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Hameed J, Nazir R. Probiotic Potential of Lactobacillus and Enterococcus Strains Isolated From the Faecal Microbiota of Critically Endangered Hangul Deer (Cervus hanglu hanglu): Implications for Conservation Management. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10325-0. [PMID: 39046670 DOI: 10.1007/s12602-024-10325-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2024] [Indexed: 07/25/2024]
Abstract
The mammalian gut microbiota plays a crucial role in promoting host health, and lactic acid bacteria (LAB) are commonly employed as probiotics for their beneficial effects. The Hangul deer (Cervus hanglu hanglu), a critically endangered red deer subspecies found in the Indian subcontinent, requires meticulous health management for its conservation. This pioneering study aimed to isolate, identify, and evaluate the in-vitro probiotic functional properties of LAB strains from the faeces of Hangul deer. A total of 27 LAB strains were isolated and identified using 16S rDNA gene sequencing, followed by comprehensive probiotic characterization and safety assessment. Remarkably, four species exhibited robust resistance and survivability against varying pH levels and bile salts, along with high aggregation and co-aggregation capacities. Notably, Lactobacillus acidophilus and Enterococcus mundtii strains displayed antibacterial activities. Safety assessment revealed the absence of hemolytic activity and virulence genes in all four strains. Antibiotic susceptibility testing showed that Lactobacillus acidophilus and Enterococcus casseliflavus were susceptible to all tested antibiotics, while Enterococcus mundtii exhibited resistance to clindamycin, and Enterococcus gallinarum exhibited resistance to erythromycin. These findings suggest that the isolated LAB strains possess advantageous probiotic characteristics and hold potential as dietary supplements for promoting the health and disease management of Hangul deer.
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Affiliation(s)
- Javaid Hameed
- Microbiology Research Laboratory, Centre of Research for Development (CORD), University of Kashmir, Srinagar, 190006, J&K, India
| | - Ruqeya Nazir
- Microbiology Research Laboratory, Centre of Research for Development (CORD), University of Kashmir, Srinagar, 190006, J&K, India.
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2
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Anka IZ, Uren Webster TM, Berbel-Filho WM, Hitchings M, Overland B, Weller S, Garcia de Leaniz C, Consuegra S. Microbiome and epigenetic variation in wild fish with low genetic diversity. Nat Commun 2024; 15:4725. [PMID: 38830879 PMCID: PMC11148108 DOI: 10.1038/s41467-024-49162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
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Affiliation(s)
- Ishrat Z Anka
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Department of Aquaculture, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Tamsyn M Uren Webster
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Biology, University of West Florida, Pensacola, FL, USA
| | - Matthew Hitchings
- Institute of Life Science, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Benjamin Overland
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Sarah Weller
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Carlos Garcia de Leaniz
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Marine Research Centre (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Sofia Consuegra
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK.
- Grupo de Biotecnología Acuática, Departamento de Biotecnología y Acuicultura, Instituto de Investigacións Mariñas, IIM-CSIC, Vigo, Spain.
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Amin A, Mekadim C, Modrackova N, Bolechova P, Mrazek J, Neuzil-Bunesova V. Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. Anim Microbiome 2024; 6:21. [PMID: 38698458 PMCID: PMC11064412 DOI: 10.1186/s42523-024-00311-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.
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Affiliation(s)
- Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Petra Bolechova
- Department of Ethology and Companion Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic.
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Jenkins L, McKnight DT, Parks M, Byer NW, Oliaro FJ, Thompson D, Scott R. Variable effects of captivity on microbiomes in populations of IUCN-endangered Blanding's turtles (Emydoidea blandingii). J Appl Microbiol 2024; 135:lxae121. [PMID: 38755020 DOI: 10.1093/jambio/lxae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/26/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024]
Abstract
AIMS Microbiome composition is increasingly considered in species reintroduction efforts and may influence survival and reproductive success. Many turtle species are threatened by anthropogenic pressures and are frequently raised in captivity for reintroduction efforts, yet little is known about turtle microbiome composition in either wild or captive settings. Here, we investigated trends in microbiome composition of captive and wild IUCN-endangered Blanding's turtles (Emydoidea blandingii). METHODS AND RESULTS We amplified and sequenced the V4 region of the 16S rDNA locus from plastron, cloaca, and water samples of wild E. blandingii adults and two populations of captive E. blandingii juveniles being raised for headstarting. Plastron, cloaca, and water-associated microbiomes differed strongly from each other and were highly variable among captive sites and between captive and wild sites. Across plastron, cloaca, and water-associated microbial communities, microbial diversity changed over time, but not in a predictable direction between captive sites. Plastron beta diversity correlated with growth rate in captive samples, indicating that external microbiomes may correlate with individual fitness. CONCLUSIONS Our results indicate that external and internal microbiomes vary between captive and wild turtles and may reflect differences in fitness of captive-raised individuals.
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Affiliation(s)
- Lauren Jenkins
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States
- Department of Biology, Wheaton College, Wheaton, IL 60187, United States
| | | | - Matthew Parks
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034, United States
| | - Nathan W Byer
- Division of Natural Resources, Cleveland Metroparks, Cleveland, OH 44144, United States
| | - Francis J Oliaro
- Conservation Research Department, John G. Shedd Aquarium, Chicago, IL 60605, United States
| | - Dan Thompson
- Forest Preserve District of DuPage County, Wheaton, IL 60189, United States
| | - Rodney Scott
- Department of Biology, Wheaton College, Wheaton, IL 60187, United States
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Zhang L, Tang X, Fan C, Ren S, Cheng Q, Zhou H, Liu K, Jia S, Zhang Y. Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika. Biomolecules 2024; 14:403. [PMID: 38672421 PMCID: PMC11047922 DOI: 10.3390/biom14040403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.
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Affiliation(s)
- Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Shi’en Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China;
| | - Kai Liu
- Qinghai Provincial Grassland Station, Xining 810008, China;
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
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Gerrick ER, DeSchepper LB, Mechler CM, Joubert LM, Dunker F, Colston TJ, Howitt MR. Commensal protists in reptiles display flexible host range and adaptation to ectothermic hosts. mBio 2023; 14:e0227323. [PMID: 37962346 PMCID: PMC10746265 DOI: 10.1128/mbio.02273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Environmental factors like climate change and captive breeding can impact the gut microbiota and host health. Therefore, conservation efforts for threatened species may benefit from understanding how these factors influence animal microbiomes. Parabasalid protists are members of the mammalian microbiota that can modulate the immune system and impact susceptibility to infections. However, little is known about parabasalids in reptiles. Here, we profile reptile-associated parabasalids in wild and captive reptiles and find that captivity has minimal impact on parabasalid prevalence or diversity. However, because reptiles are cold-blooded (ectothermic), their microbiotas experience wider temperature fluctuation than microbes in warm-blooded animals. To investigate whether extreme weather patterns affect parabasalid-host interactions, we analyzed the gene expression in reptile-associated parabasalids and found that temperature differences significantly alter genes associated with host health. These results expand our understanding of parabasalids in this vulnerable vertebrate group and highlight important factors to be taken into consideration for conservation efforts.
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Affiliation(s)
- Elias R. Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Leila B. DeSchepper
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Claire M. Mechler
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Lydia-Marie Joubert
- Cell Sciences Imaging Facility (CSIF), Stanford University, Stanford, California, USA
| | - Freeland Dunker
- Steinhart Aquarium, California Academy of Sciences, San Francisco, California, USA
| | | | - Michael R. Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology, Stanford University School of Medicine, Stanford, California, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
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7
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Mulla L, Hernández-Gómez O. Wildfires disturb the natural skin microbiota of terrestrial salamanders. Environ Microbiol 2023; 25:2203-2215. [PMID: 37340556 DOI: 10.1111/1462-2920.16452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/04/2023] [Indexed: 06/22/2023]
Abstract
Environmental change can disturb natural associations between wildlife and microbial symbionts, in many cases to the detriment of host health. We used a North American terrestrial salamander system to assess how the skin microbiota of amphibians responds to wildfires. In northern California's redwood/oak forests, we assessed how recent wildfires affected the skin microbiota of three different salamander species (Taricha sp., Batrachoseps attenuatus, and Ensatina eschscholtzii) over two different sampling seasons in 2018 and 2021. We found species-specific responses to wildfire disturbance on the alpha diversity of the skin microbiota of terrestrial salamanders, although burning in general altered the composition of the skin microbiota. The effect of burning on alpha diversities and body condition indices varied by sampling season, suggesting an additional effect of annual climatic conditions on body condition and skin microbiota response. We tested all salamanders for Batrachochytrium dendrobatidis and found four infected individuals in 2018 and none in 2021. Our study documents correlations in the skin microbiota response to an increasing source of disturbance in western North American ecosystems. In addition, our results highlight the need to consider the effects of increased wildfire regimes/intensities and longitudinal effects on wildlife-associated microbiota and animal health.
