References
1. Lips K, Brem F, Brenes R, Reeve JD, Alford RA, Voyles J, et al.
Emerging infectious disease and the loss of biodiversity in a
Neotropical amphibian community. Proc Natl Acad Sci.
2006;103(9):3165–70.
2. Olson DH, Aanensen DM, Ronnenberg KL, Powell CI, Walker SF, Bielby J,
et al. Mapping the Global Emergence of Batrachochytrium
dendrobatidis , the Amphibian Chytrid Fungus. PLoS One.
2013;8(2):747–9.
3. Carvalho T, Becker CG, Toledo LF. Historical amphibian declines and
extinctions in Brazil linked to chytridiomycosis. Proc R Soc B Biol Sci.
2017;284(1848).
4. Scheele BC, Pasmans F, Skerratt LF, Berger L, Martel A, Beukema W, et
al. Amphibian fungal panzootic causes catastrophic and ongoing loss of
biodiversity. Science. 2019;363(6434):1459–63.
5. Muletz C, Caruso NM, Fleischer RC, McDiarmid RW, Lips KR. Unexpected
rarity of the pathogen Batrachochytrium dendrobatidis in
Appalachian Plethodon salamanders: 1957-2011. PLoS One.
2014;9(8):103728.
6. Harris RN, James TY, Lauer A, Simon MA, Patel A. Amphibian pathogenBatrachochytrium dendrobatidis is inhibited by the cutaneous
bacteria of amphibian species. Ecohealth. 2006;3(1):53–6.
7. Harris RN, Lauer A, Simon MA, Banning JL, Alford RA. Addition of
antifungal skin bacteria to salamanders ameliorates the effects of
chytridiomycosis. Dis Aquat Organ. 2009;83(1):11–6.
8. Muletz CR, Myers JM, Domangue RJ, Herrick JB, Harris RN. Soil
bioaugmentation with amphibian cutaneous bacteria protects amphibian
hosts from infection by Batrachochytrium dendrobatidis . Biol
Conserv. 2012;152:119–26.
9. Myers JM, Ramsey JP, Blackman AL, Nichols AE, Minbiole KPC, Harris
RN. Synergistic inhibition of the lethal fungal pathogenBatrachochytrium dendrobatidis : The combined effect of symbiotic
bacterial metabolites and antimicrobial peptides of the frog Rana
muscosa . J Chem Ecol. 2012;38(8):958–65.
10. Woodhams DC, Brandt H, Baumgartner S, Kielgast J, Küpfer E, Tobler
U, et al. Interacting symbionts and immunity in the amphibian skin
mucosome predict disease risk and probiotic effectiveness. PLoS One.
2014;9(4).
11. Bletz MC, Loudon AH, Becker MH, Bell SC, Woodhams DC, Minbiole KPC,
et al. Mitigating amphibian chytridiomycosis with bioaugmentation:
Characteristics of effective probiotics and strategies for their
selection and use. Ecol Lett. 2013;16(6):807–20.
12. Piovia-Scott J, Rejmanek D, Woodhams DC, Worth SJ, Kenny H, McKenzie
V, et al. Greater Species Richness of Bacterial Skin Symbionts Better
Suppresses the Amphibian Fungal Pathogen Batrachochytrium
dendrobatidis . Microb Ecol. 2017;74(1):217–26.
13. Voyles J, Woodhams DC, Saenz V, Byrne AQ, Perez R, Rios-Sotelo G, et
al. Shifts in disease dynamics in a tropical amphibian assemblage are
not due to pathogen attenuation. Science. 2018;359(6383):1517–9.
14. Kueneman JG, Woodhams DC, Van Treuren W, Archer HM, Knight R,
McKenzie VJ. Inhibitory bacteria reduce fungi on early life stages of
endangered Colorado boreal toads (Anaxyrus boreas ). ISME J.
2016;10(4):934–44.
