Carthey AJR, Blumstein DT, Gallagher RV, Tetu SG, Gillings MR. Conserving the holobiont. Funct Ecol. 2020;34:764–76.
Google Scholar
Mason GJ. Species differences in responses to captivity: stress, welfare and the comparative method. Trends Ecol Evol. 2010;25:713–21.
PubMed
Google Scholar
Morgan KN, Tromborg CT. Sources of stress in captivity. Appl Anim Behav Sci. 2007;102:262–302.
Google Scholar
Gore MA, Brandes F, Kaup F-J, Lenzner R, Mothes T, Osman AA. Callitrichid nutrition and food sensitivity. J Med Primatol. 2001;30:179–84.
CAS
PubMed
Google Scholar
Amato KR, Metcalf JL, Song SJ, Hale VL, Clayton J, Ackermann G, et al. Using the gut microbiota as a novel tool for examining colobine primate GI health. Glob Ecol Conserv. 2016;7:225–37.
Google Scholar
Ushida K, Segawa T, Tsuchida S, Murata K. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans. J Vet Med Sci. 2016;78:251–7.
CAS
PubMed
Google Scholar
Roth TL, Switzer A, Watanabe-Chailland M, Bik EM, Relman DA, Romick-Rosendale LE, et al. Reduced gut microbiome diversity and metabolome differences in rhinoceros species at risk for iron overload disorder. Front Microbiol. 2019;10:2291.
PubMed
PubMed Central
Google Scholar
Seibert LM. Feather-picking disorder in pet birds. In: Luescher AU, editor. Manual of parrot behavior. Wiley; 2006. p. 255–65.
Google Scholar
Yan D, Hu D, Li K, Li B, Zeng X, Chen J, et al. Effects of chronic stress on the fecal microbiome of malayan pangolins (Manis javanica) rescued from the illegal wildlife trade. Curr Microbiol. 2021;78:1017–25.
CAS
PubMed
Google Scholar
Tubbs CW, Moley LA, Ivy JA, Metrione LC, LaClaire S, Felton RG, et al. Estrogenicity of captive southern white rhinoceros diets and their association with fertility. Gen Comp Endocrinol. 2016;238:32–8.
CAS
PubMed
Google Scholar
Petter JJ. Breeding of malagasy lemurs in captivity. In: Martin RD, editor. Breeding endangered species in captivity. Academic Press; 1975. p. 187–202.
Google Scholar
Bahrndorff S, Alemu T, Alemneh T, Lund NJ. The microbiome of animals: implications for conservation biology. Int J Genomics. 2016;2016:5304028.
PubMed
PubMed Central
Google Scholar
Price EE, Stoinski TS. Group size: determinants in the wild and implications for the captive housing of wild mammals in zoos. Appl Anim Behav Sci. 2007;103:255–64.
Google Scholar
Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, et al. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015;17:72–84.
CAS
PubMed
Google Scholar
Scepanovic P, Hodel F, Mondot S, Partula V, Byrd A, Hammer C, et al. A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals. Microbiome. 2019;7:130.
PubMed
PubMed Central
Google Scholar
Diaz Heijtz R, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA. 2011;108:3047–52.
PubMed
Google Scholar
Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9:313–23.
CAS
PubMed
PubMed Central
Google Scholar
Tremaroli V, Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489:242–9.
CAS
PubMed
Google Scholar
Kohl KD, Skopec MM, Dearing MD. Captivity results in disparate loss of gut microbial diversity in closely related hosts. Conserv Physiol. 2014;2:cou009.
PubMed
PubMed Central
Google Scholar
Greene LK, Bornbusch SL, McKenney EA, Harris RL, Gorvetzian SR, Yoder AD, et al. The importance of scale in comparative microbiome research: new insights from the gut and glands of captive and wild lemurs. Am J Primatol. 2019;81:e22974.
PubMed
Google Scholar
Reese AT, Chadaideh KS, Diggins CE, Schell LD, Beckel M, Callahan P, et al. Effects of domestication on the gut microbiota parallel those of human industrialization. Elife. 2021;10:e60197.
