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Klinhom S, Sriwichaiin S, Kerdphoo S, Khonmee J, Chattipakorn N, Chattipakorn SC, Thitaram C. Characteristics of gut microbiota in captive Asian elephants (Elephas maximus) from infant to elderly. Sci Rep 2023; 13:23027. [PMID: 38155244 PMCID: PMC10754835 DOI: 10.1038/s41598-023-50429-1] [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: 08/07/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
Gut microbiota play an important role in the health and disease of Asian elephants, however, its characteristics at each stage of life have not been thoroughly investigated in maintaining and regulating health of elephants. This study, therefore, aimed to characterize the profiles of the gut microbiota of captive Asian elephants from infants to the elderly. Gut microbiota were identified by 16S rRNA sequencing from the feces of captive Asian elephants with varying age groups, including infant calves, suckling calves, weaned calves, subadult and adult elephants, and geriatric elephants. The diversity of the gut microbiota was lowest in infants, stable during adulthood, and slightly decreased in the geriatric period. The gut microbiota of the infant elephants was dominated by milk-fermenting taxa including genus Bifidobacterium of family Bifidobacteriaceae together with genus Akkermansia. The fiber-fermenting taxa such as Lachnospiraceae_NK3A20_group were found to be increased in suckling elephants in differential abundance analysis by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). The gut microbiota profiles after weaning until the adult period has been uniform as indicated by no significant differences in beta diversity between groups. However, the composition of the gut microbiota was found to change again in geriatric elephants. Understanding of the composition of the gut microbiota of captive Asian elephants at various life stages could be beneficial for promoting good health throughout their lifespan, as well as ensuring the welfare of captive elephants.
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Affiliation(s)
- Sarisa Klinhom
- Center of Elephant and Wildlife Health, Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Sirawit Sriwichaiin
- Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sasiwan Kerdphoo
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jaruwan Khonmee
- Center of Elephant and Wildlife Health, Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
- Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriporn C Chattipakorn
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Chatchote Thitaram
- Center of Elephant and Wildlife Health, Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.
- Elephant, Wildlife and Companion Animals Research Group, Chiang Mai University, Chiang Mai, 50100, Thailand.
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Klinsawat W, Uthaipaisanwong P, Jenjaroenpun P, Sripiboon S, Wongsurawat T, Kusonmano K. Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing. Sci Rep 2023; 13:17685. [PMID: 37848699 PMCID: PMC10582034 DOI: 10.1038/s41598-023-44981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.
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Affiliation(s)
- Worata Klinsawat
- Conservation Ecology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supaphen Sripiboon
- Department of Large Animal and Wildlife Clinical Science, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Kanthida Kusonmano
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
- Bioinformatics and Systems Biology Program, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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Li X, Sun P, Gong L, Shi W, Xiang Z, Li M, Su L, Qin C. Bacteroides rhinocerotis sp. nov., isolated from the fresh feces of rhinoceros in Beijing Zoo. Arch Microbiol 2023; 205:169. [PMID: 37017778 DOI: 10.1007/s00203-023-03513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/06/2023]
Abstract
A Gram-negative strain, anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain named as NGMCC 1.200684 T was isolated from the fresh feces of rhinoceros in Beijing Zoo. Based on 16S rRNA gene sequences, phylogenetic analysis indicated that strain NGMCC 1.200684 T belonged to the genus Bacteroides and was most strongly related to the type strain of Bacteroides uniformis ATCC 8492 T (96.88%). The G + C content of the genomic DNA was determined to be 46.62%. Between strains NGMCC 1.200684 T and B. uniformis ATCC 8492 T, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 93.89 and 67.60%, respectively. Strain NGMCC 1.200684 T can produce acid from fermentation of several substrates, including glucose, mannitol, lactose, saccharose, maltose, salicin, xylose, cellobiose, mannose, raffinose, sorbitol, trehalose, D-galactose, and maltotriose. The major cellular fatty acids (> 10%) were identified as anteiso-C15:0, iso-C15:0, iso-C14:0, and iso-C17:0 3-OH. The polar lipid profiles of strain NGMCC 1.200684 T were determined to contain diphosphatidyl glycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, and two unknown amino-phospholipids. Based on phenotypic, phylogenetic, and chemotaxonomic characteristics, a novel species of the genus Bacteroides, Bacteroides rhinocerotis sp. nov. is proposed. The type strain is NGMCC 1.200684 T (= CGMCC 1.18013 T = JCM 35702 T).
