The structural discrepancy between the small and large gut microbiota of Asiatic toad (Bufo gargarizans) during hibernation

Banas JA, Loesche WJ, Nace GW (1988) Classification and distribution of large intestinal bacteria in nonhibernating and hibernating leopard frogs (Rana pipiens). Appl Environ Microbiol 54:2305–2310. https://doi.org/10.1128/aem.54.9.2305-2310.1988

Article  CAS  Google Scholar 

Bharti R, Grimm DG (2019) Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 22:178–193. https://doi.org/10.1093/bib/bbz155

Article  CAS  Google Scholar 

Bletz MC, Goedbloed DJ, Sanchez E et al (2016) Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nat Commun 7:13699. https://doi.org/10.1038/ncomms13699

Article  CAS  Google Scholar 

Bolyen E, Rideout JR, Dillon MR et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. https://doi.org/10.1038/s41587-019-0209-9

Article  CAS  Google Scholar 

Boutilier RG (2001) Mechanisms of metabolic defense against hypoxia in hibernating frogs. Respir Physiol 128:365–377. https://doi.org/10.1016/S0034-5687(01)00312-7

Article  CAS  Google Scholar 

Chai L, Dong Z, Chen A, Wang H (2018) Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis. Arch Microbiol 200:1087–1099. https://doi.org/10.1007/s00203-018-1523-1

Article  CAS  Google Scholar 

Che J, Wang K (2016) AmphibiaChina: an online database of Chinese Amphibians. Zool Res 37:57–59. https://doi.org/10.13918/j.issn.2095-8137.2016.1.57

Costanzo JP, do Amaral MCF, Rosendale AJ, Lee RE (2014) Seasonality of freeze tolerance in a subarctic population of the wood frog, Rana sylvatica. Intern J Zool 750153. https://doi.org/10.1155/2014/750153

Ding J, Dai R, Yang L et al (2017) Inheritance and establishment of gut microbiota in chickens. Front Microbiol 8. https://doi.org/10.3389/fmicb.2017.01967

Donaldson GP, Lee SM, Mazmanian SK (2016) Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 14:20–32. https://doi.org/10.1038/nrmicro3552

Article  CAS  Google Scholar 

Geiser F (2013) Hibernation. Curr Biol 23:R188–R193. https://doi.org/10.1016/j.cub.2013.01.062

Article  CAS  Google Scholar 

Guo X, Chen F, Gao F et al (2020) CNSA: a data repository for archiving omics data. Database 2020. https://doi.org/10.1093/database/baaa055

Jiang H-Y, Ma J-E, Li J et al (2017) Diets alter the gut microbiome of crocodile lizards. Front Microbiol 8. https://doi.org/10.3389/fmicb.2017.02073

Kim D, Hofstaedter CE, Zhao C et al (2017) Optimizing methods and dodging pitfalls in microbiome research. Microbiome 5:52. https://doi.org/10.1186/s40168-017-0267-5

Article  Google Scholar 

Kim KK, Lee J-S, Stevens DA (2013) Microbiology and epidemiology of Halomonas species. Future Microbiol 8:1559–1573. https://doi.org/10.2217/fmb.13.108

Article  CAS  Google Scholar 

Knight R, Vrbanac A, Taylor BC et al (2018) Best practices for analysing microbiomes. Nat Rev Microbiol 16:410–422. https://doi.org/10.1038/s41579-018-0029-9

Article  CAS  Google Scholar 

Knutie SA, Wilkinson CL, Kohl KD, Rohr JR (2017) Early-life disruption of amphibian microbiota decreases later-life resistance to parasites. Nat Commun 8:86. https://doi.org/10.1038/s41467-017-00119-0

Article  CAS  Google Scholar 

Kohl KD, Cary TL, Karasov WH, Dearing MD (2013) Restructuring of the amphibian gut microbiota through metamorphosis. Environ Microbiol Rep 5:899–903. https://doi.org/10.1111/1758-2229.12092