CAS
PubMed
PubMed Central
Google Scholar
Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, et al. Evaluating the impact of domestication and captivity on the horse gut microbiome. Sci Rep. 2017;7:15497.
PubMed
PubMed Central
Google Scholar
Munson L. Diseases of captive cheetahs (Acinonyx jubatus): results of the cheetah research council pathology survey, 1989–1992. Zoo Biol. 1993;12:105–24.
Google Scholar
Terio KA, Munson L, Moore PF. Characterization of the gastric immune response in cheetahs (Acinonyx jubatus) with helicobacter-associated gastritis. Vet Pathol. 2012;49:824–33.
CAS
PubMed
Google Scholar
Cabana F, Maguire R, Hsu C-D, Plowman A. Identification of possible nutritional and stress risk factors in the development of marmoset wasting syndrome. Zoo Biol. 2018;37:98–106.
PubMed
Google Scholar
McKenney EA, Greene LK, Drea CM, Yoder AD. Down for the count: cryptosporidium infection depletes the gut microbiome in Coquerel’s sifakas. Microb Ecol Health Dis. 2017;28:1335165.
PubMed
PubMed Central
Google Scholar
West AG, Waite DW, Deines P, Bourne DG, Digby A, McKenzie VJ, et al. The microbiome in threatened species conservation. Biol Conserv. 2019;229:85–98.
Google Scholar
Trevelline BK, Fontaine SS, Hartup BK, Kohl KD. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc R Soc B Biol Sci. 2019;286:20182448.
Google Scholar
Fisher M. Defining animal welfare—does consistency matter? N Z Vet J. 2009;57:71–3.
CAS
PubMed
Google Scholar
Eisenstein M. The hunt for a healthy microbiome. Nature. 2020;577:S6-8.
CAS
PubMed
Google Scholar
Bragg M, Freeman EW, Lim HC, Songsasen N, Muletz-Wolz CR. Gut microbiomes differ among dietary types and stool consistency in the captive red wolf (Canis rufus). Front Microbiol. 2020;11:590212.
PubMed
PubMed Central
Google Scholar
Williams CL, Ybarra AR, Meredith AN, Durrant BS, Tubbs CW. Gut microbiota and phytoestrogen-associated infertility in southern white rhinoceros. MBio. 2019;10:e00311-e319.
CAS
PubMed
PubMed Central
Google Scholar
Becker MH, Richards-Zawacki CL, Gratwicke B, Belden LK. The effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki). Biol Conserv. 2014;176:199–206.
Google Scholar
Bates KA, Shelton JMG, Mercier VL, Hopkins KP, Harrison XA, Petrovan SO, et al. Captivity and infection by the fungal pathogen batrachochytrium salamandrivorans perturb the amphibian skin microbiome. Front Microbiol. 2019;10:1834.
PubMed
PubMed Central
Google Scholar
Eisenhofer R, Helgen KM, Taggart D. Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons). Anim Microbiome. 2021;3:4.
PubMed
PubMed Central
Google Scholar
Wienemann T, Schmitt-Wagner D, Meuser K, Segelbacher G, Schink B, Brune A, et al. The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds. Syst Appl Microbiol. 2011;34:542–51.
PubMed
Google Scholar
Oliveira BCM, Murray M, Tseng F, Widmer G. The fecal microbiota of wild and captive raptors. Anim Microbiome. 2020;2:15.
PubMed
PubMed Central
Google Scholar
Gibson KM, Nguyen BN, Neumann LM, Miller M, Buss P, Daniels S, et al. Gut microbiome differences between wild and captive black rhinoceros—implications for rhino health. Sci Rep. 2019;9:7570.
PubMed
PubMed Central
Google Scholar
Nelson TM, Rogers TL, Carlini AR, Brown MV. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ Microbiol. 2013;15:1132–45.
CAS
PubMed
Google Scholar
Tsukayama P, Boolchandani M, Patel S, Pehrsson EC, Gibson MK, Chiou KL, et al. Characterization of wild and captive baboon gut microbiota and their antibiotic resistomes. mSystems. 2018;3:e00016-18.