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Affiliation(s)
- Xue Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Peilin Sun
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Liang Gong
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Weixiong Shi
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Zhiguang Xiang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Ming Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Technology Support Platform, Beijing, 100193, China
| | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China.
- Changping National Laboratory (CPNL), Beijing, 102299, China.
| | - Chuan Qin
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
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Common SM, Yun Y, Silva-Fletcher A, Thitaram C, Janyamethakul T, Khammesri S, Molenaar FM. Developing a non-invasive method of detecting elephant endotheliotropic herpesvirus infections using faecal samples. Vet Rec 2021; 190:e833. [PMID: 34472109 DOI: 10.1002/vetr.833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/07/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Elephant endotheliotropic herpesvirus (EEHV)-associated haemorrhagic disease (EEHV-HD) is a leading cause of death in Asian elephant calves across the world. Cases of EEHV-HD have been detected in free-living calves through post-mortem examination (PME) indicating the presence of the virus in the wild. In the absence of a non-invasive sampling method, little research into free-living populations has been possible. This study aimed to provide evidence that faeces can be used as a non-invasive sampling method for the detection of EEHV excretion using quantitative polymerase chain reaction. METHODS Serial saliva swabs and faecal samples were taken from five captive Asian elephants in Thailand over 12 weeks. To ensure the presence of detectable elephant DNA within the sample, qPCR was run for amplification of the Asian elephant tumour necrosis factor (TNF-α) gene, EEHV1 and EEHV4. RESULTS Of 28 sample pairs, seven saliva samples were positive for EEHV, of which two had paired positive faecal samples. CONCLUSIONS This study presents the first evidence that EEHV is excreted in faeces at detectable levels. This method may in future be used for improved understanding of the epidemiology of EEHV in free-living elephant populations, as well as detection of EEHV excretion in captive herds.
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Affiliation(s)
- Sophie M Common
- Institute of Zoology, Zoological Society of London, Regents Park, London, NW8 7LS, UK.,The Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - Yaoprapa Yun
- Center of Elephant and Wildlife Research, Faculty of Veterinary Medicine, Chiang Mai University (FVM-CMU), Chiang Mai, Thailand
| | | | - Chatchote Thitaram
- Center of Elephant and Wildlife Research, Faculty of Veterinary Medicine, Chiang Mai University (FVM-CMU), Chiang Mai, Thailand
| | | | - Siripat Khammesri
- Center of Elephant and Wildlife Research, Faculty of Veterinary Medicine, Chiang Mai University (FVM-CMU), Chiang Mai, Thailand
| | - Fieke M Molenaar
- Whipsnade Zoo, Zoological Society of London, Dunstable, Bedfordshire, UK
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Eveno M, Salouhi A, Belguesmia Y, Bazinet L, Gancel F, Fliss I, Drider D. Biodiversity and Phylogenetic Relationships of Novel Bacteriocinogenic Strains Isolated from Animal's Droppings at the Zoological Garden of Lille, France. Probiotics Antimicrob Proteins 2021; 13:218-228. [PMID: 32388703 DOI: 10.1007/s12602-020-09657-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This study aimed at exploring droppings of animals living in captivity in the zoological garden (Zoo) of Lille (France), as novel sources of bacteriocinogenic strains. A collection of 295 bacterial isolates was constituted from droppings of capybara, alpaca, muntjac, zebra, tapir, rhinoceros, binturong, armadillo, saki monkey and cockatoo. Of 295 isolates, 51 exhibited antagonism against a panel of pathogenic target bacteria like Escherichia coli MC4100, Clostridium perfringens DSM 756 and Salmonella enterica subsp. enterica Newport ATCC6962. Remarkably, within this collection, only 2 Gram-negative bacilli exhibited activity against E. coli MC4100 strain used as target organism. Then, the 16S rDNA sequencing revealed these thereafter cited species, Pediococcus pentosaceus, Weissella cibaria, E. coli, Lactobacillus reuteri, Enterococcus hirae and Enterococcus faecalis. Characterization of this antagonism has revealed 11 strains able producing extracellular protease-sensitive inhibitory compounds. These strains included E. coli ICVB442 and ICVB443, Ent. faecalis ICVB472, ICVB474, ICVB477 ICVB479, ICVB481, ICVB497 and ICVB501 and Ped. pentosaceus ICVB491 and ICVB492. The genomes of the 5 most promising bacteriocinogenic strains were sequenced and analysed with Bagel4 software. Afterwards, this bioinformatics analysis permitted to locate genes encoding bacteriocins like colicin Y (E. coli), enterocin 1071A, enterocin 107 B (Ent. faecalis) and penocin A (Ped. pentosaceus), associating the above-mentioned antibacterial activity of proteinaceous nature to possible production of bacteriocins. All these results enabled us to select different bacteriocinogenic strains for a further characterization in terms of beneficial traits.
