Table 1 Papers comparing the gut microbiomes of captive animals and their wild counterparts
From: Possibilities and limits for using the gut microbiome to improve captive animal health
| Â | Author | Year | Citation | Sample type | Species | Difference in captive/wild microbial diversity? | Difference in captive/wild microbial composition? | Functional implications discussed? |
|---|---|---|---|---|---|---|---|---|
Mammals | Alfano et al. | 2015 | [113] | rectal | Koala | Not reported | N | Not discussed |
Allan et al. | 2018 | [114] | fecal | Amargosa vole | No difference | Y | Discussed | |
Allan et al. | 2018 | [114] | foregut | Amargosa vole | No difference | N | Discussed (metabolic function) | |
Amato et al. | 2016 | [5] | fecal and intestinal | Various colobine species | No difference | Y | Discuss (metabolic function) | |
Benno et al. | 1987 | [115] | fecal | Japanese macaque | Higher in captivity | Y | Discussed (metabolic function) | |
Bik et al. | 2016 | [116] | rectal | Bottlenose dolphin | Not reported | N | Not discussed | |
Borbon-Garcia et al. | 2017 | [73] | fecal | Andean bear | Lower in captivity | Y | Assessed (predicted metabolic functions—KEGG pathways/PICRUSt) | |
Cheng et al. | 2015 | [72] | fecal | Tasmanian devil | Lower in captivity | Y | Assessed (predicted metabolic functions—KEGG pathways/PICRUSt) | |
Clayton et al. | 2018 | [44] | fecal | Red-shanked douc | Lower in captivity | Y | Assessed (predicted metabolic and antibiotic resistance functions—KEGG pathways/PICRUSt) | |
Clayton et al. | 2016 | [55] | fecal | Red-shanked douc, Mantled howling monkey | Lower in captivity | Y | Assessed (predicted metabolic functions—PICRUSt) | |
De Jesus-Laboy et al. | 2011 | [117] | fecal | Goat | Not reported | N | Assessed (Assess presence of antibiotic resistance genes) | |
Delport et al. | 2016 | [118] | fecal | Australian sea lion | Not reported | Y | Not discussed | |
Delsuc et al. | 2013 | [119] | fecal | Various myrmecophagous mammals | Not reported | Y | Not discussed | |
Eigeland et al. | 2012 | [120] | fecal | Dugong | Lower in captivity | Y | Not discussed | |
Eisenhofer et al. | 2021 | [35] | fecal | Southern hairy-nosed wombat | Lower in captivity | Y | Discussed (metabolic function) | |
Frankel et al. | 2019 | [121] | fecal | 5 primate species | Lower in captivity | Y | Discussed (metabolic function) | |
Gao et al. | 2019 | [87] | fecal | Tibetan wild ass | Lower in captivity | Y | Discussed (immune function) | |
Gibson et al. | 2019 | [38] | fecal | Black rhinoceros | No difference | Y | Assessed (functional metagenomics—metabolic) | |
Greene et al. | 2019 | [20] | fecal | Various lemur species | Not reported | Y | Discussed (metabolic function) | |
Guan et al. | 2016 | [122] | fecal | Sable | Not reported | Y | Discussed (metabolic function) | |
Guan et al. | 2017 | [123] | fecal | Sika deer | Higher in captivity | Y | Discussed (metabolic function) | |
Guo et al. | 2019 | [124] | fecal | Giant Panda | Lower in captivity | Y | Assessed (functional metagenomics—metabolic and immune) | |
Hale et al. | 2019 | [125] | fecal | Snub-nosed monkey | Lower in captivity | Y | Discussed (metabolic and immune function) | |
Haworth et al. | 2019 | [126] | fecal | Mountain goat | No difference | Y | Discussed | |
Kong et al. | 2014 | [127] | fecal | Red panda | Lower in captivity | Y | Assessed (associated present OTUs with cellulose degradation ability (GenBank/Kimura—phylogenetic analysis based on 16S)) | |
Li et al. | 2017 | [86] | fecal | Forest musk deer | No difference | Y | Discussed (metabolic function) | |
McKenzie et al. | 2017 | [42] | fecal | 41 mammal species | Inconsistent between species | Y (except even-toed ungulates) | Discussed (metabolic function) | |
Metcalf et al. | 2017 | [22] | fecal | Przewalski's horse | Lower in captivity | Y | Not discussed | |
