google Scholar
19.Douglas AJ, Hug LA, Katzenback BA. Composition of the North American wood frog (Rana sylvatica) bacterial skin microbiome and seasonal variation in community structure. Microb Ecol. 2021;81:78–92.CAS
PubMed
Article
Google Scholar
20.Estrada A, Hughey MC, Medina D, Rebollar EA, Walke JB, Harris RN, et al. Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling. PeerJ. 2019;2019:1–20.
Google Scholar
21.Longo AV, Zamudio KR. Temperature variation, bacterial diversity and fungal infection dynamics in the amphibian skin. Mol Ecol. 2017;26:4787–97.PubMed
Article
Google Scholar
22.Vredenburg VT, Bingham R, Knapp R, Morgan JAT, Moritz C, Wake D. Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog. J Zool. 2007;271:361–74.Article
Google Scholar
23.Vredenburg VT, McNally S, Sulaeman H, Butler HM, Yap T, Koo MS, et al. Pathogen invasion history elucidates contemporary host pathogen dynamics. PLoS ONE. 2019;14:1–14.Article
CAS
Google Scholar
24.Vredenburg VT, Knapp RA, Tunstall TS, Briggs CJ. Dynamics of an emerging disease drive large-scale amphibian population extinctions. Proc Natl Acad Sci USA. 2010;107:9689–94.CAS
PubMed
PubMed Central
Article
Google Scholar
25.Briggs CJ, Knapp RA, Vredenburg VT. Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians. Proc Natl Acad Sci USA. 2010;107:9695–700.CAS
PubMed
PubMed Central
Article
Google Scholar
26.Knapp RA, Fellers GM, Kleeman PM, Miller DA, Vredenburg VT, Rosenblum EB, et al. Large-scale recovery of an endangered amphibian despite ongoing exposure to multiple stressors. Proc Natl Acad Sci USA. 2016;113:11889–94.CAS
PubMed
PubMed Central
Article
Google Scholar
27.Jani AJ, Briggs CJ. The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection. Proc Natl Acad Sci USA. 2014;111:E5049–E5058.CAS
PubMed
PubMed Central
Article
Google Scholar
28.Ellison S, Knapp RA, Sparagon W, Swei A, Vredenburg VT. Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host. Mol Ecol. 2019;28:127–40.PubMed
Article
Google Scholar
29.Jani AJ, Briggs CJ. Host and aquatic environment shape the amphibian skin microbiome but effects on downstream resistance to the pathogen Batrachochytrium dendrobatidis are variable. Front Microbiol. 2018;9:1–17.Article
Google Scholar
30.Jani AJ, Knapp RA, Briggs CJ. Epidemic and endemic pathogen dynamics correspond to distinct host population microbiomes at a landscape scale. Proc R Soc B Biol Sci. 2017;284:20170944.31.Vredenburg VT. Reversing introduced species effects: experimental removal of introduced fish leads to rapid recovery of a declining frog. Proc Natl Acad Sci USA. 2004;101:7646–50.CAS
PubMed
PubMed Central
Article
Google Scholar
32.Joseph MB, Knapp RA. Disease and climate effects on individuals drive post-reintroduction population dynamics of an endangered amphibian. Ecosphere 2018;9:e02499.33.Boyle DG, Boyle DB, Olsen V, Morgan JAT, Hyatt AD. Rapid quantitative detection of chytridiomycosis (Batrachochytrium dendrobatidis) in amphibian samples using real-time Taqman PCR assay. Dis Aquat Organ. 2004;60:141–8.CAS
PubMed
Article
Google Scholar
34.Hyatt AD, Boyle DG, Olsen V, Boyle DB, Berger L, Obendorf D, et al. Diagnostic assays and sampling protocols for the detection of Batrachochytrium dendrobatidis. Dis Aquat Organ. 2007;73:175–92.CAS
PubMed
Article
Google Scholar
35.Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.CAS
PubMed
PubMed Central
Article
Google Scholar
36.Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS
PubMed
PubMed Central
Article
Google Scholar
37.Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.CAS
PubMed
PubMed Central
Article
Google Scholar
38.Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.PubMed
PubMed Central
Article
CAS
Google Scholar
39.McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.CAS
Article
Google Scholar
40.Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6:90.PubMed
PubMed Central
Article
Google Scholar
41.Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: machine learning in Python. J Mach Learn Res. 2011;12:2825–30.
Google Scholar
42.Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5:27.PubMed
PubMed Central
Article
Google Scholar
43.Faith DP. Conservation evaluation and phylogenetic diversity. Biol Conserv. 1992;61:1–10.Article
Google Scholar
44.Pielou EC. The measurement of diversity in different types of biological collections. J Theor Biol. 1966;13:131–44.Article
Google Scholar
45.Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228–35.CAS
PubMed
PubMed Central
Article
Google Scholar
46.Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007;73:1576–85.CAS
PubMed
PubMed Central
Article
Google Scholar
47.Chang Q, Luan Y, Sun F. Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinformatics. 2011;12:118.PubMed
PubMed Central
Article
Google Scholar
48.Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012;28:2106–13.CAS
PubMed
PubMed Central
Article
Google Scholar
49.McDonald D, Vázquez-Baeza Y, Koslicki D, McClelland J, Reeve N, Xu Z, et al. Striped UniFrac: enabling microbiome analysis at unprecedented scale. Nat Methods. 2018;15:847–48.CAS
PubMed
PubMed Central
Article
Google Scholar
50.Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Heal Dis. 2015;26:1–7.
Google Scholar
51.Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10:57–59.CAS
PubMed
Article
Google Scholar
52.Woodhams DC, Alford RA, Antwis RE, Archer H, Becker MH, Belden LK, et al. Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens. Ecology. 2015;96:595.Article
Google Scholar
53.Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.PubMed
PubMed Central
Article
Google Scholar
54.R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020.55.Lee G, You HJ, Bajaj JS, Joo SK, Yu J, Park S, et al. Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD. Nat Commun. 2020;11:1–13.
Google Scholar
56.Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017;550:61–66.CAS
PubMed
PubMed Central
Article
Google Scholar
57.Knapp RA, Briggs CJ, Smith TC, Maurer JR. Nowhere to hide: impact of a temperature-sensitive amphibian pathogen along an elevation gradient in the temperate zone. Ecosphere. 2011;2:art93.Article
Google Scholar
58.Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al. Topographical and temporal diversity of the human skin microbiome. Science. 2009;324:1190–2.CAS
PubMed
PubMed Central
Article
Google Scholar
59.Bates KA, Clare FC, O’Hanlon S, Bosch J, Brookes L, Hopkins K, et al. Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure. Nat Commun. 2018;9:1–11.CAS
Article
Google Scholar
60.Kinney VC, Heemeyer JL, Pessier AP, Lannoo MJ, Samples F. Seasonal pattern of Batrachochytrium dendrobatidis infection and mortality in Lithobates areolatus: affirmation of Vredenburg’ s “10, 000 Zoospore Rule”. PLoS ONE. 2011;6:e16708.CAS
PubMed
PubMed Central
Article
Google Scholar More