15. Kearns PJ, Fischer S, Fernández-Beaskoetxea S, Gabor CR, Bosch J,
Bowen JL, et al. Fight fungi with fungi: Antifungal properties of the
amphibian mycobiome. Front Microbiol. 2017;8:1–12.
16. Kueneman JG, Weiss S, McKenzie VJ. Composition of micro-eukaryotes
on the skin of the cascades frog (Rana cascadae ) and patterns of
correlation between skin microbes and Batrachochytrium
dendrobatidis . Front Microbiol. 2017;8:1–10.
17. Belasen AM, Bletz MC, Leite D da S, Toledo LF, James TY. Long-Term
Habitat Fragmentation Is Associated With Reduced MHC IIB Diversity and
Increased Infections in Amphibian Hosts. Front Ecol Evol. 2019;6:1–12.
18. Gao F-K, Dai C-C, Liu X-Z. Mechanisms of fungal endophytes in plant
protection against pathogens. African J Microbiol Res.
2010;4(13):1346–51.
19. Newsham KK, Fitter AH, Watkinson AR. Arbuscular Mycorrhiza Protect
an Annual Grass from Root Pathogenic Fungi in the Field. J Ecol.
1995;83(6):991.
20. Gleason FH, Carney LT, Lilje O, Glockling SL. Ecological potentials
of species of Rozella (Cryptomycota). Fungal Ecol.
2012;5(6):651–6.
21. Hoffmann AR, Patterson AP, Diesel A, Lawhon SD, Ly HJ, Stephenson
CE, et al. The skin microbiome in healthy and allergic dogs. PLoS One.
2014;9(1).
22. Holler E, Butzhammer P, Schmid K, Hundsrucker C, Koestler J, Peter
K, et al. Metagenomic Analysis of the Stool Microbiome in Patients
Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is
Associated with Use of Systemic Antibiotics and More Pronounced in
Gastrointestinal Graft-versus-Host Disease. Biol Blood Marrow
Transplant. 2014;20(5):640–5.
23. Graham AL. Ecological rules governing helminth microparasite
coinfection. Proc Natl Acad Sci. 2008;105(2):566–70.
24. Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, et al.
Individuality in gut microbiota composition is a complex polygenic trait
shaped by multiple environmental and host genetic factors. Proc Natl
Acad Sci. 2010;107(44):18933–8.
25. Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, et al.
Host genetic variation impacts microbiome composition across human body
sites. Genome Biol. 2015;16(1).
26. Marietta E, Rishi A, Taneja V. Immunogenetic control of the
intestinal microbiota. Immunology. 2015;145(3):313–22.
27. Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie
VJ. The amphibian skin-associated microbiome across species, space and
life history stages. Mol Ecol. 2014;23(6):1238–50.
28. Walke JB, Becker MH, Loftus SC, House LL, Cormier G, Jensen R V, et
al. Amphibian skin may select for rare environmental microbes. ISME J.
2014;8(11):1–11.
29. Griffiths SM, Harrison XA, Weldon C, Wood MD, Pretorius A, Hopkins
K, et al. Genetic variability and ontogeny predict microbiome structure
in a disease-challenged montane amphibian. ISME J. 2018;1–12.
30. Barribeau SM, Villinger J, Waldman B. Ecological immunogenetics of
life-history traits in a model amphibian. Biol Lett. 2012;8(3):405–7.
31. Allentoft ME, O’Brien J. Global amphibian declines, loss of genetic
diversity and fitness: A review. Diversity. 2010;2(1):47–71.
32. Tilman D, May RM, Lehman CL, Nowak MA. Habitat destruction and the
extinction debt. Nature. 1994;371(6492):65–6.
33. Suguio K, Angulo RJ, Carvalho AM, Corrêa ICS, Tomazeli LJ, Willwock
JA, et al. Paleoníveis do mar e paleolinhas da costa. In: Quaternário do
Brasil. 2005. p. 378.
