Ley, R. et al. Evolution of mammals and their gut microbes. Science 320, 1647–1651 (2008).
Google Scholar
Robinson, C. J., Bohannan, B. J. M. & Young, V. B. From structure to function: The ecology of host-associated microbial communities. Microbiol. Mol. Biol. Rev. 74, 453–476 (2010).
Google Scholar
Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006).
Google Scholar
Pryor, G. & Bjorndal, K. Symbiotic fermentation, digesta passage, and gastrointestinal morphology in bullfrog tadpoles (Rana catesbeiana). Physiol. Biochem. Zool. 78, 201–215 (2005).
Google Scholar
Claus, S. P., Guillou, H. & Ellero-Simatos, S. The gut microbiota: A major player in the toxicity of environmental pollutants?. NPJ Biofilms Microbiomes 2, 16003 (2016).
Google Scholar
Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107–118 (2005).
Google Scholar
Alberdi, A., Aizpurua, O., Bohmann, K., Zepeda-Mendoza, M. L. & Gilbert, M. T. P. Do vertebrate gut metagenomes confer rapid ecological adaptation?. Trends Ecol. Evol. 31, 689–699 (2016).
Google Scholar
Bourguignon, T. et al. Rampant host switching shaped the termite gut microbiome. Curr. Biol. 28, 649-654.e2 (2018).
Google Scholar
Amato, K. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 1 (2018).
Sullam, K. E. et al. Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis. Mol. Ecol. 21, 3363–3378 (2012).
Google Scholar
Bolnick, D. I. et al. Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecol. Lett. 17, 979–987 (2014).
Google Scholar
Grond, K., Sandercock, B. K., Jumpponen, A. & Zeglin, L. H. The avian gut microbiota: Community, physiology and function in wild birds. J. Avian Biol. 49, e01788 (2018).
Google Scholar
Michel, A. et al. The gut of the finch: Uniqueness of the gut microbiome of the Galápagos vampire finch. Microbiome 6, 1–14 (2018).
Google Scholar
Delsuc, F. et al. Convergence of gut microbiomes in myrmecophagous mammals. Mol. Ecol. 23, 1301–1317 (2014).
Google Scholar
Carmody, R. N. et al. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 17, 72–84 (2015).
Google Scholar
Kohl, K., Amaya, J., Passement, C., Dearing, M. D. & Mccue, M. Unique and shared responses of the gut microbiota to prolonged fasting: A comparative study across five classes of vertebrate hosts. FEMS Microbiol. Ecol. 90, 883–894 (2014).
Google Scholar
Vences, M. et al. Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas. Sci. Nat. 103, 25 (2016).
Google Scholar
Li, G. et al. Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species. ISME J. 14, 1795–1808 (2020).
Google Scholar
Rawls, J., Mahowald, M., Ley, R. & Gordon, J. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127, 423–433 (2006).
Google Scholar
Bletz, M. C. et al. Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nat. Commun. 7, 13699 (2016).
Google Scholar
Woodhams, D. C. et al. Host-associated microbiomes are predicted by immune system complexity and climate. Genome Biol. 21, 23 (2020).
Google Scholar
Adlerberth, I. & Wold, A. E. Establishment of the gut microbiota in Western infants. Acta Paediatr. Int. J. Paediatr. 98, 229–238 (2009).
Google Scholar
Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).
Google Scholar
Stuart, S. N. et al. Status and trends of amphibian declines and extinctions worldwide. Science 306, 1783 (2004).
Google Scholar
Lips, K. R. et al. Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community. Proc. Natl. Acad. Sci. USA. 103, 3165 (2006).
Google Scholar
Bishop, P. et al. The amphibian extinction crisis -what will it take to put the action into the amphibian conservation action plan?. Surv. Perspect. Integr. Environ. Soc. 5, 97–111 (2012).
Kats, L. & Ferrer, R. Alien predators and amphibian declines: Review of two decades of science and the transition to conservation. Divers. Distrib. 9, 99–110 (2003).