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Affiliation(s)
- Mégane Eveno
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, F-59000, Lille, France.,Pavillon Paul-Comtois, Université Laval, 2425 Rue de l'Agriculture, Local 1413, Québec, Canada
| | - Amine Salouhi
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, F-59000, Lille, France
| | - Yanath Belguesmia
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, F-59000, Lille, France
| | - Laurent Bazinet
- Pavillon Paul-Comtois, Université Laval, 2425 Rue de l'Agriculture, Local 1413, Québec, Canada
| | - Frédérique Gancel
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, F-59000, Lille, France
| | - Ismail Fliss
- Pavillon Paul-Comtois, Université Laval, 2425 Rue de l'Agriculture, Local 1413, Québec, Canada
| | - Djamel Drider
- Pavillon Paul-Comtois, Université Laval, 2425 Rue de l'Agriculture, Local 1413, Québec, Canada. .,Université de Lille, Cité Scientifique/Avenue Paul Langevin, Polytech-Lille, Bureau C315, 59655, Villeneuve d'Ascq, France.
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Segawa T, Fukuchi S, Bodington D, Tsuchida S, Mbehang Nguema PP, Mori H, Ushida K. Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior. Microorganisms 2019; 7:microorganisms7040099. [PMID: 30987363 PMCID: PMC6518056 DOI: 10.3390/microorganisms7040099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/18/2023] Open
Abstract
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan.
| | - Dylan Bodington
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
| | | | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
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Thoemmes MS, Stewart FA, Hernandez-Aguilar RA, Bertone MA, Baltzegar DA, Borski RJ, Cohen N, Coyle KP, Piel AK, Dunn RR. Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180382. [PMID: 29892462 PMCID: PMC5990838 DOI: 10.1098/rsos.180382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we consider the microbes and arthropods found in chimpanzee beds, relative to the surrounding environment (n = 41 and 15 beds, respectively). Based on the study of human homes, we hypothesized that the microbes found in chimpanzee beds would be less diverse than those on nearby branches and leaves and that their beds would be primarily composed of body-associated organisms. However, we found that differences between wet and dry seasons and elevation above sea level explained nearly all of the observed variation in microbial diversity and community structure. While we can identify the presence of a chimpanzee based on the assemblage of bacteria, the dominant signal is that of environmental microbes. We found just four ectoparasitic arthropod specimens, none of which appears to be specialized on chimpanzees or their structures. These results suggest that the life to which chimpanzees are exposed while in their beds is predominately the same as that of the surrounding environment.
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Affiliation(s)
- Megan S. Thoemmes
- Department of Applied Ecology and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
| | - Fiona A. Stewart
- Ugalla Primate Project, Katavi Region, Tanzania
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - R. Adriana Hernandez-Aguilar
- Ugalla Primate Project, Katavi Region, Tanzania
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew A. Bertone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - David A. Baltzegar
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Genomic Sciences Laboratory, Office of Research, Innovation and Economic Development, North Carolina State University, Raleigh, NC, USA
| | - Russell J. Borski
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Naomi Cohen
- Ugalla Primate Project, Katavi Region, Tanzania
| | - Kaitlin P. Coyle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Alexander K. Piel
- Ugalla Primate Project, Katavi Region, Tanzania
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Robert R. Dunn
- Department of Applied Ecology and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
- The Center for Macroecology, Ecology and Conservation, Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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