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Affiliation(s)
- Lubna Mulla
- Department of Natural Sciences and Mathematics, School of Health and Natural Sciences, Dominican University of California, San Rafael, California, USA
| | - Obed Hernández-Gómez
- Department of Natural Sciences and Mathematics, School of Health and Natural Sciences, Dominican University of California, San Rafael, California, USA
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Tang L, Yan L, Jia H, Xiong Y, Ma X, Chu H, Sun Z, Wang L, Shalitanati M, Li K, Hu D, Zhang D. Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China. Integr Zool 2023; 18:1027-1040. [PMID: 36606497 DOI: 10.1111/1749-4877.12699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.
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Affiliation(s)
- Liping Tang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Huiping Jia
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu Xiong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xinping Ma
- Xinjiang Mountain Ungulate Nature Reserve Management Center, Urumqi, China
| | - Hongjun Chu
- Institute of Forestry Ecology, Xinjiang Academy of Forestry Sciences, Urumqi, China
| | - Zhicheng Sun
- Administrative Bureau of Dunhuang Xihu National Nature Reserve, Dunhuang, China
| | - Liang Wang
- Administration of Gansu Anxi Extra-arid Desert National Nature Reserve, Guazhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mubalake Shalitanati
- Xinjiang Uygur Autonomous Region Wild Horse Breeding Research Center, Urumqi, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Maigoro AY, Muhammad M, Bello B, Useh U, Lee S. Exploration of Gut Microbiome Research in Africa: A Scoping Review. J Med Food 2023; 26:616-623. [PMID: 37523293 DOI: 10.1089/jmf.2023.k.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
Abstract
The crucial role of the gut microbiome in various diseases has led to increased interest in interventions and therapeutics targeting the human microbiome. Accordingly, the current scoping review analyzed the diseases and interventions involved in gut microbiome research in Africa. The electronic databases of PubMed, Google Scholar, and Scopus were searched from inception to October 2021. This study identified 48 studies involving 7073 study participants. Of the 48 studies, 20 (42%) used interventions to modulate gut microbiota, whereas the remaining 28 (58%) did not. Out of the total African countries, only 13% were involved in intervention-based gut microbiome research, whereas a larger proportion of 67% were not involved in any gut microbiome research. The interventions used in gut microbiome research in Africa include supplements, natural products, educational approaches, associated pathogens, albendazole, fresh daily yogurt, iron-containing lipid-based nutrient supplements, fecal microbiota transplant, and prophylactic cotrimoxazole. This scoping review highlights the current state of gut microbiome research in Africa. The findings of this review can inform the design of future studies and interventions aimed at improving gut health in African populations.
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Affiliation(s)
- Abdulkadir Yusif Maigoro
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Korea
| | - Mubarak Muhammad
- Department of Physiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Bashir Bello
- Lifestyle Diseases Research Entity, Faculty of Health Sciences, North-West University, Vanderbijlpark, South Africa
| | - Ushotanefe Useh
- Lifestyle Diseases Research Entity, Faculty of Health Sciences, North-West University, Vanderbijlpark, South Africa
| | - Soojin Lee
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Korea
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10
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Oliveros A, Terraube J, Levengood AL, Powell D, Frère CH. Influence of scat ageing on the gut microbiome: how old is too old? BMC Genomics 2023; 24:427. [PMID: 37525141 PMCID: PMC10388479 DOI: 10.1186/s12864-023-09520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus). RESULTS We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery. CONCLUSION We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.
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Affiliation(s)
- Alejandro Oliveros
- The School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
| | - Julien Terraube
- Vulture Conservation Foundation, Wuhrstrasse 12, Zürich, CH-8003, Switzerland
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Alexis L Levengood
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Daniel Powell
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Céline H Frère
- The School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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11
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Redford KH. Extending conservation to include Earth's microbiome. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14088. [PMID: 37009683 DOI: 10.1111/cobi.14088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 05/30/2023]
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12
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Gerrick ER, DeSchepper LB, Mechler CM, Joubert LM, Dunker F, Colston TJ, Howitt MR. Commensal protists in reptiles display flexible host range and adaptation to ectothermic hosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542353. [PMID: 37292851 PMCID: PMC10245904 DOI: 10.1101/2023.05.25.542353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Parabasalid protists recently emerged as keystone members of the mammalian microbiota with important effects on their host's health. However, the prevalence and diversity of parabasalids in wild reptiles and the consequences of captivity and other environmental factors on these symbiotic protists are unknown. Reptiles are ectothermic, and their microbiomes are subject to temperature fluctuations, such as those driven by climate change. Thus, conservation efforts for threatened reptile species may benefit from understanding how shifts in temperature and captive breeding influence the microbiota, including parabasalids, to impact host fitness and disease susceptibility. Here, we surveyed intestinal parabasalids in a cohort of wild reptiles across three continents and compared these to captive animals. Reptiles harbor surprisingly few species of parabasalids compared to mammals, but these protists exhibited a flexible host-range, suggesting specific adaptations to reptilian social structures and microbiota transmission. Furthermore, reptile-associated parabasalids are adapted to wide temperature ranges, although colder temperatures significantly altered the protist transcriptomes, with increased expression of genes associated with detrimental interactions with the host. Our findings establish that parabasalids are widely distributed in the microbiota of wild and captive reptiles and highlight how these protists respond to temperature swings encountered in their ectothermic hosts.
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Affiliation(s)
- Elias R Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leila B DeSchepper
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Claire M Mechler
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lydia-Marie Joubert
- Cell Sciences Imaging Facility (CSIF), Stanford University, Stanford, CA 94305, USA
| | - Freeland Dunker
- Steinhart Aquarium, California Academy of Science, San Francisco, CA 94118, USA
| | - Timothy J Colston
- Biology Department, University of Puerto Rico at Mayagüez, Call Box 9000, 00681-9000 Mayagüez, Puerto Rico
| | - Michael R Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Lead Contact
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13
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By Bits and Pieces: The Contributions of Zoos and Aquariums to Science and Society via Biomaterials. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2023. [DOI: 10.3390/jzbg4010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Scientific research has long been recognized as one of the four pillars of the zoo or aquarium mission, alongside recreation, conservation, and education. This study sought to quantify a sample of zoos’ participation in scientific research via the provision of biomaterials from animals to outside scientists and the associated training of undergraduate and graduate students that resulted from these projects. A convenience sample of zoos provided data on their participation in biomaterials-related projects and a focused analysis of biomaterials-related research facilitated by the Saint Louis Zoo was conducted. In addition, the Association of Zoos & Aquariums’ conservation & science database was queried to uncover what research projects AZA members engaged in over the last five years that likely involved biomaterials research and training of students. Results demonstrate that zoos are making significant contributions to science by agreeing to participate in large numbers of biomaterials-related projects across different areas of focus involving a variety of animal species annually, with results applicable to human and non-human animals. Support of such research often involves student thesis projects, thus contributing to the education of future scientists.
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14
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Eisenhofer R, Brice KL, Blyton MDJ, Bevins SE, Leigh K, Singh BK, Helgen KM, Hough I, Daniels CB, Speight N, Moore BD. Individuality and stability of the koala ( Phascolarctos cinereus) faecal microbiota through time. PeerJ 2023; 11:e14598. [PMID: 36710873 PMCID: PMC9879153 DOI: 10.7717/peerj.14598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/29/2022] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kylie L. Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Michaela DJ Blyton
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, Brisbane, Queensland, Australia
| | - Scott E. Bevins
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kellie Leigh
- Science for Wildlife Ltd, Sydney, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia,Global Centre for Land Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Kristofer M. Helgen
- Australian Museum Research Institute, Sydney, New South Wales, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia,Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Ian Hough
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Christopher B. Daniels
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
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15
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Gaughan S, Kyndt JA, Haas JD, Steffensen KD, Kočovský PM, Pope KL. Using the Gut Microbiome to Assess Stocking Efforts of the Endangered Pallid Sturgeon, Scaphirhynchus albus. Life (Basel) 2023; 13:life13020309. [PMID: 36836665 PMCID: PMC9967686 DOI: 10.3390/life13020309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The endangered Pallid Sturgeon, Scaphirhynchus albus, has been actively managed to prevent population declines, including stocking of hatchery-raised fish. The gut microbiome plays an innate role in an organism's absorption of nutrients by increasing nutrient availability and can provide new insights for Pallid Sturgeon management. In this study, the Pallid Sturgeon's microbiome is dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. It was also determined that the gut bacterial diversity in hatchery-raised Pallid Sturgeon was not significantly different from wild Pallid Sturgeon, supporting that hatchery-raised Pallid Sturgeon are transitioning effectively to wild diets. There is also a high degree of intraspecific variation in the bacterial and eukaryotic sequences amongst individual Pallid Sturgeon microbiomes, suggesting the Pallid Sturgeon may be omnivorous. This study demonstrated that genetic markers may be used to effectively describe the dietary requirements for wild Pallid Sturgeon and provides the first genetic evidence that Pallid Sturgeons are effectively transitioning from hatchery-raised environments to the wild.