Google Scholar
Chanson, J., Hoffman, M., Cox, N. & Stuart, S. The State of the World’s Amphibians. In Threatened Amphibians of the World 33–44 (Lynx Edicions, Barcelona, Spain, 2015)
Rollins-Smith, L. A. & Woodhams, D. C. Amphibian immunity: Staying in tune with the environment. In Ecoimmunology ( eds Demas, G. & Nelson, R.) 92–143 (Oxford University press, Oxford, UK, 2011).
Martel, A. et al. Recent introduction of a chytrid fungus endangers Western Palearctic salamanders. Science 346, 630 (2014).
Google Scholar
Birnie-Gauvin, K., Peiman, K. S., Raubenheimer, D. & Cooke, S. J. Nutritional physiology and ecology of wildlife in a changing world. Conserv. Physiol. 5, cox030 (2017).
Google Scholar
Scheele, B. C. et al. Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity. Science 363, 1459 (2019).
Google Scholar
Whiles, M. R. et al. The effects of amphibian population declines on the structure and function of Neotropical stream ecosystems. Front. Ecol. Environ. 4, 27–34 (2006).
Google Scholar
Hocking, D. & Babbitt, K. Amphibian contributions to ecosystem services. Herpetol. Conserv. Biol. 9, 1–17 (2014).
Burton, T. M. & Likens, G. E. Energy flow and nutrient cycling in salamander populations in the Hubbard Brook experimental forest, New Hampshire. Ecology 56, 1068–1080 (1975).
Google Scholar
Reagan, D. P. & Waide, R. B. The Food Web of a Tropical Rain Forest (University of Chicago Press, 1996).
Stebbins, R. C. & Cohen, N. W. A Natural History of Amphibians (Princeton University Press, 1997).
Flecker, A. S., Feifarek, B. P. & Taylor, B. W. Ecosystem engineering by a tropical tadpole: Density-dependent effects on habitat structure and larval growth rates. Copeia 1999, 495–500 (1999).
Google Scholar
Beard, K., Vogt, K. & Kulmatiski, A. Top-down effects of a terrestrial frog on nutrient dynamics. Oecologia 133, 583–593 (2002).
Google Scholar
Davic, R. & Welsh, H. On the ecological role of salamanders. Annu. Rev. Ecol. Syst. 12, 405–434 (2004).
Google Scholar
Reinhardt, T., Steinfartz, S., Paetzold, A. & Weitere, M. Linking the evolution of habitat choice to ecosystem functioning: Direct and indirect effects of pond-reproducing fire salamanders on aquatic-terrestrial subsidies. Oecologia 173, 281–291 (2013).
Google Scholar
Buckley, D. & Alcobendas, M. Salamandra salamandra (Linnaeus, 1758). (2002).
Fryxell, J. & Lundberg, P. Diet choice and predator—prey dynamics. Evol. Ecol. 8, 407–421 (1994).
Google Scholar
Deagle, B. E. et al. Studying seabird diet through genetic analysis of faeces: A case study on macaroni penguins (Eudyptes chrysolophus). PLoS ONE 2, e831 (2007).
Google Scholar
Botzler, R. G., Wetzler, T. F. & Cowan, A. B. Yersinia enterocolitica and yersinia-like organisms isolated from frogs and snails. Bull. Wildl. Dis. Assoc. 4, 110–115 (1968).
Google Scholar
Cooper, J. E., Needham, J. R. & Griffin, J. A bacterial disease of the Darwin’s frog (Rhinoderma darwini). Lab. Anim. 12, 91–93 (1978).
Google Scholar
Hird, D. et al. Enterobacteriacae and Aeromonas hydrophila in Minnesota frogs and tadpoles (Rana papiens). Appl. Environ. Microbiol. 46, 1423–1425 (1984).
Google Scholar
Olson, M., Gard, S., Brown, M., Hampton, R. & Morck, D. Flavobacterium indologenes infection in leopard frogs. J. Am. Vet. Med. Assoc. 201, 1766–1770 (1992).