CAS
PubMed
PubMed Central
Google Scholar
Xenoulis PG, Gray PL, Brightsmith D, Palculict B, Hoppes S, Steiner JM, et al. Molecular characterization of the cloacal microbiota of wild and captive parrots. Vet Microbiol. 2010;146:320–5.
CAS
PubMed
Google Scholar
McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, et al. The effects of captivity on the mammalian gut microbiome. Integr Comp Biol. 2017;57:690–704.
PubMed
PubMed Central
Google Scholar
Alberdi A, Garazi MB, Aizpurua O. Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis. Sci Rep. 2021;11:22660.
Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, et al. Captivity humanizes the primate microbiome. Proc Natl Acad Sci USA. 2016;113:10376–81.
CAS
PubMed
PubMed Central
Google Scholar
Houtz JL, Sanders JG, Denice A, Moeller AH. Predictable and host-species specific humanization of the gut microbiota in captive primates. Mol Ecol. 2021;30:3677–87.
CAS
PubMed
Google Scholar
Kohl KD, Dearing MD. Wild-caught rodents retain a majority of their natural gut microbiota upon entrance into captivity. Environ Microbiol Rep. 2014;6:191–5.
PubMed
Google Scholar
Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, et al. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol. 2017;26:1175–89.
PubMed
Google Scholar
Moeller AH, Suzuki TA, Phifer-Rixey M, Nachman MW. Transmission modes of the mammalian gut microbiota. Science. 2018;362:453–7.
CAS
PubMed
Google Scholar
Bär J, Leung JM, Hansen C, Loke P, Hall AR, Conour L, et al. Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection. FEMS Microbiol Ecol. 2020;96:fiaa167.
PubMed
Google Scholar
Chong R, Grueber CE, Fox S, Wise P, Barrs VR, Hogg CJ, et al. Looking like the locals—gut microbiome changes post-release in an endangered species. Anim Microbiome. 2019;1:8.
PubMed
PubMed Central
Google Scholar
van Leeuwen P, Mykytczuk N, Mastromonaco GF, Schulte-Hostedde AI. Effects of captivity, diet, and relocation on the gut bacterial communities of white-footed mice. Ecol Evol. 2020;10:4677–90.
PubMed
PubMed Central
Google Scholar
Moeller AH, Suzuki TA, Lin D, Lacey EA, Wasser SK, Nachman MW. Dispersal limitation promotes the diversification of the mammalian gut microbiota. Proc Natl Acad Sci. 2017;114:13768–73.
CAS
PubMed
PubMed Central
Google Scholar
Linnenbrink M, Wang J, Hardouin EA, Künzel S, Metzler D, Baines JF. The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Mol Ecol. 2013;22:1904–16.
PubMed
Google Scholar
Hu X, Liu G, Li Y, Wei Y, Lin S, Liu S, et al. High-throughput analysis reveals seasonal variation of the gut microbiota composition within forest musk deer (Moschus berezovskii). Front Microbiol. 2018;9:1674.
PubMed
PubMed Central
Google Scholar
Clayton JB, Al-Ghalith GA, Long HT, Tuan BV, Cabana F, Huang H, et al. Associations between nutrition, gut microbiome, and health in a novel nonhuman primate model. Sci Rep. 2018;8:11159.
PubMed
PubMed Central
Google Scholar
Martínez-Mota R, Kohl KD, Orr TJ, Denise DM. Natural diets promote retention of the native gut microbiota in captive rodents. ISME J. 2020;14:67–78.
PubMed
Google Scholar
Greene LK, McKenney EA, O’Connell TM, Drea CM. The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas. Sci Rep. 2018;8:14482.
PubMed
PubMed Central
Google Scholar
Narat V, Amato KR, Ranger N, Salmona M, Mercier-Delarue S, Rupp S, et al. A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo. Sci Rep. 2020;10:19107.