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Affiliation(s)
- Sarah Gaughan
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
| | - John A Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
| | - Justin D Haas
- Nebraska Game and Parks Commission, Lincoln, NE 68501, USA
| | | | | | - Kevin L Pope
- U.S. Geological Survey-Nebraska Cooperative Fish and Wildlife Research Unit, School of Natural Resources, Lincoln, NE 68583, USA
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16
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Greenspan SE, Peloso P, Fuentes-González JA, Bletz M, Lyra ML, Machado IF, Martins RA, Medina D, Moura-Campos D, Neely WJ, Preuss J, Sturaro MJ, Vaz RI, Navas CA, Toledo LF, Tozetti AM, Vences M, Woodhams DC, Haddad CFB, Pienaar J, Becker CG. Low microbiome diversity in threatened amphibians from two biodiversity hotspots. Anim Microbiome 2022; 4:69. [PMID: 36582011 PMCID: PMC9801548 DOI: 10.1186/s42523-022-00220-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil's Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.
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Affiliation(s)
- Sasha E. Greenspan
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Pedro Peloso
- grid.452671.30000 0001 2175 1274Programa de Pós Gradução em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, Pará 66077-530 Brazil ,Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Jesualdo A. Fuentes-González
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - Molly Bletz
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Mariana L. Lyra
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Ibere F. Machado
- Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Renato A. Martins
- grid.411247.50000 0001 2163 588XPrograma de Pós-Graduação em Conservação da Fauna, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905 Brazil
| | - Daniel Medina
- Sistema Nacional de Investigación, SENACYT; City of Knowledge, Clayton, Panama, Republic of Panama ,grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
| | - Diego Moura-Campos
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil ,grid.1001.00000 0001 2180 7477Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601 Australia
| | - Wesley J. Neely
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Jackson Preuss
- grid.412292.e0000 0004 0417 7532Departamento de Ciências da Vida, Universidade do Oeste de Santa Catarina, São Miguel Do Oeste, Santa Catarina 89900-000 Brazil
| | - Marcelo J. Sturaro
- grid.411249.b0000 0001 0514 7202Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo 09972-270 Brazil
| | - Renata I. Vaz
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Carlos A. Navas
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Luís Felipe Toledo
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil
| | - Alexandro M. Tozetti
- grid.412302.60000 0001 1882 7290Programa de Pos-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, Rio Grande Do Sul 93022-750 Brazil
| | - Miguel Vences
- grid.6738.a0000 0001 1090 0254Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, Brunswick, Germany
| | - Douglas C. Woodhams
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Célio F. B. Haddad
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Jason Pienaar
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - C. Guilherme Becker
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
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17
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Lee SK, Woo C, Lee EJ, Yamamoto N. Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison. Sci Rep 2022; 12:22271. [PMID: 36564425 PMCID: PMC9789119 DOI: 10.1038/s41598-022-26862-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN's red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.
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Affiliation(s)
- Seung-Kyung Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Cheolwoon Woo
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea
| | - Eun Ju Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Institute of Health and Environment, Seoul National University, Seoul, South Korea
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18
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Kumar MS, Slud EV, Hehnly C, Zhang L, Broach J, Irizarry RA, Schiff SJ, Paulson JN. Differential richness inference for 16S rRNA marker gene surveys. Genome Biol 2022; 23:166. [PMID: 35915508 PMCID: PMC9344657 DOI: 10.1186/s13059-022-02722-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is essential. While microbiome data generated using high-throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa. Results When this artificial inflation in the observed number of taxa is ignored, we find that changes in the abundance of detected taxa confound current methods for inferring differences in richness. Experimental evidence, theory-guided exploratory data analyses, and existing literature support the conclusion that most sub-genus discoveries are spurious artifacts of clustering 16S sequencing reads. We proceed to model a 16S survey’s systematic patterns of sub-genus taxa generation as a function of genus abundance to derive a robust control for false taxa accumulation. These controls unlock classical regression approaches for highly flexible differential richness inference at various levels of the surveyed microbial assemblage: from sample groups to specific taxa collections. The proposed methodology for differential richness inference is available through an R package, Prokounter. Conclusions False species discoveries bias richness estimation and confound differential richness inference. In the case of 16S microbiome surveys, supporting evidence indicate that most sub-genus taxa are spurious. Based on this finding, a flexible method is proposed and is shown to overcome the confounding problem noted with current approaches for differential richness inference. Package availability: https://github.com/mskb01/prokounter Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02722-x.
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19
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Zeng Y, Xiong Y, Yang C, He N, He J, Luo W, Chen Y, Zeng X, Wu Z. Investigation of Parasitic Infection in Crocodile Lizards ( Shinisaurus crocodilurus) Using High-Throughput Sequencing. Animals (Basel) 2022; 12:ani12202726. [PMID: 36290112 PMCID: PMC9597849 DOI: 10.3390/ani12202726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The highly endangered crocodile lizard (Shinisaurus crocodilurus) continues to be impacted by disease, especially in captive breeding populations. In this paper, based on high-throughput sequencing, we investigated parasitic infections in captive and wild crocodile lizard populations in the Daguishan National Nature Reserve and Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The results show that the overall parasitic infection rate in crocodile lizards was 33.33% (23/69). Four parasite genera were detected, including Eimeria, Cryptosporidium, Nematopsis, and Acanthamoeba, with infection rates of 15.94% (11/69), 17.39% (12/69), 7.25% (5/69), and 4.35% (3/69), respectively. Significant differences in the infection rate were found between the different parasite species (χ2 = 8.54, p < 0.05, chi-squared test). The parasitic infection rates in the captive and wild populations were 39.29% (22/56) and 7.69% (1/13), respectively, which were significantly different (p < 0.05, Fisher’s exact test). However, no significant differences in the infection rates of the four parasite genera were found between the captive and wild populations (p > 0.05, Fisher’s exact test). The parasitic infection rates in Daguishan and Luokeng were 34.09% (15/44) and 32.00% (8/25), respectively, which were not significantly different (p > 0.05, Fisher’s exact test). However, significant differences in terms of species were found in the two reserves (p < 0.01, Fisher’s exact test). Only Cryptosporidium infection showed a significant difference between the two regions (p < 0.01, Fisher’s exact test). Our results suggest that captive crocodile lizards are more susceptible to parasitic diseases than wild crocodile lizards and that Cryptosporidium infection varies by geographical region. This study provides basic information about the parasites of endangered crocodile lizards, as well as a reference for disease control and conservation.
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Affiliation(s)
- Yongru Zeng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Yi Xiong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Chunsheng Yang
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou 542824, China
| | - Nan He
- Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve, Shaoguan 512100, China
| | - Jiasong He
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou 542824, China
| | - Wenxian Luo
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou 542824, China
| | - Yaohuan Chen
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou 542824, China
| | - Xiaochen Zeng
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou 542824, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
- Correspondence: ; Tel.: +86-135-1783-6091
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20
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Ni Q, Dong S, Xing B, Zeng B, Kong F, Xu H, Yao Y, Li D, Zhang M, Fan X, Yang D, Yang M, Xie M. Oral and fecal microbiome of confiscated Bengal slow lorises in response to confinement duration. Front Microbiol 2022; 13:941261. [PMID: 36238588 PMCID: PMC9553000 DOI: 10.3389/fmicb.2022.941261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Slow lorises are small arboreal and nocturnal primates. Due to the illegal trade, a large number of slow lorises were confiscated into wildlife sanctuaries or rescue centers. The re-release has been considered a preferable approach for alleviating the captive pressure, but inappropriate and long-term confinement make it difficult to achieve this goal. In this study, we investigated and compared the fecal and oral microbiome of Bengal slow lorises (Nycticebus bengalensis) under long-term captivity (LC) and short-term captivity (SC) groups based on 16s rRNA high-throughput gene sequencing. The oral microbiome displayed higher Chao1 richness but lower Shannon and Simpson indices than the fecal microbiome. The Bengal slow lorises under long-term captivity had abundant pathogenic genera in both gut and oral microbiomes, such as Desulfovibrio, Actinomyces, Capnocytophaga, Neisseria, and Fusobacterium, while some specific bacterial taxa associated with intestinal balance were more enriched in the SC group. Due to the plant gum scarcity in the diet, both groups had a low abundance of Bifidobacterium. Function profile prediction indicated that the LC group was enriched with genetic information processing and metabolism pathways due to the stable food intake. The increased membrane transport and xenobiotic metabolism and degradation functions in the SC group could be explained by the function of the host microbiome in facilitating adaptation to changing environments and diets. The results demonstrated that the oral microbiome had the potential to be used as a regular surveillance tool. Also, current captive management should be improved to ensure reintroduction success.