Google Scholar
Pearson, M. D. Motile Aeromonas septicaemia of farmed Rana spp. (1998).
Green, S. et al. Identification and management of an outbreak of Flavobacterium meningosepticum infection in a colony of South African clawed frogs (Xenopus laevis). J. Am. Vet. Med. Assoc. 214(1833–8), 1792–1793 (1999).
Bernardet, J.-F. et al. Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals. Syst. Appl. Microbiol. 28, 640–660 (2005).
Google Scholar
Pasteris, S., Guidoli, M., Otero, M., Bühler, M. & Nader-Macías, M. In vitro inhibition of Citrobacter freundii, a red-leg syndrome associated pathogen in raniculture, by indigenous Lactococcus lactis CRL 1584. Vet. Microbiol. 151, 336–344 (2011).
Google Scholar
Kirk, K. et al. Chryseobacterium angstadtii sp. nov., isolated from a newt tank. Int. J. Syst. Evol. Microbiol. 63, 4777–4783 (2013).
Google Scholar
Suzina, N. E. et al. Cytophysiological characteristics of the vegetative and dormant cells of Stenotrophomonas sp. strain FM3, a bacterium isolated from the skin of a Xenopus laevis frog. Microbiology 87, 339–349 (2018).
Google Scholar
Hallinger, M., Taubert, A. & Hermosilla, C. Endoparasites infecting exotic captive amphibian pet and zoo animals (Anura, Caudata) in Germany. Parasitol. Res. 119, 3659–3673 (2020).
Google Scholar
Deagle, B. E., Chiaradia, A., McInnes, J. & Jarman, S. N. Pyrosequencing faecal DNA to determine diet of little penguins: Is what goes in what comes out?. Conserv. Genet. 11, 2039–2048 (2010).
Google Scholar
Deagle, B. E., Thomas, A. C., Shaffer, A. K., Trites, A. W. & Jarman, S. N. Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: Which counts count?. Mol. Ecol. Resour. 13, 620–633 (2013).
Google Scholar
Nakahara, F. et al. The applicability of DNA barcoding for dietary analysis of sika deer. DNA Barcodes 3, 200–206 (2015).
Google Scholar
Deagle, B., Kirkwood, R. & Jarman, S. Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Mol. Ecol. 18, 2022–2038 (2009).
Google Scholar
Pompanon, F. et al. Who is eating what: Diet assessment using next generation sequencing. Mol. Ecol. 21, 1931–1950 (2012).
Google Scholar
Thomas, A. C., Jarman, S. N., Haman, K. H., Trites, A. W. & Deagle, B. E. Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias. Mol. Ecol. 23, 3706–3718 (2014).
Google Scholar
Deagle, B. & Tollit, D. Quantitative analysis of prey DNA in pinniped faeces: Potential to estimate diet composition?. Conserv. Genet. 8, 743–747 (2007).
Google Scholar
Ando, H. et al. Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding. Environ. DNA 2, 391–406 (2020).
Google Scholar
Deagle, B. et al. Molecular scatology as a tool to study diet: Analysis of prey DNA in scats from captive Steller sea lions. Mol. Ecol. 14, 1831–1842 (2005).
Google Scholar
Parsons, K., Piertney, S., Middlemas, S., Hammond, P. & Armstrong, J. DNA-based identification of salmonid prey species in seal faeces. J. Zool. 266, 275–281 (2005).
Google Scholar
Meekan, M., Jarman, S., McLean, C. & Schultz, M. DNA evidence of whale sharks (Rhincodon typus) feeding on red crab (Gecarcoidea natalis) larvae at Christmas Island, Australia. Mar. Freshw. Res. 60, 607–609 (2009).
Google Scholar
Guillerault, N., Bouletreau, S., Iribar, A., Valentini, A. & Santoul, F. Application of DNA metabarcoding on faeces to identify European catfish Silurus glanis diet. J. Fish Biol. 90, 2214–2219 (2017).