Article  Google Scholar 

Kohl KD, Cary TL, Karasov WH, Dearing MD (2015) Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota. Environ Toxicol Chem 34:1113–1118. https://doi.org/10.1002/etc.2905

Article  CAS  Google Scholar 

Li J, Rui J, Li Y et al (2020) Ambient temperature alters body size and gut microbiota of Xenopus tropicalis. Sci China Life Sci 63:915–925. https://doi.org/10.1007/s11427-019-9540-y

Article  Google Scholar 

Liu C, Cui Y, Li X, Yao M (2020) microeco: an R package for data mining in microbial community ecology. FEMS Microbiol Ecol 97. https://doi.org/10.1093/femsec/fiaa255

Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. https://doi.org/10.1093/bioinformatics/btr507

Article  CAS  Google Scholar 

Martinez-Guryn K, Leone V, Chang EB (2019) Regional diversity of the gastrointestinal microbiome. Cell Host Microbe 26:314–324. https://doi.org/10.1016/j.chom.2019.08.011

Article  CAS  Google Scholar 

Milsom WK, Jackson DC (2011) Hibernation and gas exchange. In Comprehensive Physiology pp. 397–420

Naya DE, Veloso C, Sabat P, Bozinovic F (2009) The effect of short- and long-term fasting on digestive and metabolic flexibility in the Andean toad, Bufo spinulosus. J Exp Biol 212:2167–2175. https://doi.org/10.1242/jeb.030650

Article  CAS  Google Scholar 

Ning D, Yuan M, Wu L et al (2020) A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nat Commun 11:4717. https://doi.org/10.1038/s41467-020-18560-z

Article  CAS  Google Scholar 

Oksanen J, Blanchet FG, Friendly M et al (2020) Vegan: Community Ecology Package. R package version 2.5–7

Pruesse E, Peplies J, Glöckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829. https://doi.org/10.1093/bioinformatics/bts252

Article  CAS  Google Scholar 

Regan MD, Chiang E, Liu Y et al (2022) Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season. Science 375:460–463. https://doi.org/10.1126/science.abh2950

Article  CAS  Google Scholar 

Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. Peer J 4:e2584. https://doi.org/10.7717/peerj.2584

Salter SJ, Cox MJ, Turek EM et al (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87. https://doi.org/10.1186/s12915-014-0087-z

Article  CAS  Google Scholar 

Schroeder BO (2019) Fight them or feed them: how the intestinal mucus layer manages the gut microbiota. Gastroenterol Rep (oxf) 7:3–12. https://doi.org/10.1093/gastro/goy052

Article  Google Scholar 

Schwartz C, Andrews MT (2013) Chapter nine - circannual transitions in gene expression: lessons from seasonal adaptations. In Curr Top Dev Biol (Rougvie AE, O'Connor MB eds.), pp 247–273. Academic Press

Segata N, Izard J, Waldron L et al (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. https://doi.org/10.1186/gb-2011-12-6-r60

Article  Google Scholar 

Shi Q, Zhu Y, Wang J, Yang H, Wang J, Zhu W (2019) Protein restriction and succedent realimentation affecting ileal morphology, ileal microbial composition and metabolites in weaned piglets. Animal 13:2463–2472. https://doi.org/10.1017/S1751731119000776

Article  CAS  Google Scholar 

Sommer F, Ståhlman M, Ilkayeva O et al (2016) The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos. Cell Rep 14:1655–1661. https://doi.org/10.1016/j.celrep.2016.01.026

Article  CAS  Google Scholar 

Song X, Song J, Song H, Zeng Q, Shi K (2018) A robust noninvasive approach to study gut microbiota structure of amphibian tadpoles by feces. Asian Herpetol Res 9:1–12. https://doi.org/10.16373/j.cnki.ahr.170062

Song X, Zhang J, Song J, Zhai Y (2021) Decisive effects of life stage on the gut microbiota discrepancy between two wild populations of hibernating Asiatic toads (Bufo gargarizans). Front Microbiol 12. https://doi.org/10.3389/fmicb.2021.665849

