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Sariyati NH, Othman N, Abdullah-Fauzi NAF, Chan E, Md-Zain BM, Karuppannan KV, Abdul-Latiff MAB. Characterizing the gastrointestinal microbiome diversity in endangered Malayan Siamang (Symphalangus syndactylus): Insights into group composition, age variability and sex-related patterns. J Med Primatol 2024; 53:e12730. [PMID: 39148344 DOI: 10.1111/jmp.12730] [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: 04/14/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus. METHODS This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region. RESULTS A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut. CONCLUSIONS This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.
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Affiliation(s)
- Nur Hartini Sariyati
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Eddie Chan
- Treks Event Sdn Bhd, Lot AW/G5.00, GF, Awana Hotel Genting Highlands Resort, Genting Highlands, Pahang, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
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Tingga RCT, Gani M, Mohd-Ridwan AR, Aifat NR, Matsuda I, Md-Zain BM. Gut microbial assessment among Hylobatidae at the National Wildlife Rescue Centre, Peninsular Malaysia. J Vet Sci 2024; 25:25.e65. [PMID: 39231790 DOI: 10.4142/jvs.23312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/04/2024] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
IMPORTANCE Recent developments in genetic analytical techniques have enabled the comprehensive analysis of gastrointestinal symbiotic bacteria as a screening tool for animal health conditions, especially the endangered gibbons at the National Wildlife Rescue Centre (NWRC). OBJECTIVE High-throughput sequencing based on 16S ribosomal RNA genes was used to determine the baseline gut bacterial composition and identify potential pathogenic bacteria among three endangered gibbons housed in the NWRC. METHODS Feces were collected from 14 individuals (Hylobates lar, n = 9; Hylobates agilis, n = 4; and Symphalangus syndactylus, n = 1) from March to November 2022. Amplicon sequencing were conducted by targeting V3-V4 region. RESULTS The fecal microbial community of the study gibbons was dominated by Bacteroidetes and Firmicutes (phylum level), Prevotellaceae and Lachnospiraceae/Muribaculaceae (family level), and Prevotella (and its subgroups) (genera level). This trend suggests that the microbial community composition of the study gibbons differed insignificantly from previously reported conspecific or closely related gibbon species. CONCLUSIONS AND RELEVANCE This study showed no serious health problems that require immediate attention. However, relatively low alpha diversity and few potential bacteria related to gastrointestinal diseases and streptococcal infections were detected. Information on microbial composition is essential as a guideline to sustain a healthy gut condition of captive gibbons in NWRC, especially before releasing this primate back into the wild or semi-wild environment. Further enhanced husbandry environments in the NWRC are expected through continuous health monitoring and increase diversity of the gut microbiota through diet diversification.
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Affiliation(s)
- Roberta Chaya Tawie Tingga
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan 94300, Malaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks Peninsular Malaysia (PERHILITAN), Kuala Lumpur 56100, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan 94300, Malaysia
| | - Nor Rahman Aifat
- Faculty of Tropical Forestry, Universiti Malaysia Sabah (UMS), Kota Kinabalu 88400, Malaysia
| | - Ikki Matsuda
- Wildlife Research Center of Kyoto University, Kyoto 606-8203, Japan
- Chubu Institute for Advanced Studies, Chubu University, Kasugai 4878501, Japan
- Chubu University Academy of Emerging Sciences, Kasugai 4878501, Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah (UMS), Kota Kinabalu 88400, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
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Jose L, Lee W, Hanya G, Tuuga A, Goossens B, Tangah J, Matsuda I, Kumar VS. Gut microbial community in proboscis monkeys ( Nasalis larvatus): implications for effects of geographical and social factors. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231756. [PMID: 39050721 PMCID: PMC11265907 DOI: 10.1098/rsos.231756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/23/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024]
Abstract
Recent technological advances have enabled comprehensive analyses of the previously uncharacterized microbial community in the gastrointestinal tracts of numerous animal species; however, the gut microbiota of several species, such as the endangered proboscis monkey (Nasalis larvatus) examined in this study, remains poorly understood. Our study sought to establish the first comprehensive data on the gut microbiota of free-ranging foregut-fermenting proboscis monkeys and to determine how their microbiota are affected locally by environmental factors, i.e. geographical distance, and social factors, i.e. the number of adult females within harem groups and the number of adults and subadults within non-harem groups, in a riverine forest in Sabah, Malaysian Borneo. Using 16S rRNA gene sequencing of 264 faecal samples collected from free-ranging proboscis monkeys, we demonstrated the trend that their microbial community composition is not particularly distinctive compared with other foregut- and hindgut-fermenting primates. The microbial alpha diversity was higher in larger groups and individuals inhabiting diverse vegetation (i.e. presumed to have a diverse diet). For microbial beta diversity, some measures were significant, showing higher values with larger geographical distances between samples. These results suggest that social factors such as increased inter-individual interactions, which can occur with larger groups, as well as physical distances between individuals or differences in dietary patterns, may affect the gut microbial communities.