Milovic et al. | 2020 | [128] | fecal | White-footed mouse | Lower in captivity | Y | Not discussed | |
Minich et al. | 2021 | [78] | fecal | White-tailed deer | Higher in captivity | Y | Discussed (metabolic and immune function) | |
Moustafa et al. | 2021 | [129] | fecal | Asian elephant | No difference | Y | Discussed (metabolic function) | |
Nakamura et al. | 2011 | [130] | fecal | Black howler monkey | Lower in captivity | Y | Discussed (metabolic function) | |
Narat et al. | 2020 | [58] | fecal | Chimpanzee | No difference | Y | Discussed (metabolic function) | |
Narat et al. | 2020 | [58] | fecal | Western lowland gorilla | Higher in captivity | Y | Discussed (metabolic function) | |
Nelson et al. | 2012 | [39] | fecal | Elephant seal and Leopard seal | Higher in captivity | Y | Discussed (immune function) | |
Ning et al. | 2020 | [88] | fecal | Amur Tiger | Higher in captivity | Y | Assessed (functional metagenomics—metabolic) | |
Prabhu et al. | 2020 | [131] | fecal | Gaur | No difference | Y | Assessed (predicted metabolic and immune functions—PICRUSt/KEGG) | |
Rosshart et al. | 2017 | [79] | ileocecal | House mouse | Not reported | Y | Assessed (transplant experiment with immune readouts) | |
Schwab et al. | 2011 | [132] | fecal | Grizzly bear | Not reported | Y | Discussed (immune function) | |
Sun et al. | 2019 | [74] | fecal | Alpine musk deer | Not reported | Y | Assessed (functional metagenomics—metabolic) | |
Sun et al. | 2019 | [76] | fecal | Père David’s deer | No difference | Y | Assessed (predicted metabolic functions—PICRUSt/KEGG) | |
Tang et al. | 2020 | [133] | fecal | Giant panda | Lower in captivity | Y | Discussed (metabolic and immune function) | |
Tsukayama et al. | 2018 | [40] | fecal | Kinda and grayfoot chacma baboon | Higher in captivity | Y | Assessed (functional metagenomics—abx resistance) | |
Uenishi et al. | 2007 | [134] | fecal | Chimpanzee | Not reported | Y | Discussed (metabolic function) | |
Wasimuddin et al. | 2017 | [135] | fecal | Cheetah | No difference | Y | Assessed (predicted metabolic and immune functions—PICRUSt/KEGG) | |
Xiao et al. | 2019 | [136] | fecal | 6 bat species | Higher in captivity | Did not compare | Assessed (predicted metabolic functions—PICRUSt/KEGG) | |
Yan et al. | 2021 | [9] | fecal | Pangolin | Higher in captivity | Y | Not discussed | |
Birds | Oliveira et al. | 2020 | [37] | fecal | Various raptor species | No difference | Y | Not discussed |
San Juan et al. | 2021 | [137] | fecal | Brown kiwi | Lower in captivity | Y | Not discussed | |
Scupham et al. | 2008 | [138] | cecal | Turkey | No difference | Y | Discussed (metabolic function) | |
Ushida et al. | 2016 | [6] | cecal | Japanese and Svalbard rock ptarmigan | Not reported | Y | Discussed (metabolic function) | |
Wienemann et al. | 2011 | [36] | cecal | Capercaillie | Lower in captivity | Y | Discussed (metabolic function) | |
Xenoulis et al. | 2010 | [41] | cloacal | 3 parrot species | Higher in captivity | Y | Not discussed | |
Xie et al. | 2016 | [139] | fecal | Red-crowned crane | Higher in captivity | Y | Discussed (immune function) | |
Reptiles | Campos et al. | 2018 | [140] | fecal and rectal | Green turtle | No difference | N | Discussed (metabolic function) |
Garcia-De la Pena et al. | 2019 | [141] | fecal | Bolson tortoise | No difference | Y | Discussed (metabolic function) | |
Sandri et al. | 2020 | [142] | fecal | Aldabra giant tortoise | No difference | Y | Discussed (metabolic function) | |
Tang et al. | 2020 | [143] | fecal | Crocodile lizard | Higher in captivity | Y | Assessed (predicted metabolic functions—PICRUSt/KEGG) | |
Amphibians | Tong et al. | 2019 | [144] | intestinal | Dybowski's brown frog | No difference | Y | Assessed (predicted metabolic and immune functions—PICRUSt/KEGG) |