CAS
PubMed
PubMed Central
Google Scholar
Hyde ER, Navas-Molina JA, Song SJ, Kueneman JG, Ackermann G, Cardona C, et al. The oral and skin microbiomes of captive komodo dragons are significantly shared with their habitat. mSystems. 2016;1:e00046-e116.
PubMed
PubMed Central
Google Scholar
Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA. Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka. Proc Biol Sci. 2017;284:20172274.
PubMed
PubMed Central
Google Scholar
Tung J, Barreiro LB, Burns MB, Grenier J-C, Lynch J, Grieneisen LE, et al. Social networks predict gut microbiome composition in wild baboons. Elife. 2015;4:e05224.
PubMed Central
Google Scholar
Raulo A, Allen BE, Troitsky T, Husby A, Firth JA, Coulson T, et al. Social networks strongly predict the gut microbiota of wild mice. ISME J. 2021;15:2601–13.
PubMed
PubMed Central
Google Scholar
Caruso R, Ono M, Bunker ME, Núñez G, Inohara N. Dynamic and asymmetric changes of the microbial communities after cohousing in laboratory mice. Cell Rep. 2019;27:3401-3412.e3.
CAS
PubMed
PubMed Central
Google Scholar
Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341:1241214.
PubMed
Google Scholar
Wernimont SM, Radosevich J, Jackson MI, Ephraim E, Badri DV, MacLeay JM, et al. The effects of nutrition on the gastrointestinal microbiome of cats and dogs: impact on health and disease. Front Microbiol. 2020;11:1266.
PubMed
PubMed Central
Google Scholar
Willing BP, Russell SL, Finlay BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol. 2011;9:233–43.
CAS
PubMed
Google Scholar
Eleftheriou A. Implications for one health of anthelmintic use in wildlife conservation programs. EcoHealth. 2021. https://doi.org/10.1007/s10393-021-01556-6.
Article
PubMed
Google Scholar
Leung JM, Loke P. A role for IL-22 in the relationship between intestinal helminths, gut microbiota and mucosal immunity. Int J Parasitol. 2013;43:253–7.
CAS
PubMed
Google Scholar
Allen-Blevins CR, You X, Hinde K, Sela DA. Handling stress may confound murine gut microbiota studies. PeerJ. 2017;2017:e2876.
Google Scholar
Murakami T, Kamada K, Mizushima K, Higashimura Y, Katada K, Uchiyama K, et al. Changes in intestinal motility and gut microbiota composition in a rat stress model. Digestion. 2017;95:55–60.
CAS
PubMed
Google Scholar
Reese AT, Dunn RR. Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance. MBio. 2018;9:e01294-e1318.
PubMed
PubMed Central
Google Scholar
Cheng Y, Fox S, Pemberton D, Hogg C, Papenfuss AT, Belov K. The Tasmanian devil microbiome—implications for conservation and management. Microbiome. 2015;3:76.
PubMed
PubMed Central
Google Scholar
Borbón-García A, Reyes A, Vives-Flórez M, Caballero S. Captivity shapes the gut microbiota of andean bears: insights into health surveillance. Front Microbiol. 2017;8:1316.
PubMed
PubMed Central
Google Scholar
Sun Y, Sun Y, Shi Z, Liu Z, Zhao C, Lu T, et al. Gut microbiota of wild and captive alpine musk deer (Moschus chrysogaster). Front Microbiol. 2020;10:3156.
PubMed
PubMed Central
Google Scholar
Yao R, Xu L, Hu T, Chen H, Qi D, Gu X, et al. The “wildness” of the giant panda gut microbiome and its relevance to effective translocation. Glob Ecol Conserv. 2019;18:e00644.
Google Scholar
Sun C-H, Liu H-Y, Liu B, Yuan B-D, Lu C-H. Analysis of the gut microbiome of wild and captive Père David’s deer. Front Microbiol. 2019;10:2331.
PubMed
PubMed Central
Google Scholar
Reese AT, Kearney SM. Incorporating functional trade-offs into studies of the gut microbiota. Curr Opin Microbiol. 2019;50:20–7.