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Affiliation(s)
- Qingyong Ni
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Qingyong Ni,
| | - Shasha Dong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bolin Xing
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Diyan Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Deying Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingyao Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Yaan, China
- Meng Xie,
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21
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Wuerthner VP, Hua J, Hernández‐Gómez O. Life stage and proximity to roads shape the skin microbiota of eastern newts (Notophthalmus viridescens). Environ Microbiol 2022; 24:3954-3965. [PMID: 35355399 PMCID: PMC9790580 DOI: 10.1111/1462-2920.15986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 12/30/2022]
Abstract
Host-associated microbiomes play an essential role in the health of organisms, including immune system activation, metabolism and energy uptake. It is well established that microbial communities differ depending on the life stage and natural history of the organism. However, the effects of life stage and natural history on microbial communities may also be influenced by human activities. We investigated the effects of amphibian life stage (terrestrial eft vs. aquatic adult) and proximity to roadways on newt skin bacterial communities. We found that the eft and adult life stages differed in bacterial community composition; however, the effects of roads on community composition were more evident in the terrestrial eft stage compared to the aquatic adult stage. Terrestrial efts sampled close to roads possessed richer communities than those living further away from the influence of roads. When accounting for amplicon sequence variants with predicted antifungal capabilities, in the adult life stage, we observed a decrease in anti-fungal bacteria with distance to roads. In contrast, in the eft stage, we found an increase in anti-fungal bacteria with distance to roads. Our results highlight the need to consider the effects of human activities when evaluating how host-associated microbiomes differ across life stages of wildlife.
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Affiliation(s)
| | - Jessica Hua
- Department of Biological SciencesBinghamton UniversityBinghamtonNY,Department of Forest and Wildlife EcologyUniversity of Wisconsin‐MadisonMadisonWI
| | - Obed Hernández‐Gómez
- Department of Environmental Sciences, Policy, and ManagementUniversity of California‐BerkeleyBerkeleyCA,Department of Natural Sciences and MathematicsDominican University of CaliforniaSan RafaelCA
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22
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Estrada A, Medina D, Gratwicke B, Ibáñez R, Belden LK. Body condition, skin bacterial communities and disease status: insights from the first release trial of the limosa harlequin frog,
Atelopus limosus. Proc Biol Sci 2022; 289:20220586. [PMID: 35858072 PMCID: PMC9277274 DOI: 10.1098/rspb.2022.0586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many endangered amphibian species survive in captive breeding facilities, but there have been few attempts to reintroduce captive-born individuals to rebuild wild populations. We conducted a soft-release trial of limosa harlequin frogs,
Atelopus limosus,
which are highly susceptible to the amphibian chytrid fungus
Batrachochytrium dendrobatidis
(Bd), to understand changes associated with the transition from captivity to the wild. Specifically, we assessed changes in body condition, skin-associated bacterial communities and disease status after release. Frogs were housed individually in field mesocosms and monitored for 27 days. Body condition did not significantly change in the mesocosms, and was similar to, or higher than, that of wild conspecifics at day 27. The skin bacteria of captive-born frogs, based on 16S rRNA gene amplicons, became similar to that of wild conspecifics after 27 days in mesocosms. Prevalence of Bd in wild conspecifics was 13–27%, and 15% of the
A. limosus
in mesocosms became infected with Bd, but no mortality of infected frogs was observed. We conclude that mesocosms are suitable for systematically and repeatedly monitoring amphibians during release trials, and that body condition, the skin microbiome, and Bd status can all change within one month of placement of captive-born individuals back into the wild.
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Affiliation(s)
- Angie Estrada
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
- Sistema Nacional de Investigación, SENACYT, Panama
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA 22630, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
- Sistema Nacional de Investigación, SENACYT, Panama
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
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23
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de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL. The Gut Microbiome of 54 Mammalian Species. Front Microbiol 2022; 13:886252. [PMID: 35783446 PMCID: PMC9246093 DOI: 10.3389/fmicb.2022.886252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon sequencing. The composition of the gut microbiota clearly reflects diet and the structure of the gastrointestinal system, and it is to a certain degree more similar between closely related animals. Specific clusters of taxa were observed across animals of the same species, diet, and gut morphology. The microbiota retained regardless of captivity status is hypothesized to cover important symbiotic relationships with the host, while the remaining part reflects the artificial living conditions and can therefore be used as a future tool for conservation biologists. For five animal species (giraffes, horses, baboons, elephants, and zebras), it was possible to compare the microbiota of wild and captive individuals. Differences were observed in the proportion of microbiota detected between wild and captive specimens of the same animal species. We propose that the gut microbiota harbours important species, which can potentially serve as indicators for the well-being of the animal and the effect of living in captivity.
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Affiliation(s)
- Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Benjamin Carlsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Aalborg Zoo, Aalborg, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- *Correspondence: Jeppe Lund Nielsen
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24
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Ørsted M, Yashiro E, Hoffmann AA, Kristensen TN. Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness. PLoS Genet 2022; 18:e1010206. [PMID: 35604942 PMCID: PMC9166449 DOI: 10.1371/journal.pgen.1010206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/03/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
It is becoming increasingly clear that microbial symbionts influence key aspects of their host’s fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations. It is becoming increasingly clear that organisms and the microbes that live on or in them–their microbiome–affect each other in profound ways that we are just beginning to understand. For instance, a diverse microbiome can help maintain metabolic functions or fight pathogens causing diseases. A disrupted microbiome may be especially critical for animals and plants that occur in low numbers because of threats from e.g. human exploitation or climate change, as they may already suffer from genetic challenges such as inbreeding and reduced evolutionary potential. The importance of such a reduction in population size, called a bottleneck, on the microbial diversity and the potential interactive effects on host health remains unexplored. Here we experimentally test these associations by investigating the microbiomes of 50 inbred or non-inbred populations of vinegar flies. We found that restricting the population size constrain the host’s genetic variation and simultaneously decreases the diversity of the microbiome that they harbor, and that both effects were detrimental to host fitness. The microbial communities in inbred host populations were less robust than in their non-inbred counterparts, suggesting that we should increasingly consider the microbiome diversity, which may ultimately influence the health and persistence of threatened species.
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Affiliation(s)
- Michael Ørsted
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- * E-mail:
| | - Erika Yashiro
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Institute for Plant Sciences, Department of Biology, University of Cologne, Cologne, Germany
| | - Ary A. Hoffmann
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Torsten Nygaard Kristensen
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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25
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Zhang L, Yang F, Li T, Dayananda B, Lin L, Lin C. Lessons from the diet: Captivity and sex shape the gut microbiota in an oviparous lizard (
Calotes versicolor
). Ecol Evol 2022; 12:e8586. [PMID: 35169453 PMCID: PMC8840884 DOI: 10.1002/ece3.8586] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
Studies have indicated that the abundance and community structure of gut microbiota are altered by diet. In this study, next‐generation sequencing of the 16S rRNA gene amplicon was performed to evaluate variations in the gut microbiota of wild and captive individuals of both sexes of Calotes versicolor. The results showed that there was a significant sex difference in microbial community structure for wild C. versicolor, Bacteroide was the dominant genus in wild females (WF), whereas Ochrobactrum was the dominant genus in wild males (WM). Acinetobacter and Hymenobacter were the dominant genera in WF, while Clostridium was the dominant genus in captive females (CF). The results indicated that differences in diet between wild and captive C. versicolor also resulted in variations in gut microbiota. Thus, it was not surprising that captivity and sex shape the gut microbiota in C. versicolor. In summary, the fundamental information presented about the gut microbiota of both sexes of wild (and captive females) C. versicolor, indicates that the artificial environments are not suitable for the wild C. versicolor.