Stegen JC, Lin X, Fredrickson JK et al (2013) Quantifying community assembly processes and identifying features that impose them. ISME J 7:2069–2079. https://doi.org/10.1038/ismej.2013.93

Article  Google Scholar 

Team RC (2020) R: a language and environment for statistical computing

Tong Q, Cui L-Y, Hu Z-F, Du X-P, Abid HM, Wang H-B (2020a) Environmental and host factors shaping the gut microbiota diversity of brown frog Rana dybowskii. Sci Total Environ 741:140142. https://doi.org/10.1016/j.scitotenv.2020a.140142

Tong Q, Hu Z-F, Du X-P, Bie J, Wang H-B (2020b) Effects of seasonal hibernation on the similarities between the skin microbiota and gut microbiota of an amphibian (Rana dybowskii). Microb Ecol 79:898–909. https://doi.org/10.1007/s00248-019-01466-9

Article  Google Scholar 

Tong Q, Liu X-N, Hu Z-F et al (2019) Effects of captivity and season on the gut microbiota of the brown frog (Rana dybowskii). Front Microbiol 10. https://doi.org/10.3389/fmicb.2019.01912

Wagener C, du Plessis M, Measey J (2021) Invasive amphibian gut microbiota and functions shift differentially in an expanding population but remain conserved across established populations. Microb Ecol. https://doi.org/10.1007/s00248-021-01896-4

Article  Google Scholar 

Wagner Mackenzie B, Waite DW, Taylor MW (2015) Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences. Front Microbiol 6. https://doi.org/10.3389/fmicb.2015.00130

Wan X-L, McLaughlin RW, Zheng J-S et al (2018) Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri). Sci Rep 8:14142. https://doi.org/10.1038/s41598-018-32512-0

Article  CAS  Google Scholar 

Wang Y, LêCao K-A (2019) Managing batch effects in microbiome data. Brief Bioinform 21:1954–1970. https://doi.org/10.1093/bib/bbz105

Article  Google Scholar 

Warne RW, Kirschman L, Zeglin L (2019) Manipulation of gut microbiota during critical developmental windows affects host physiological performance and disease susceptibility across ontogeny. J Anim Ecol 88:845–856. https://doi.org/10.1111/1365-2656.12973

Article  Google Scholar 

Weng FC-H, Yang Y-J, Wang D (2016) Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. BMC Genomics 17:1024. https://doi.org/10.1186/s12864-016-3318-6

Article  CAS  Google Scholar 

Wesolowska-Andersen A, Bahl MI, Carvalho V et al (2014) Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome 2:19. https://doi.org/10.1186/2049-2618-2-19

Article  Google Scholar 

Wiebler JM, Kohl KD, Lee RE, Costanzo JP (2018) Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia. Proc R Soc B Biol Sci 285:20180241. https://doi.org/10.1098/rspb.2018.0241

Article  CAS  Google Scholar 

Xu LL, Chen H, Zhang M et al (2020) Changes in the community structure of the symbiotic microbes of wild amphibians from the eastern edge of the Tibetan Plateau. MicrobiologyOpen 9:e1004. https://doi.org/10.1002/mbo3.1004

Yang P, Hu H, Li Y et al (2019) Effect of dietary xylan on immune response, tight junction protein expression and bacterial community in the intestine of juvenile turbot (Scophthalmus maximus L.). Aquaculture 512:734361. https://doi.org/10.1016/j.aquaculture.2019.734361

Zhang M, Gaughan S, Chang Q et al (2018) Age-related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus). MicrobiologyOpen 0:e778. https://doi.org/10.1002/mbo3.778

Zhou J, Nelson TM, Rodriguez Lopez C, Sarma RR, Zhou SJ, Rollins LA (2020) A comparison of nonlethal sampling methods for amphibian gut microbiome analyses. Mol Ecol Resour 20:844–855. https://doi.org/10.1111/1755-0998.13139

Article  CAS  Google Scholar 

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