CAS
PubMed
Google Scholar
Minich D, Madden C, Evans MV, Ballash GA, Barr DJ, Poulsen KP, et al. Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus). BioRxiv. 2021;11:13218.
CAS
Google Scholar
Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, et al. Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell. 2017;171:1015-1028.e13.
CAS
PubMed
PubMed Central
Google Scholar
Blyton MDJ, Soo RM, Whisson D, Marsh KJ, Pascoe J, Le Pla M, et al. Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Anim Microbiome. 2019;1:6.
PubMed
PubMed Central
Google Scholar
Koeppel KN, Bertschinger H, Van Vuuren M, Picard J, Steiner J, Williams D, et al. The use of a probiotic in captive cheetahs (Acinonyx jubatus). J S Afr Vet Assoc. 2006;77:127–30.
CAS
PubMed
Google Scholar
Weimer PJ, Stevenson DM, Mantovani HC, Man SLC. Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents1. J Dairy Sci. 2010;93:5902–12.
CAS
PubMed
Google Scholar
Hook SE, Northwood KS, Wright A-DG, McBride BW. Long-term Monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow. Appl Environ Microbiol. 2009;75:374–80.
CAS
PubMed
Google Scholar
Danielsson R, Dicksved J, Sun L, Gonda H, Müller B, Schnürer A, et al. Methane production in dairy cows correlates with rumen methanogenic and bacterial community structure. Front Microbiol. 2017;8:226.
PubMed
PubMed Central
Google Scholar
Clemmons BA, Voy BH, Myer PR. Altering the gut microbiome of cattle: considerations of host-microbiome interactions for persistent microbiome manipulation. Microb Ecol. 2019;77:523–36.
CAS
PubMed
Google Scholar
Li Y, Hu X, Yang S, Zhou J, Zhang T, Qi L, et al. Comparative analysis of the gut microbiota composition between captive and wild forest musk deer. Front Microbiol. 2017;8:1705.
PubMed
PubMed Central
Google Scholar
Gao H, Chi X, Qin W, Wang L, Song P, Cai Z, et al. Comparison of the gut microbiota composition between the wild and captive Tibetan wild ass (Equus kiang). J Appl Microbiol. 2019;126:1869–78.
CAS
PubMed
PubMed Central
Google Scholar
Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, et al. Comparative analysis of microbial community structure and function in the gut of wild and captive Amur tiger. Front Microbiol. 2020;11:1665.
PubMed
PubMed Central
Google Scholar
Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol. 2016;31:689–99.
PubMed
Google Scholar
Kohl KD, Weiss RB, Cox J, Dale C, Dearing MD. Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol Lett. 2014;17:1238–46.
PubMed
Google Scholar
Louca S, Polz MF, Mazel F, Albright MBN, Huber JA, O’Connor MI, et al. Function and functional redundancy in microbial systems. Nat Ecol Evol. 2018;2:936–43.
PubMed
Google Scholar
Guo W, Ren K, Ning R, Li C, Zhang H, Li D, et al. Fecal microbiota transplantation provides new insight into wildlife conservation. Glob Ecol Conserv. 2020;24:e01234.
Google Scholar
Martín R, Bermúdez-Humarán LG, Langella P. Gnotobiotic rodents: an in vivo model for the study of microbe–microbe interactions. Front Microbiol. 2016;7:409.
PubMed
PubMed Central
Google Scholar
Iyer N. Methods in microbiome research. Lab Anim. 2016;45:323–6.
Google Scholar
Greyson-Gaito CJ, Bartley TJ, Cottenie K, Jarvis WMC, Newman AEM, Stothart MR. Into the wild: microbiome transplant studies need broader ecological reality. Proc R Soc B Biol Sci. 2020;287:20192834.
Google Scholar
Auchtung JM, Robinson CD, Britton RA. Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs). Microbiome. 2015;3:42.
PubMed
PubMed Central
Google Scholar
Auchtung JM, Robinson CD, Farrell K, Britton RA. MiniBioReactor Arrays (MBRAs) as a tool for studying C. difficile physiology in the presence of a complex community. Methods Mol Biol Clifton NJ. 2016;1476:235–58.