34. Bell RC, Brasileiro CA, Haddad CFB, Zamudio KR. Evolutionary history
of Scinax treefrogs on land-bridge islands in south-eastern
Brazil. J Biogeogr. 2012;39(9):1733–42.
35. Duryea MC, Zamudio KR, Brasileiro CA. Vicariance and marine
migration in continental island populations of a frog endemic to the
Atlantic Coastal forest. Heredity. 2015;115(3):225–34.
36. Duryea MC, Zamudio KR, Brasileiro CA. Characterization of
microsatellite markers for Thoropa taophora (Anura, Cycloramphidae), a
frog endemic to the Brazilian Atlantic Rain Forest. Mol Ecol Resour.
2008;8(3):663–5.
37. Hyatt AD, Boyle DG, Olsen V, Boyle DB, Berger L, Obendorf D, et al.
Diagnostic assays and sampling protocols for the detection ofBatrachochytrium dendrobatidis . Dis Aquat Organ.
2007;73(3):175–92.
38. Vences M, Lyra ML, Kueneman JG, Bletz MC, Archer HM, Canitz J, et
al. Gut bacterial communities across tadpole ecomorphs in two diverse
tropical anuran faunas. Sci Nat. 2016;103(3).
39. Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, et al.
Multiple marker parallel tag environmental DNA sequencing reveals a
highly complex eukaryotic community in marine anoxic water. Mol Ecol.
2010;19(SUPPL. 1):21–31.
40. 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(510).
41. 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(1):57–9.
42. Edgar RC. UCHIME2: improved chimera prediction for amplicon
sequencing. 2016;
43. 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(2):595–595.
44. Dray S, Dufour AB. The ade4 package: implementing the duality
diagram for ecologists. J Stat Softw. 2007;22(4):1–20.
45. Chessel D, Dufour AB, Thioulouse J. The ade4 package-I- One-table
methods. R News. 2004;4:5–10.
46. Dray S, Dufour AB, Chessel D. The ade4 package-II: Two-table and
K-table methods. R News. 2007;7(2):47–52.
47. R Core Team. R: A language and environment for statistical
computing. R Found Stat Comput Vienna, Austria. 2018;
48. Hunter JD. Matplotlib: A 2D Graphics Environment. Comput Sci Eng.
2007;9:90–5.
49. van Rossum G. Python Tutorial, Technical Report CS-R9526. 1995.
50. Petersen J. Die Theorie der regulären graphs. Acta Math.
1891;15(1):193–220.
51. Besag J, Clifford P. Generalized Monte Carlo significance tests.
Biometrika. 1989;76(4):633–42.
52. Fosdick BK, Larremore DB, Nishimura J, Ugander J. Configuring Random
Graph Models with Fixed Degree Sequences. SIAM Rev. 2018;60(2):315–55.
53. Hagberg AA, Schult DA. Exploring network structure, dynamics, and
function using NetworkX. In: Proceedings of the 7th Python in Science
Conference (SciPy2008). 2008. p. 11–5.
54. Federici E, Rossi R, Fidati L, Paracucchi R, Scargetta S, Montalbani
E, et al. Characterization of the Skin Microbiota in Italian Stream
Frogs (Rana italica ) infected and uninfected by a cutaneous
parasitic disease. Microbes Environ. 2015;30(3):262–9.
55. McKenzie VJ, Bowers RM, Fierer N, Knight R, Lauber CL. Co-habiting
amphibian species harbor unique skin bacterial communities in wild
populations. ISME J. 2012;6(3):588–96.
56. Abarca JG, Vargas G, Zuniga I, Whitfield SM, Woodhams DC, Kerby J,
et al. Assessment of bacterial communities associated with the skin of
Costa Rican amphibians at La Selva Biological Station. Front Microbiol.
2018;9:1–12.