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Affiliation(s)
- Lin Zhang
- School of Basic Medical Sciences Hubei University of Chinese Medicine WuhanChina
| | - Fang Yang
- School of Laboratory Medicine Hubei University of Chinese Medicine WuhanChina
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology Shandong University QingdaoChina
| | - Buddhi Dayananda
- School of Agriculture and Food Sciences The University of Queensland Brisbane QLDAustralia
| | - Longhui Lin
- College of Life and Environmental Sciences Hangzhou Normal University HangzhouChina
| | - Chixian Lin
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources Hainan Key Laboratory of Herpetological Research College of Fisheries and Life Science Hainan Tropical Ocean University SanyaChina
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26
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Pannoni SB, Proffitt KM, Holben WE. Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis. Ecol Evol 2022; 12:e8564. [PMID: 35154651 PMCID: PMC8826075 DOI: 10.1002/ece3.8564] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023] Open
Abstract
Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body-fat). We paired a feature-selection algorithm with an LDA-classifier trained on elk differential bacterial abundance (16S-rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave-one-out cross-validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body-fat, sex, and age-class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non-invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome-based monitoring of wildlife populations and supports hypothetical expectations found in host-microbiome theory.
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Affiliation(s)
- Samuel B. Pannoni
- Franke College of Forestry and ConservationUniversity of MontanaMissoulaMontanaUSA
| | | | - William E. Holben
- Cellular, Molecular and Microbial Biology ProgramUniversity of MontanaMissoulaMontanaUSA
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27
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McManus N, Holmes SM, Louis EE, Johnson SE, Baden AL, Amato KR. The gut microbiome as an indicator of habitat disturbance in a Critically Endangered lemur. BMC Ecol Evol 2021; 21:222. [PMID: 34915861 PMCID: PMC8680155 DOI: 10.1186/s12862-021-01945-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Habitat disturbance affects the biology and health of animals globally. Understanding the factors that contribute to the differential responses of animals to habitat disturbance is critical for conservation. The gut microbiota represents a potential pathway through which host responses to habitat disturbance might be mediated. However, a lack of quantitative environmental data in many gut microbiome (GM) studies of wild animals limits our ability to pinpoint mechanisms through which habitat disturbance affects the GM. Here, we examine the impact of anthropogenic habitat disturbance on the diet and GM of the Critically Endangered black-and-white ruffed lemur (Varecia variegata editorum). We collected fecal samples and behavioral data from Varecia occupying habitats qualitatively categorized as primary forest, moderately disturbed forest, and heavily disturbed forest. RESULTS Varecia diet and GM composition differed substantially across sites. Dietary richness predicted GM richness across sites, and overall GM composition was strongly correlated to diet composition. Additionally, the consumption of three specific food items positively correlated to the relative abundances of five microbial strains and one microbial genus across sites. However, diet did not explain all of the GM variation in our dataset, and differences in the GM were detected that were not correlated with diet, as measured. CONCLUSIONS Our data suggest that diet is an important influence on the Varecia GM across habitats and thus could be leveraged in novel conservation efforts in the future. However, other factors such as contact with humans should also be accounted for. Overall, we demonstrate that quantitative data describing host habitats must be paired with GM data to better target the specific mechanisms through which environmental change affects the GM.
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Affiliation(s)
- Nicolette McManus
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Sheila M Holmes
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo, Omaha, NE, 68107, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York, NY, 10065, USA.
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA.
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28
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Toro‐Valdivieso C, Toro F, Stubbs S, Castro‐Nallar E, Blacklaws B. Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii). Microbiologyopen 2021; 10:e1215. [PMID: 34459554 PMCID: PMC8302013 DOI: 10.1002/mbo3.1215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host-microbial-environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 region of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla: Firmicutes (40% ±24), Fusobacteria (30% ±17), Bacteroidetes (22% ±10), Proteobacteria (6% ±4), and Actinobacteria (2% ±3). Alpha diversity was higher in Tierras Blancas. However, location was not found to be a dominant driver of microbial composition. Interestingly, the strongest signal in the data was a negative association between the genera Peptoclostridium and Fusobacterium, which explained 29.7% of the total microbial composition variability between samples. The genus Peptoclostridium has not been reported in other pinniped studies, and its role here is unclear, with interpretation challenging due to a lack of information regarding microbiome functionality in marine mammals. As a first insight into the JFFS fecal microbiome, these results contribute towards our understanding of the natural microbial diversity and composition in free-ranging pinnipeds.
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Affiliation(s)
| | - Frederick Toro
- Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
- Escuela de Medicina VeterinariaFacultad de Recursos Naturales y Medicina VeterinariaUniversidad Santo TomásViña del MarChile
- ONG PanthalassaRed de Estudios de Vertebrados Marinos en ChileSantiagoChile
- Ph.D. Program in Conservation MedicineFacultad de Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | - Samuel Stubbs
- Department of Infectious Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eduardo Castro‐Nallar
- Center for Bioinformatics and Integrative BiologyUniversidad Andres BelloSantiagoChile
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29
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Betts EL, Hoque S, Torbe L, Bailey JR, Ryan H, Toller K, Breakell V, Carpenter AI, Diana A, Matechou E, Gentekaki E, Tsaousis AD. Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles. BIOLOGY 2021; 10:457. [PMID: 34067374 PMCID: PMC8224621 DOI: 10.3390/biology10060457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022]
Abstract
(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.
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Affiliation(s)
- Emma L. Betts
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Sumaiya Hoque
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Lucy Torbe
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Jessica R. Bailey
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Hazel Ryan
- Wildwood Trust, Herne Common, Herne Bay CT6 7LQ, UK; (H.R.); (K.T.); (V.B.)
| | - Karen Toller
- Wildwood Trust, Herne Common, Herne Bay CT6 7LQ, UK; (H.R.); (K.T.); (V.B.)
| | - Vicki Breakell
- Wildwood Trust, Herne Common, Herne Bay CT6 7LQ, UK; (H.R.); (K.T.); (V.B.)
| | - Angus I. Carpenter
- School of Animal, Rural and Environmental Sciences, Brackenhurst Campus, Nottingham Trent University, Nottinghamshire NG1 4FQ, UK;
| | - Alex Diana
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury CT2 7NJ, UK; (A.D.); (E.M.)
| | - Eleni Matechou
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury CT2 7NJ, UK; (A.D.); (E.M.)
| | - Eleni Gentekaki
- School of Science and Human Gut Microbiome for Health Research Unit, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Anastasios D. Tsaousis
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
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30
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Gut microbiota of frugo-folivorous sifakas across environments. Anim Microbiome 2021; 3:39. [PMID: 34006323 PMCID: PMC8132362 DOI: 10.1186/s42523-021-00093-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/04/2021] [Indexed: 12/16/2022] Open
Abstract
Background Captive animals, compared to their wild counterparts, generally harbor imbalanced gut microbiota owing, in part, to their altered diets. This imbalance is particularly striking for folivores that fundamentally rely on gut microbiota for digestion, yet rarely receive sufficient dietary fiber in captivity. We examine the critically endangered Coquerel’s sifaka (Propithecus coquereli), an anatomically specialized, rather than facultative, folivore that consumes a seasonal frugo-folivorous diet in the wild, but is provisioned predominantly with seasonal foliage and orchard vegetables in captivity. Using amplicon and metagenomic sequencing applied to fecal samples collected from two wild and one captive population (each comprising multiple groups), we clarify how dietary variation underlies the perturbational effect of captivity on the structure and function of this species’ gut microbiota. Results The gut microbiota of wild sifakas varied by study population, most notably in community evenness and in the abundance of diet-associated microbes from Prevotellaeceae and Lachnospiraceae. Nevertheless, the differences among wild subjects were minor compared to those evident between wild and captive sifakas: Unusually, the consortia of captive sifakas were the most diverse, but lacked representation of endemic Bacteroidetes and metagenomic capacity for essential amino-acid biosynthesis. Instead, they were enriched for complex fiber metabolizers from the Firmicutes phylum, for archaeal methanogens, and for several metabolic pathways putatively linked to plant fiber and secondary compound metabolism. Conclusions The relatively minor differences in gut microbial structure and function between wild sifaka populations likely reflect regional and/or temporal environmental variability, whereas the major differences observed in captive conspecifics, including the loss of endemic microbes, but gain in low-abundance taxa, likely reflect imbalanced or unstable consortia. Indeed, community perturbation may not necessarily entail decreased community diversity. Moreover, signatures of greater fiber degradation indicate that captive sifakas consume a more fibrous diet compared to their wild counterparts. These results do not mirror those typically reported for folivores and herbivores, suggesting that the direction and strength of captivity-induced ‘dysbiosis’ may not be universal across species with similar feeding strategies. We propose that tailored, species-specific dietary interventions in captivity, aimed at better approximating naturally foraged diets, could functionally ‘rewild’ gut microbiota and facilitate successful management of diverse species. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00093-5.