Google Scholar
Bishop J, Hosey G, Plowman A. Handbook of zoo research, guidelines for conducting research in zoos. BIAZA; 2013.
Google Scholar
Ericsson AC, Hart ML, Kwan J, Lanoue L, Bower LR, Araiza R, et al. Supplier-origin mouse microbiomes significantly influence locomotor and anxiety-related behavior, body morphology, and metabolism. Commun Biol. 2021;4:1–12.
Google Scholar
Ding R, Goh W-R, Wu R, Yue X, Luo X, Khine WWT, et al. Revisit gut microbiota and its impact on human health and disease. J Food Drug Anal. 2019;27:623–31.
CAS
PubMed
Google Scholar
Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech. 2015;8:1–16.
CAS
PubMed
PubMed Central
Google Scholar
Celi P, Verlhac V, Pérez Calvo E, Schmeisser J, Kluenter A-M. Biomarkers of gastrointestinal functionality in animal nutrition and health. Anim Feed Sci Technol. 2019;250:9–31.
Google Scholar
Fry TL, Dunbar MR. A review of biomarkers used for wildlife damage and disease management. USDA Natl Wildl Res Cent - Staff Publ; 2007.
Google Scholar
Olifiers N, Jansen AM, Herrera HM, Bianchi RC, D’Andrea PS, Mourão GM, et al. Co-infection and wild animal health: effects of trypanosomatids and gastrointestinal parasites on coatis of the Brazilian pantanal. PLoS ONE. 2015;10:e0143997.
PubMed
PubMed Central
Google Scholar
Knutie SA. Food supplementation affects gut microbiota and immunological resistance to parasites in a wild bird species. J Appl Ecol. 2020;57:536–47.
CAS
Google Scholar
Aouissi HA, Ababsa M, Gaagai A, Bouslama Z, Farhi Y, Chenchouni H. Does melanin-based plumage coloration reflect health status of free-living birds in urban environments? Avian Res. 2021;12:45.
Google Scholar
Lane EP, Miller S, Lobetti R, Caldwell P, Bertschinger HJ, Burroughs R, et al. Effect of diet on the incidence of and mortality owing to gastritis and renal disease in captive cheetahs (Acinonyx jubatus) in South Africa. Zoo Biol. 2012;31:669–82.
CAS
PubMed
Google Scholar
Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365:eaaw4361.
CAS
PubMed
PubMed Central
Google Scholar
De Araujo Lima Constantino P. Deforestation and hunting effects on wildlife across Amazonian indigenous lands. Ecol Soc. 2016;21:3.
Google Scholar
Taylor-Brown A, Booth R, Gillett A, Mealy E, Ogbourne SM, Polkinghorne A, et al. The impact of human activities on Australian wildlife. PLoS ONE. 2019;14:e0206958.
CAS
PubMed
PubMed Central
Google Scholar
Daszak P, Cunningham AA, Hyatt AD. Emerging infectious diseases of wildlife—threats to biodiversity and human health. Science. 2000;287:443–9.
CAS
PubMed
Google Scholar
Thornes T. Animals and climate change. J Anim Ethics. 2016;6:81–8.
Google Scholar
Alfano N, Courtiol A, Vielgrader H, Timms P, Roca AL, Greenwood AD. Variation in koala microbiomes within and between individuals: effect of body region and captivity status. Sci Rep. 2015;5:10189.
CAS
PubMed
PubMed Central
Google Scholar
Allan N, Knotts TA, Pesapane R, Ramsey JJ, Castle S, Clifford D, et al. Conservation implications of shifting gut microbiomes in captive-reared endangered voles intended for reintroduction into the wild. Microorganisms. 2018;6:94.
CAS
PubMed Central
Google Scholar
Benno Y, Itoh K, Miyao Y, Mitsuoka T. Comparison of fecal microflora between wild Japanese monkeys in a snowy area and laboratory-reared Japanese monkeys. Jpn J Vet Sci. 1987;49:1059–64.