Google Scholar
Brown, D. S., Jarman, S. N. & Symondson, W. O. C. Pyrosequencing of prey DNA in reptile faeces: Analysis of earthworm consumption by slow worms. Mol. Ecol. Resour. 12, 259–266 (2012).
Google Scholar
Ferenti, S., Cicort-Lucaciu, A. S., Dobre, F., Paina, C. & Covaci, R. The food of four Salamandra salamandra populations from Defileul Jiului National Park (Gorj County). Olten. Stud. Si Comun. Stiintele Nat. 2008, 153–160 (2008).
Ferenti, S., David, A. & Nagy, D. Feeding-behaviour responses to anthropogenic factors on Salamandra salamandra (Amphibia, Caudata). Biharean Biol. 4, 139–143 (2010).
Lezău, O. et al. The feeding of two Salamandra salamandra (Linnaeus, 1758) populations from Jiului Gorge National Park (Romania), South West. J. Hortic. Biol. Environ. 1, 143–152 (2010).
Balogová, M., Maxinová, E., Orendáš, P. & Uhrin, M. Trophic spectrum of adult Salamandra salamandra in the Carpathians with the first note on food intake by the species during winter. Herpetol. Notes 8, 371–377 (2015).
Sebastiano, S., Antonio, R., Fabrizio, O., Dario, O. & Roberta, M. Different season, different strategies: Feeding ecology of two syntopic forest-dwelling salamanders. Acta Oecologica 43, 42–50 (2012).
Google Scholar
Lunghi, E. et al. Field-recorded data on the diet of six species of European Hydromantes cave salamanders. Sci. Data 5, 1–7 (2018).
Google Scholar
Lunghi, E. et al. What shapes the trophic niche of European plethodontid salamanders?. PLoS ONE 13, e0205672 (2018).
Google Scholar
Measey, G. Diet of feral Xenopus laevis (Daudin) in South Wales, UK. J. Zool. 246, 287–298 (1998).
Google Scholar
Le, D. T. T., Rowley, J. J., Tran, D. T. A. & Hoang, H. D. The diet of a forest-dependent frog species, Odorrana morafkai (Anura: Ranidae), in relation to habitat disturbance. Amphib. Reptil. 41, 29–41 (2020).
Google Scholar
Pamintuan, P. E. & Starr, C. K. Diet of the giant toad, Bufo marinus (Amphibia: Salientia), in a coastal habitat of the Philippines. Trop. AgricTrinidad 93, 323–327 (2016).
Plummer, M. & Farrar, D. Sexual dietary differences in a population of Trionyx muticus. J. Herpetol. 15, 175–179 (1981).
Google Scholar
Shetty, S. & Shine, R. Activity patterns of yellow-lipped sea Kraits (Laticauda colubrina) on a Fijian island. Copeia 2002, 77–85 (2002).
Google Scholar
Vincent, S., Herrel, A. & Irschick, D. Sexual dimorphism in head shape and diet in the Cottonmouth Snake (Agkistrodon piscivorus). J. Zool. 264, 53–59 (2004).
Google Scholar
Manenti, R., Conti, A. & Pennati, R. Fire salamander (Salamandra salamandra) males’ activity during breeding season: Effects of microhabitat features and body size. Acta Herpetol. 12, 29–36 (2017).
Keen, W. H. Feeding and activity patterns in the salamander Desmognathus ochrophaeus (Amphibia, Urodela, Plethodontidae). J. Herpetol. 13, 461–467 (1979).
Google Scholar
Forester, D. C. Parental care in the salamander Desmognathus ochrophaeus: Female activity pattern and trophic behavior. J. Herpetol. 15, 29–34 (1981).
Google Scholar
Harris, W. E. Spermatophore deposition behaviour in an explosive breeder, the Small mouthed salamander, Ambystom texanum. Herpetologica 64, 149–155 (2008).
Google Scholar
Anderson, T. & Mathis, A. Diets of two sympatric neotropical salamanders, bolitoglossa mexicana and B. rufescens, with notes on reproduction for B. rufescens. J. Herpetol. 33, 601 (1999).