57. Belden LK, Hughey MC, Rebollar EA, Umile TP, Loftus SC, Burzynski
EA, et al. Panamanian frog species host unique skin bacterial
communities. Front Microbiol. 2015;6:1–21.
58. Bletz MC, Archer H, Harris RN, McKenzie VJ, Rabemananjara FCE,
Rakotoarison A, et al. Host ecology rather than host phylogeny drives
amphibian skin microbial community structure in the biodiversity hotspot
of Madagascar. Front Microbiol. 2017;8:1–14.
59. Varela BJ, Lesbarrères D, Ibáñez R, Green DM. Environmental and host
effects on skin bacterial community composition in Panamanian frogs.
Front Microbiol. 2018;9:1–13.
60. Becker MH, Walke JB, Murrill L, Woodhams DC, Reinert LK,
Rollins-Smith LA, et al. Phylogenetic distribution of symbiotic bacteria
from Panamanian amphibians that inhibit growth of the lethal fungal
pathogen Batrachochytrium dendrobatidis . Mol Ecol.
2015;24(7):1628–41.
61. Brucker RM, Baylor CM, Walters RL, Lauer A, Harris RN, Minbiole KPC.
The identification of 2,4-diacetylphloroglucinol as an antifungal
metabolite produced by cutaneous bacteria of the salamanderPlethodon cinereus . J Chem Ecol. 2008;34(1):39–43.
62. Amend AS, Seifert KA, Bruns TD. Quantifying microbial communities
with 454 pyrosequencing: Does read abundance count? Mol Ecol.
2010;19(24):5555–65.
63. Hernández-Gómez O, Briggler JT, Williams RN. Influence of
immunogenetics, sex and body condition on the cutaneous microbial
communities of two giant salamanders. Mol Ecol. 2018;27(8):1915–29.
64. Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S,
et al. Bacterial-fungal interactions: Ecology, mechanisms and
challenges. FEMS Microbiol Rev. 2018;42(3):335–52.
65. Frey-Klett P, Garbaye J. Mycorrhiza helper bacteria: A promising
model for the genomic analysis of fungal-bacterial interactions. New
Phytol. 2005;168(1):4–8.
66. Walke JB, Belden LK. Harnessing the microbiome to prevent fungal
infections: Lessons from amphibians. PLoS Pathog. 2016;12(9):6–11.
67. Rowley JJL, Gleason FH, Andreou D, Marshall WL, Lilje O, Gozlan R.
Impacts of mesomycetozoean parasites on amphibian and freshwater fish
populations. Vol. 27, Fungal Biology Reviews. 2013. p. 100–11.
68. Badali H, Bonifaz A, Barrn-Tapia T, Vzquez-Gonzlez D,
Estrada-Aguilar L, Cavalcante Oliveira NM, et al. Rhinocladiella
aquaspersa, proven agent of verrucous skin infection and a novel type of
chromoblastomycosis. Med Mycol. 2010;48(5):696–703.
69. Seyedmousavi S, Guillot J, Tolooe A, Verweij PE. Neglected fungal
zoonoses: hidden threats to man and animals. Clin Microbiol Infect.
2015;21:416–25.
70. Gram L, Melchiorsen J, Spanggaard B, Huber I, Al GET, Icrobiol
APPLENM. AH2 , a possible probiotic treatment of fish.
1999;65(3):969–73.
71. Ghadban GS. Probiotics in broiler production - A review. Arch fur
Geflugelkd. 2002;66(2):49–58.
72. Cheng TL, Mayberry H, McGuire LP, Hoyt JR, Langwig KE, Nguyen H, et
al. Efficacy of a probiotic bacterium to treat bats affected by the
disease white-nose syndrome. J Appl Ecol. 2017;54(3):701–8.
73. Belasen AM, Riolo MA, Lyra ML, Toledo LF, James TY. 2020.Thoropa taophora genetic
and microbiome data. Dryad [identifier to be added upon article
acceptance].