CAS
Google Scholar
Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, et al. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun. 2016;7:10516.
CAS
PubMed
PubMed Central
Google Scholar
De Jesús-Laboy KM, Godoy-Vitorino F, Piceno YM, Tom LM, Pantoja-Feliciano IG, Rivera-Rivera MJ, et al. Comparison of the fecal microbiota in feral and domestic goats. Genes. 2012;3:1–18.
Google Scholar
Delport TC, Power ML, Harcourt RG, Webster KN, Tetu SG. Colony location and captivity influence the gut microbial community composition of the Australian sea lion (Neophoca cinerea). Appl Environ Microbiol. 2016;82:3440–9.
CAS
PubMed
PubMed Central
Google Scholar
Delsuc F, Metcalf JL, Parfrey LW, Song SJ, González A, Knight R. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol. 2014;23:1301–17.
CAS
PubMed
Google Scholar
Eigeland K, Lanyon J, Trott D, Ouwerkerk D, Blanshard W, Milinovich G, et al. Bacterial community structure in the hindgut of wild and captive dugongs (Dugong dugon). Aquat Mamm. 2012;38:402–411402.
Google Scholar
Frankel JS, Mallott EK, Hopper LM, Ross SR, Amato KR. The effect of captivity on the primate gut microbiome varies with host dietary niche. Am J Primatol. 2019;81:e23061.
PubMed
Google Scholar
Guan Y, Zhang H, Gao X, Shang S, Wu X, Chen J, et al. Comparison of the bacterial communities in feces from wild versus housed sables (Martes zibellina) by high-throughput sequence analysis of the bacterial 16S rRNA gene. AMB Express. 2016;6:98.
PubMed
PubMed Central
Google Scholar
Guan Y, Yang H, Han S, Feng L, Wang T, Ge J. Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing. AMB Express. 2017;7:212.
PubMed
PubMed Central
Google Scholar
Guo W, Mishra S, Wang C, Zhang H, Ning R, Kong F, et al. Comparative study of gut microbiota in wild and captive giant pandas (Ailuropoda melanoleuca). Genes. 2019;10:827.
CAS
PubMed Central
Google Scholar
Hale VL, Tan CL, Niu K, Yang Y, Zhang Q, Knight R, et al. Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi. Am J Primatol. 2019;81:e22989.
CAS
PubMed
Google Scholar
Haworth SE, White KS, Côté SD, Shafer ABA. Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate. FEMS Microbiol Ecol. 2019;95:fiz095.
CAS
PubMed
Google Scholar
Kong F, Zhao J, Han S, Zeng B, Yang J, Si X, et al. Characterization of the gut microbiota in the Red Panda (Ailurus fulgens). PLoS ONE. 2014;9:e87885.
PubMed
PubMed Central
Google Scholar
Milovic A, Bassam K, Shao H, Chatzistamou I, Tufts DM, Diuk-Wasser M, et al. Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America. PLoS ONE. 2020;15:e0231801.
CAS
PubMed
PubMed Central
Google Scholar
Moustafa MAM, Chel HM, Thu MJ, Bawm S, Htun LL, Win MM, et al. Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments. Sci Rep. 2021;11:741.
CAS
PubMed
PubMed Central
Google Scholar
Nakamura N, Amato KR, Garber P, Estrada A, Mackie RI, Gaskins HR. Analysis of the hydrogenotrophic microbiota of wild and captive black howler monkeys (Alouatta pigra) in palenque national park, Mexico. Am J Primatol. 2011;73:909–19.
PubMed
Google Scholar
Prabhu VR, Wasimuddin, Kamalakkannan R, Arjun MS, Nagarajan M. Consequences of domestication on gut microbiome: a comparative study between wild gaur and domestic Mithun. Front Microbiol. 2020;11:133.
PubMed
PubMed Central
Google Scholar
Schwab C, Cristescu B, Northrup JM, Stenhouse GB, Gänzle M. Diet and environment shape fecal bacterial microbiota composition and enteric pathogen load of grizzly bears. PLoS ONE. 2011;6:e27905.