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31
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Eliades SJ, Brown JC, Colston TJ, Fisher RN, Niukula JB, Gray K, Vadada J, Rasalato S, Siler CD. Gut microbial ecology of the Critically Endangered Fijian crested iguana ( Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes. Ecol Evol 2021; 11:4731-4743. [PMID: 33976843 PMCID: PMC8093715 DOI: 10.1002/ece3.7373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 02/01/2023] Open
Abstract
Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.
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Affiliation(s)
- Samuel J. Eliades
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Joseph C. Brown
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
- Hope Zoo Preservation FoundationKingstonJamaica
| | | | - Robert N. Fisher
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCaliforniaUSA
| | | | - Kim Gray
- San Diego Zoo Wildlife AllianceSan DiegoCaliforniaUSA
| | | | | | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
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32
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Quiroga-González C, Cardenas LAC, Ramírez M, Reyes A, González C, Stevenson PR. Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process. Sci Rep 2021; 11:6522. [PMID: 33753830 PMCID: PMC7985493 DOI: 10.1038/s41598-021-85990-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Microbiome is known to play an important role in the health of organisms and different factors such as diet have been associated with modifications in microbial communities. Differences in the microbiota composition of wild and captive animals has been evaluated; however, variation during a reintroduction process in primates has never been reported. Our aim was to identify changes in the bacterial composition of three individuals of reintroduced woolly monkeys (Lagothrix lagothricha) and the variables associated with such changes. Fecal samples were collected and the V4 region of the 16S rRNA gene was sequenced to determine gut microbial composition and functionality. Individual samples from released individuals showed a higher microbial diversity after being released compared to before liberation, associated with changes in their diet. Beta diversity and functionality analysis showed separation of samples from released and captive conditions and the major factor of variation was the moment of liberation. This study shows that intestinal microbiota varies depending on site conditions and is mainly associated with diet diversity. The intake of food from wild origin by released primates may promote a positive effect on gut microbiota, improving health, and potentially increasing success in reintroduction processes.
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Affiliation(s)
- Camilo Quiroga-González
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia.
| | - Luis Alberto Chica Cardenas
- Grupo de Investigación en Biología Computacional y Ecología Microbiana (BCEM), Max Planck Tandem Research Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
| | - Mónica Ramírez
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Grupo de Investigación en Biología Computacional y Ecología Microbiana (BCEM), Max Planck Tandem Research Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| | - Pablo R Stevenson
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
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33
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Parke EC. Trivial, Interesting, or Overselling? The Microbiome and “What It Means to Be Human”. Bioscience 2021. [DOI: 10.1093/biosci/biab009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Discussions of microbiome research increasingly refer to the microbiome's impact on what it means to be human. These claims are rarely carefully explained or justified. Given the increasing importance of microbiome research across the life sciences, philosophy, and the public sphere, it is worth exercising more care in these discussions. This article offers a guide for doing so. There are many different ways to interpret the details of ambiguous claims about the microbiome and what it means to be human. I discuss some possible interpretations and show how the resulting claims can range from trivial to suggestive of interesting research to controversial and overhyped. I recommend greater caution and clarity in ongoing discussions of microbiome research and its implications.
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Affiliation(s)
- Emily C Parke
- Department of Philosophy, School of Humanities, University of Auckland, Auckland, New Zealand
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34
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Majewska R, Ashworth MP, Bosak S, Goosen WE, Nolte C, Filek K, Van de Vijver B, Taylor JC, Manning SR, Nel R. On Sea Turtle-associated Craspedostauros (Bacillariophyta), with Description of Three Novel Species. JOURNAL OF PHYCOLOGY 2021; 57:199-218. [PMID: 33098095 DOI: 10.1111/jpy.13086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
The current study focuses on four species from the primarily marine diatom genus Craspedostauros that were observed growing attached to numerous sea turtles and sea turtle-associated barnacles from Croatia and South Africa. Three of the examined taxa, C. danayanus sp. nov., C. legouvelloanus sp. nov., and C. macewanii sp. nov., are described based on morphological and, whenever possible, molecular characteristics. The new taxa exhibit characters not previously observed in other members of the genus, such as the presence of more than two rows of cribrate areolae on the girdle bands, shallow perforated septa, and a complete reduction of the stauros. The fourth species, C. alatus, itself recently described from museum sea turtle specimens, is reported for the first time from loggerhead sea turtles rescued in Europe. A 3-gene phylogenetic analysis including DNA sequence data for three sea turtle-associated Craspedostauros species and other marine and epizoic diatom taxa indicated that Craspedostauros is monophyletic and sister to Achnanthes. This study, being based on a large number of samples and animal specimens analyzed and using different preservation and processing methods, provides new insights into the ecology and biogeography of the genus and sheds light on the level of intimacy and permanency in the host-epibiont interaction within the epizoic Craspedostauros species.
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Affiliation(s)
- Roksana Majewska
- Unit for Environmental Sciences and Management, School of Biological Sciences, North-West University, Potchefstroom, 2520, South Africa
- South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, 6140, South Africa
| | - Matt P Ashworth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, 10000, Croatia
| | - William E Goosen
- Centre for High Resolution Transmission Electron Microscopy, Faculty of Science, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Christopher Nolte
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Klara Filek
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, 10000, Croatia
| | - Bart Van de Vijver
- Research Department, Botanic Garden Meise, B-1860, Meise, Belgium
- Department of Biology, University of Antwerp, ECOBE, 2020, Antwerpen, Belgium
| | - Jonathan C Taylor
- Unit for Environmental Sciences and Management, School of Biological Sciences, North-West University, Potchefstroom, 2520, South Africa
- South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, 6140, South Africa
| | - Schonna R Manning
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ronel Nel
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, 6031, South Africa
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35
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Weiss S, Taggart D, Smith I, Helgen KM, Eisenhofer R. Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons). Anim Microbiome 2021; 3:13. [PMID: 33500001 PMCID: PMC7836174 DOI: 10.1186/s42523-021-00074-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 01/08/2021] [Indexed: 01/17/2023] Open
Abstract
Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00074-8.
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Affiliation(s)
- Sesilje Weiss
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - David Taggart
- School of Animal and Veterinary Sciences (Waite), University of Adelaide, Adelaide, South Australia, Australia.,FAUNA Research Alliance, Ltd, PO Box 98, Callaghan, NSW, 2308, Australia
| | - Ian Smith
- School of Animal and Veterinary Sciences (Waite), University of Adelaide, Adelaide, South Australia, Australia.,Zoos South Australia, Frome Rd, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, 1 William St, Sydney, New South Wales, Australia.,Australian Research Council Centre for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. .,Australian Research Council Centre for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia.
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36
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Shi Y, Miao ZY, Su JP, Wasser SK. Shift of Maternal Gut Microbiota of Tibetan Antelope (Pantholops hodgsonii) During the Periparturition Period. Curr Microbiol 2021; 78:727-738. [PMID: 33410953 DOI: 10.1007/s00284-020-02339-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]
Abstract
The maternal gut microbiota can influence and be affected by the substantial physiological changes taking place during the periparturition period. However, little information is known about the changes in the maternal gut microbiota and hormonal variations during this period in nonmodel organisms. Tibetan antelope (Pantholops hodgsonii) provide a unique system to address this issue because their summer migration cycle is synchronized with the periparturition period. Here, we used fecal microbiota as a proxy of gut microbiota. We characterized fecal microbial community of female migratory Tibetan antelope in the late pregnancy and postpartum periods using 16S rRNA gene sequencing and quantified fecal glucocorticoids (GCs) and triiodothyronine (T3) metabolite concentrations through enzyme immunoassays to identify the associations between maternal gut microbiota and physiological changes related with reproduction. We found that the fecal microbiota of Tibetan antelope was dominated by Firmicutes and Bacteroidetes. The microbial composition was significantly altered during the transition from late pregnancy to the postpartum period. Fecal T3 concentration was significantly higher in the postpartum period compared to late pregnancy, whereas GC metabolite concentration did not significantly differ between two reproductive states. We identified six genera (Anaerofustis, Bacteroides, Coprococcus_2, Ruminiclostridium_5, Ruminococcaceae_UCG-007, and Tyzzerella) that were significantly associated with reproductive states. We also found two genera (Christensenellaceae_R-7_group and Rikenellaceae_RC9_gut_group) significantly associated with GC metabolite concentration and two genera (Agathobacter and Papillibacter) significantly associated with T3 metabolite concentration, though these correlations were weak with coefficient values ranging from - 0.007 to 0.03. Our results indicate that many members of the gut microbiota are associated with the physiological changes in the transition from late pregnancy to the postpartum period, likely reflecting the metabolic and immune system dynamics during the periparturition period. This study highlights the importance of integrating microbiota, hormones and migration pattern to study the reproductive health of wildlife. By establishing a baseline of the physiological changes during the migration/periparturition period, we can have a better understanding of the impacts of increasing human activities on the Tibetan Plateau on the reproductive health of Tibetan antelope.