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Affiliation(s)
- Lilian Jose
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah88400, Malaysia
| | - Wanyi Lee
- National Taiwan University, Taipei10617, Taiwan
- Center for Ecological Research, Kyoto University, Inuyama484-8506, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama484-8506, Japan
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu, Sabah88100, Malaysia
| | - Benoit Goossens
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu, Sabah88100, Malaysia
- Danau Girang Field Centre, Sabah Wildlife Department, Wisma Muis, Kota Kinabalu, Sabah88100, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, CardiffCF10 3AX, UK
| | - Joseph Tangah
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - Ikki Matsuda
- Wildlife Research Center of Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto606-8203, Japan
- Chubu Institute for Advanced Studies, Chubu University, 1200, Matsumoto-cho, Kasugai-shi, Aichi487-8501, Japan
- Chubu University Academy of Emerging Sciences, 1200, Matsumoto-cho, Kasugai-shi, Aichi487-8501, Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah88400, Malaysia
| | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah88400, Malaysia
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Kondo K, Suzuki M, Amadaira M, Araki C, Watanabe R, Murakami K, Ochiai S, Ogura T, Hayakawa T. Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas. PeerJ 2024; 12:e17385. [PMID: 38818452 PMCID: PMC11138522 DOI: 10.7717/peerj.17385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Background Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection. Methods Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala's gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection. Results and Discussion This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection. Conclusion We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.
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Affiliation(s)
- Kotaro Kondo
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mirei Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mana Amadaira
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Chiharu Araki
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Rie Watanabe
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | | | | | - Tadatoshi Ogura
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [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: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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Bi X, Zhou L, Zhang JJ, Feng S, Hu M, Cooper DN, Lin J, Li J, Wu DD, Zhang G. Lineage-specific accelerated sequences underlying primate evolution. SCIENCE ADVANCES 2023; 9:eadc9507. [PMID: 37262186 PMCID: PMC10413682 DOI: 10.1126/sciadv.adc9507] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. Here, we investigated the evolutionary landscape of lineage-specific accelerated regions (LinARs) across 49 primate species. Genomic comparison with dense taxa sampling of primate species significantly improved LinAR detection accuracy and revealed many novel human LinARs associated with brain development or disease. Our study also yielded detailed maps of LinARs in other primate lineages that may have influenced lineage-specific phenotypic innovation and adaptation. Functional experimentation identified gibbon LinARs, which could have participated in the developmental regulation of their unique limb structures, whereas some LinARs in the Colobinae were associated with metabolite detoxification which may have been adaptive in relation to their leaf-eating diet. Overall, our study broadens knowledge of the functional roles of LinARs in primate evolution.