CAS
PubMed
PubMed Central
Google Scholar
Tang J, Wang C, Zhang H, Zhao J, Guo W, Mishra S, et al. Gut microbiota in reintroduction of giant panda. Ecol Evol. 2020;10:1012–28.
PubMed
PubMed Central
Google Scholar
Uenishi G, Fujita S, Ohashi G, Kato A, Yamauchi S, Matsuzawa T, et al. Molecular analyses of the intestinal microbiota of chimpanzees in the wild and in captivity. Am J Primatol. 2007;69:367–76.
CAS
PubMed
Google Scholar
Wasimuddin, Menke S, Melzheimer J, Thalwitzer S, Heinrich S, Wachter B, et al. Gut microbiomes of free-ranging and captive Namibian cheetahs: diversity, putative functions and occurrence of potential pathogens. Mol Ecol. 2017;26:5515–27.
CAS
PubMed
Google Scholar
Xiao Y, Xiao G, Liu H, Zhao X, Sun C, Tan X, et al. Captivity causes taxonomic and functional convergence of gut microbial communities in bats. PeerJ. 2019;7:e6844.
PubMed
PubMed Central
Google Scholar
San Juan PA, Castro I, Dhami MK. Captivity reduces diversity and shifts composition of the Brown Kiwi microbiome. Anim Microbiome. 2021;3:48.
PubMed
PubMed Central
Google Scholar
Scupham AJ, Patton TG, Bent E, Bayles DO. Comparison of the cecal microbiota of domestic and wild turkeys. Microb Ecol. 2008;56:322–31.
PubMed
Google Scholar
Xie Y, Xia P, Wang H, Yu H, Giesy JP, Zhang Y, et al. Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis). Sci Rep. 2016;6:33350.
CAS
PubMed
PubMed Central
Google Scholar
Campos P, Guivernau M, Prenafeta-Boldú FX, Cardona L. Fast acquisition of a polysaccharide fermenting gut microbiome by juvenile green turtles Chelonia mydas after settlement in coastal habitats. Microbiome. 2018;6:69.
PubMed
PubMed Central
Google Scholar
García-De la Peña C, Garduño-Niño E, Vaca-Paniagua F, Díaz-Velásquez C, Barrows CW, Gomez-Gil B, et al. Comparison of the fecal bacterial microbiota composition between wild and captive bolson tortoises (Gopherus flavomarginatus). Herpetol Conserv Biol. 2019;14:587–600.
Google Scholar
Sandri C, Correa F, Spiezio C, Trevisi P, Luise D, Modesto M, et al. Fecal microbiota characterization of seychelles giant tortoises (Aldabrachelys gigantea) living in both wild and controlled environments. Front Microbiol. 2020;11:569249.
PubMed
PubMed Central
Google Scholar
Tang G-S, Liang X-X, Yang M-Y, Wang T-T, Chen J-P, Du W-G, et al. Captivity influences gut microbiota in crocodile lizards (Shinisaurus crocodilurus). Front Microbiol. 2020;11:550.
PubMed
PubMed Central
Google Scholar
Tong Q, Liu X-N, Hu Z-F, Ding J-F, Bie J, Wang H-B, et al. Effects of captivity and season on the gut microbiota of the brown frog (Rana dybowskii). Front Microbiol. 2019;10:1912.
PubMed
PubMed Central
Google Scholar
Edenborough KM, Mu A, Mühldorfer K, Lechner J, Lander A, Bokelmann M, et al. Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity. PLoS ONE. 2020;15:e0223629.
CAS
PubMed
PubMed Central
Google Scholar
Schmidt E, Mykytczuk N, Schulte-Hostedde A. Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus). ISME J. 2019;13:1293–305.
CAS
PubMed
PubMed Central
Google Scholar
Dhanasiri AKS, Brunvold L, Brinchmann MF, Korsnes K, Bergh Ø, Kiron V. Changes in the intestinal microbiota of wild Atlantic cod Gadus morhua L. Upon Captive Rearing Microb Ecol. 2011;61:20–30.
PubMed
Google Scholar