Google Scholar
Shu, Y. et al. Comparison of intestinal microbes in female and male Chinese concave-eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities. MicrobiologyOpen 8, e00749 (2019).
Google Scholar
Zhou, J. et al. A comparison of nonlethal sampling methods for amphibian gut microbiome analyses. Mol. Ecol. Resour. 20, 844–855 (2020).
Google Scholar
Huang, C. & Liao, W. Seasonal variation in gut microbiota related to diet in Fejervarya limnocharis. Animals 11, 1393 (2021).
Google Scholar
Chang, C.-W., Huang, B.-H., Lin, S.-M., Huang, C.-L. & Liao, P.-C. Changes of diet and dominant intestinal microbes in farmland frogs. BMC Microbiol. 16, 33 (2016).
Google Scholar
Kohl, K. D., Cary, T. L., Karasov, W. H. & Dearing, M. D. Restructuring of the amphibian gut microbiota through metamorphosis. Environ. Microbiol. Rep. 5, 899–903 (2013).
Google Scholar
Colombo, B. M., Scalvenzi, T., Benlamara, S. & Pollet, N. Microbiota and mucosal immunity in amphibians. Front. Immunol. 6, 111–111 (2015).
Google Scholar
Novoslavskij, A. et al. Major foodborne pathogens in fish and fish products: a review. Ann. Microbiol. 66, 1–15 (2015).
Google Scholar
Standish, I. et al. Yersinia ruckeri isolated from common mudpuppy necturus maculosus. J. Aquat. Anim. Health 31, 71–74 (2019).
Google Scholar
Hird, D. W. et al. Enterobacteriaceae and Aeromonas hydrophila in Minnesota frogs and tadpoles (Rana pipiens). Appl. Environ. Microbiol. 46, 1423–1425 (1983).
Google Scholar
Heiman, M. L. & Greenway, F. L. A healthy gastrointestinal microbiome is dependent on dietary diversity. Mol. Metab. 5, 317–320 (2016).
Google Scholar
Amato, K. & Righini, N. The howler monkey as a model for exploring host-gut microbiota interactions in primates.https://doi.org/10.1007/978-1-4939-1957-4_9 (2015).
Kartzinel, T. R., Hsing, J. C., Musili, P. M., Brown, B. R. P. & Pringle, R. M. Covariation of diet and gut microbiome in African megafauna. Proc. Natl. Acad. Sci. 116, 23588 (2019).
Google Scholar
Tiede, J., Scherber, C., Mutschler, J., McMahon, K. D. & Gratton, C. Gut microbiomes of mobile predators vary with landscape context and species identity. Ecol. Evol. 7, 8545–8557 (2017).
Google Scholar
Peig, J. & Green, A. J. New perspectives for estimating body condition from mass/length data: The scaled mass index as an alternative method. Oikos 118, 1883–1891 (2009).
Google Scholar
Vences, M. et al. Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene. Conserv. Genet. Resour. 8, 323–327 (2016).
Google Scholar
Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W. & Huse, S. M. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE 4, e6372 (2009).
Google Scholar
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Google Scholar
Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2, e00191-16 (2017).
Google Scholar
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).
Google Scholar
Aguirre, A. A. et al. The One Health Approach to toxoplasmosis: Epidemiology, control, and prevention strategies. EcoHealth 16, 378–390 (2019).
Google Scholar
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
Google Scholar
Vavrek, M. J. Fossil: Palaeoecological and palaeogeographical analysis tools. Palaeontol. Electron. 14, 16 (2011).
McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Google Scholar
Jaccard, P. The distribution of the flora of the Alpine zone. New Phytol. 11, 37–50 (1912).
Google Scholar
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-5. 2019 (2020).
Dray, S. & Dufour, A.-B. The ade4 package: Implementing the duality diagram for ecologists. J. Stat. Softw. 22, 1–20 (2007).
Google Scholar
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