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Affiliation(s)
- Yue Shi
- Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195, USA. .,College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801, USA.
| | - Zi-Yan Miao
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China.,Museum of Natural Resources of Qinghai Province, Xining, 810008, Qinghai, China
| | - Jian-Ping Su
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, Qinghai, China
| | - Samuel K Wasser
- Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195, USA
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37
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Guo W, Ren K, Ning R, Li C, Zhang H, Li D, Xu L, Sun F, Dai M. Fecal microbiota transplantation provides new insight into wildlife conservation. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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38
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Narat V, Amato KR, Ranger N, Salmona M, Mercier-Delarue S, Rupp S, Ambata P, Njouom R, Simon F, Giles-Vernick T, LeGoff J. A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo. Sci Rep 2020; 10:19107. [PMID: 33154444 PMCID: PMC7645722 DOI: 10.1038/s41598-020-75847-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, UMR7206 CNRS/MNHN/Université de Paris, Site du Musée de L'Homme, Paris, France
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, USA
- Humans and the Microbiome, CIFAR, Toronto, Canada
| | - Noémie Ranger
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Maud Salmona
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France
| | | | - Stephanie Rupp
- Department of Anthropology, City University of New York - Lehman College, New York, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Tamara Giles-Vernick
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France.
- Humans and the Microbiome, CIFAR, Toronto, Canada.
| | - Jérôme LeGoff
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France.
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France.
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Shanmuganandam S, Hu Y, Strive T, Schwessinger B, Hall RN. Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia. PeerJ 2020; 8:e9564. [PMID: 32874776 PMCID: PMC7441920 DOI: 10.7717/peerj.9564] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/26/2020] [Indexed: 12/31/2022] Open
Abstract
Background European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. Methods We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms. Results We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.
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Affiliation(s)
- Somasundhari Shanmuganandam
- Research School of Biology, Australian National University, Acton, ACT, Australia.,Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Yiheng Hu
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Tanja Strive
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Centre for Invasive Species Solutions, Bruce, ACT, Australia
| | | | - Robyn N Hall
- Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Centre for Invasive Species Solutions, Bruce, ACT, Australia
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40
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Majewska R, Goosen WE. For Better, For Worse: Manatee-Associated Tursiocola (Bacillariophyta) Remain Faithful to Their Host. JOURNAL OF PHYCOLOGY 2020; 56:1019-1027. [PMID: 32198928 DOI: 10.1111/jpy.12993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
With the advent of more comprehensive research into the microbiome and interactions between animals and their microbiota, new solutions can be applied to address conservation challenges such as husbandry and medical care of captive animals. Although studies on epizoic algae are relatively rare, and the function and role of those mainly photosynthetic organisms in the animal microbiome is not well understood, recent surveys on epizoic diatoms show that some of them exhibit traits of obligate epibionts. This study explores diatom communities on captive-born manatees from the Africarium in Wroclaw, Poland. Light and scanning electron microscopy analyses revealed that skin of all animals sampled was dominated by apochlorotic Tursiocola cf. ziemanii, an epizoic species described recently from Florida manatees, that reached 99,9% of the total diatom abundance. Despite using media with a wide range of salinity (0-34), the isolated Tursiocola cells did not grow, whereas the normally pigmented Planothidium sp., that was only occasionally found on the animal substratum, survived in all culture media tested. Our observations provide direct evidence that manatee-associated Tursiocola endure the dramatic salinity changes that occur regularly during their host life cycle, and can thrive in an artificial captive setting, if the manatee substratum is available. The impact of practices and routines used by the Africarium on manatee-associated diatoms, as well as ultrastructure of areolae in Tursiocola, are briefly discussed.
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Affiliation(s)
- Roksana Majewska
- Unit for Environmental Sciences and Management, School of Biological Sciences, North-West University, Potchefstroom, South Africa
- South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, South Africa
| | - William E Goosen
- Centre for High Resolution Transmission Electron Microscopy, Faculty of Science, Nelson Mandela University, Port Elizabeth, South Africa
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41
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Rebollar EA, Martínez-Ugalde E, Orta AH. The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.167] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Emanuel Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Alberto H. Orta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
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42
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Chong R, Cheng Y, Hogg CJ, Belov K. Marsupial Gut Microbiome. Front Microbiol 2020; 11:1058. [PMID: 32547513 PMCID: PMC7272691 DOI: 10.3389/fmicb.2020.01058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.
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Affiliation(s)
- Rowena Chong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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43
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Budd K, Gunn JC, Finch T, Klymus K, Sitati N, Eggert LS. Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna ( Loxodonta africana) and forest elephants ( L. cyclotis). Ecol Evol 2020; 10:5637-5650. [PMID: 32607180 PMCID: PMC7319146 DOI: 10.1002/ece3.6305] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6-5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop-raiding versus noncrop-raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.
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Affiliation(s)
- Kris Budd
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Tabitha Finch
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Vermont Genetics NetworkUniversity of VermontBurlingtonVTUSA
| | - Katy Klymus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Columbia Environmental Research CenterUnited States Geological SurveyColumbiaMOUSA
| | - Noah Sitati
- World Wide Fund for NatureDar es SalaamTanzania
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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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; 10:4677-4690. [PMID: 32551052 PMCID: PMC7297780 DOI: 10.1002/ece3.6221] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes can have important impacts on their host's survival. Captive breeding programs for endangered species include periods of captivity that can ultimately have an impact on reintroduction success. No study to date has investigated the impacts of captive diet on the gut microbiota during the relocation process of generalist species. This study simulated a captive breeding program with white-footed mice (Peromyscus leucopus) to describe the variability in gut microbial community structure and composition during captivity and relocation in their natural habitat, and compared it to wild individuals. Mice born in captivity were fed two different diets, a control with dry standardized pellets and a treatment with nonprocessed components that reflect a version of their wild diet that could be provided in captivity. The mice from the two groups were then relocated to their natural habitat. Relocated mice that had the treatment diet had more phylotypes in common with the wild-host microbiota than mice under the control diet or mice kept in captivity. These results have broad implications for our understanding of microbial community dynamics and the effects of captivity on reintroduced animals, including the potential impact on the survival of endangered species. This study demonstrates that ex situ conservation actions should consider a more holistic perspective of an animal's biology including its microbes.
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Affiliation(s)
- Pauline van Leeuwen
- Department of BiologyLaurentian UniversitySudburyONCanada
- Conservation Genetics LaboratoryUniversity of LiègeLiègeBelgium
| | - Nadia Mykytczuk
- Vale Living with Lakes CentreLaurentian UniversitySudburyONCanada
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45
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Becker AAMJ, Harrison SWR, Whitehouse-Tedd G, Budd JA, Whitehouse-Tedd KM. Integrating Gut Bacterial Diversity and Captive Husbandry to Optimize Vulture Conservation. Front Microbiol 2020; 11:1025. [PMID: 32523573 PMCID: PMC7261900 DOI: 10.3389/fmicb.2020.01025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/27/2020] [Indexed: 02/01/2023] Open
Abstract
Endangered species recovery plans often include captive breeding and reintroduction, but success remains rare. Critical for effective recovery is an assessment of captivity-induced changes in adaptive traits of reintroduction candidates. The gut microbiota is one such trait and is particularly important for scavengers exposed to carcass microbiomes. We investigated husbandry-associated differences in the gut microbiota of two Old World vulture species using 16S RNA gene amplicon sequencing. Increased abundance of Actinobacteria occurred when vultures were fed quail but not rat or chicken. Conversely, diet preparation (sanitization) had no effect, although bacterial diversity differed significantly between vulture species, likely reflective of evolved feeding ecologies. Whilst the relative lack of influence of a sanitized diet is encouraging, changes in bacterial abundance associated with the type of prey occurred, representing a dietary influence on host–microbiome condition warranting consideration in ex situ species recovery plans. Incorporation of microbiome research in endangered species management, therefore, provides an opportunity to refine conservation practice.
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Affiliation(s)
- Anne A M J Becker
- One Health Center for Zoonoses and Tropical Veterinary Medicine and Center for Conservation Medicine and Ecosystem Health, Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Stephen W R Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, United Kingdom
| | | | - Jane A Budd
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
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46
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Ni Q, He X, Zeng B, Meng X, Xu H, Li Y, Yang M, Li D, Yao Y, Zhang M, Li Y, Fan X, Yang D, Xie M. Variation in Gut Microbiota of Captive Bengal Slow Lorises. Curr Microbiol 2020; 77:2623-2632. [PMID: 32440808 DOI: 10.1007/s00284-020-02035-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
Abstract
Gastrointestinal microbiome plays an important role in animal metabolism, immune system and pathology associated with health and disease. Many wild slow lorises were confiscated from illegal trade into captivities and experienced a range of changes in living environment and diet. Microbiome analysis contributes to improving captive management by identifying the alteration in their gastrointestinal microbial communities and aiding in determining the factors affecting the health of captive slow lorises. The fecal samples of eighteen Bengal slow lorises (Nycticebus bengalensis) were used to compare gut microbiota from four rescue centers located in Dehong, Gejiu, Nanning and Puer cities of China. The results showed a significant site-dependent difference in microbial community diversity. Similar to other Lorisinae species, the Phyla including Bacteroidetes, Firmicutes and Proteobacteria dominated their gut microbiome composition. The Gejiu group exhibited a higher overall diversity and the unique OTUs, which is resulted from long-term isolated husbandry and heavy human disturbances. The scarcity of gums in the captive diet was likely to cause a lower abundance of Prevotella associated with soluble fiber degradation. The variation of intestinal microbiota in different environments highlights the necessity to improve feed preparation and husbandry management for the captive Bengal slow lorises.
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Affiliation(s)
- Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China. .,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
| | - Xin He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiangyun Meng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China.
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Kambe J, Sasaki Y, Inoue R, Tomonaga S, Kinjo T, Watanabe G, Jin W, Nagaoka K. Analysis of infant microbiota composition and the relationship with breast milk components in the Asian elephant (Elephas maximus) at the zoo. J Vet Med Sci 2020; 82:983-989. [PMID: 32350162 PMCID: PMC7399312 DOI: 10.1292/jvms.20-0190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The prevention of diseases through health control is essential at zoos. Here, we investigated the gut microbiota formation during infancy in an Asian elephant and compared the
composition between infant and mother. Besides, we analyzed the components of breast milk and examined the correlation with the infant gut microbiota. Analysis revealed the gut
microbiota of the infant contained high amount of Lactobacillales and its diversity was relatively low compared to that of the mother. We found several milk
components, showed a positive correlation with the change of Lactobacillales. The present study revealed the mechanism of gut microbiota formation during infancy
in an Asian elephant and provides important insights into the health control of Asian elephants in zoos.
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Affiliation(s)
- Jun Kambe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Yu Sasaki
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Sciences, Setsunan University, Osaka 573-0101, Japan
| | - Shozo Tomonaga
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Teruo Kinjo
- Okinawa Zoo Animal Hospital, Okinawa Zoo and Museum, Okinawa 904-0021, Japan
| | - Gen Watanabe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Wanzhu Jin
- Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen West Road, Chaoyang, Beijing, China
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
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48
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Tang GS, Liang XX, Yang MY, Wang TT, Chen JP, Du WG, Li H, Sun BJ. Captivity Influences Gut Microbiota in Crocodile Lizards ( Shinisaurus crocodilurus). Front Microbiol 2020; 11:550. [PMID: 32390955 PMCID: PMC7190797 DOI: 10.3389/fmicb.2020.00550] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022] Open
Abstract
Captivity is an important measure for conservation of an endangered species, and it is becoming a hot topic in conservation biology, which integrates gut microbiota and endangered species management in captivity. As an ancient reptile, the crocodile lizard (Shinisaurus crocodilurus) is facing extreme danger of extinction, resulting in great significance to species conservation in the reserve. Thus, it is critical to understand the differences in gut microbiota composition between captive and wild populations, as it could provide fundamental information for conservative management of crocodile lizards. Here, fecal samples of crocodile lizards were collected from two wild and one captive populations with different ages (i.e., juveniles and adults) and were analyzed for microbiota composition by 16S ribosomal RNA (rRNA) gene amplicon sequencing. This study showed that the lizard gut microbiota was mainly composed of Firmicutes and Proteobacteria. The gut microbiota composition of crocodile lizard did not differ between juveniles and adults, as well as between two wild populations. Interestingly, captivity increased community richness and influenced community structures of gut microbiota in crocodile lizards, compared with wild congeners. This was indicated by higher abundances of the genera Epulopiscium and Glutamicibacter. These increases might be induced by complex integration of simple food resources or human contact in captivity. The gut microbiota functions of crocodile lizards are primarily enriched in metabolism, environmental information processing, genetic information processing, and cellular processes based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This study provides fundamental information about the gut microbiota of crocodile lizards in wild and captive populations. In the future, exploring the relationship among diet, gut microbiota, and host health is necessary for providing animal conservation strategies.
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Affiliation(s)
- Guo-Shuai Tang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Xi Liang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Meng-Yuan Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ting-Ting Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center of Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jin-Ping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Wei-Guo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huan Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Bao-Jun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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49
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Zhang Z, Hu T, Lu G, Zhu L. Lessons from bamboo-eating pandas and their gut microbiome: Gut microbiome flow and applications. Evol Appl 2020; 13:615-619. [PMID: 32211055 PMCID: PMC7086052 DOI: 10.1111/eva.12915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/26/2022] Open
Abstract
The giant panda is one of the most endangered mammals in the world, and many studies have revealed their evolutionary adaptation to the local environment (e.g., dietary cellulose and cyanide) on the evidences from population genetics and their gut microbiome. Here, based on the results of our analysis of the giant panda gut microbiome, we concluded that instability and resilience are the two primary characteristics of the giant panda gut microbiome. This basic information may have an impact on giant panda conservation, as well the management of other animal species.
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Affiliation(s)
- Zheng Zhang
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Ting Hu
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Guoqing Lu
- Department of Biology University of Nebraska Omaha Omaha NE USA
| | - Lifeng Zhu
- College of Life Sciences Nanjing Normal University Nanjing China
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50
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McKnight DT, Zenger KR, Alford RA, Huerlimann R. Microbiome diversity and composition varies across body areas in a freshwater turtle. MICROBIOLOGY-SGM 2020; 166:440-452. [PMID: 32213245 DOI: 10.1099/mic.0.000904] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is increasing recognition that microbiomes are important for host health and ecology, and understanding host microbiomes is important for planning appropriate conservation strategies. However, microbiome data are lacking for many taxa, including turtles. To further our understanding of the interactions between aquatic microbiomes and their hosts, we used next generation sequencing technology to examine the microbiomes of the Krefft's river turtle (Emydura macquarii krefftii). We examined the microbiomes of the buccal (oral) cavity, skin on the head, parts of the shell with macroalgae and parts of the shell without macroalgae. Bacteria in the phyla Proteobacteria and Bacteroidetes were the most common in most samples (particularly buccal samples), but Cyanobacteria, Deinococcus-thermus and Chloroflexi were also common (particularly in external microbiomes). We found significant differences in community composition among each body area, as well as significant differences among individuals. The buccal cavity had lower bacterial richness and evenness than any of the external microbiomes, and it had many amplicon sequence variants (ASVs) with a low relative abundance compared to other body areas. Nevertheless, the buccal cavity also had the most unique ASVs. Parts of the shell with and without algae also had different microbiomes, with particularly obvious differences in the relative abundances of the families Methylomonaceae, Saprospiraceae and Nostocaceae. This study provides novel, baseline information about the external microbiomes of turtles and is a first step in understanding their ecological roles.
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Affiliation(s)
- Donald T McKnight
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.,Present address: School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Kyall R Zenger
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Ross A Alford
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Roger Huerlimann
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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