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Affiliation(s)
- Xupeng Bi
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Long Zhou
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shaohong Feng
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Mei Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Jiangwei Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jiali Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Suzuki-Hashido N, Tsuchida S, Azumano A, Goossens B, Saldivar DAR, Stark DJ, Tuuga A, Ushida K, Matsuda I. Isolation of Bacteria from Freeze-Dried Samples and the Functional Characterization of Species-Specific Lactic Acid Bacteria with a Comparison of Wild and Captive Proboscis Monkeys. Microorganisms 2023; 11:1458. [PMID: 37374963 DOI: 10.3390/microorganisms11061458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Previously, we isolated a novel lactic acid bacteria species (Lactobacillus nasalidis) from the fresh forestomach contents of a captive proboscis monkey (Nasalis larvatus) in a Japanese zoo. In this study, we isolated two strains of L. nasalidis from the freeze-dried forestomach contents of a wild proboscis monkey inhabiting a riverine forest in Malaysia. The samples had been stored for more than six years. Phenotypic analysis showed that strains isolated from the wild individual had more diverse sugar utilization and lower salt tolerance than strains previously isolated from the captive counterpart. These phenotypic differences are most likely induced by feeding conditions; wild individuals consume a wide variety of natural food, unlike their zoo-raised counterparts that consume formula feed with sodium sufficiency. Since 16s rRNA sequences of L. nasalidis were detected in the previously created 16S rRNA libraries of wild, provisioned, and captive proboscis monkeys in Malaysia and Japan, L. nasalidis may be an essential bacterium of the foregut microbial community of the proboscis monkey. The currently established method for the isolation of gut bacteria from freeze-dried samples under storage will be applicable to many already-stored precious samples.
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Affiliation(s)
- Nami Suzuki-Hashido
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku 102-0083, Tokyo, Japan
| | - Sayaka Tsuchida
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | | | - Benoit Goossens
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Diana A Ramirez Saldivar
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Danica J Stark
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Kazunari Ushida
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | - Ikki Matsuda
- Wildlife Research Center, Kyoto University, Sakyo-ku 606-8203, Kyoto, Japan
- Academy of Emerging Sciences, Chubu University, Kasugai 487-8501, Aichi, Japan
- Chubu Institute for Advanced Studies, Chubu University, Kasugai 487-8501, Aichi, Japan
- Institute for Tropical Biology and Conservation, University Malaysia Sabah, Kota Kinabalu 88100, Malaysia
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Mori R, Hayakawa T, Hirayama M, Ozawa F, Yoshihara H, Goto S, Kitaori T, Ozaki Y, Sugiura-Ogasawara M. Cervicovaginal microbiome in patients with recurrent pregnancy loss. J Reprod Immunol 2023; 157:103944. [PMID: 37060795 DOI: 10.1016/j.jri.2023.103944] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/18/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
Abstract
There have been few studies concerning an association between unexplained recurrent pregnancy loss (RPL) and the microbiome. A recent study including 67 patients demonstrated that an increase in Ureaplasma species in the endometrium raised the risk of miscarriage with an euploid karyotype. While endometrial sampling is invasive, cervicovaginal sampling is not. We compared vaginal and cervical microbiomes with a 16 S ribosomal RNA sequence between 88 patients with unexplained RPL and 17 healthy women with no history of miscarriage. We prospectively assessed risk factors for maternal colonization at a subsequent miscarriage without an aneuploid karyotype in patients. Cervicovaginal bacteria were dominated by Lactobacillus iners, Gardnerella vaginalis, Atopobium vaginae and Bifidobacterium breve in Japanese population. The proportions of Delftia and unknown bacteria in the cervix were significantly higher in patients with RPL than in controls. Streptococcus, Microbacterium, Delftia, Anaerobacillus and Chloroplast in the cervix were significantly higher in patients with a history of chorioamnionitis compared to the controls. The abundance of Cutibacterium and Anaerobacillus in the cervix was significantly higher in patients who had subsequently miscarried compared to those who gave birth. The miscarriage rate in patients with higher proportions of both Cutibacterium and Anaerobacillus (66.7%, 2/3) was significantly greater than that of patients who lacked these bacteria (9.2%, 6/65, adjusted odds ratio 16.90, 95% confidence interval 1.27-225.47, p = 0.032). The presence of certain bacteria could be a predictor of subsequent miscarriage without an aneuploid karyotype. The cervicovaginal microbiome might be useful for investigating a possible cause of RPL.
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Affiliation(s)
- Ryosuke Mori
- Department of Obstetrics and Gynecology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Masaaki Hirayama
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya 461-8673, Japan
| | - Fumiko Ozawa
- Department of Obstetrics and Gynecology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Hiroyuki Yoshihara
- Department of Obstetrics and Gynecology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Shinobu Goto
- Department of Obstetrics and Gynecology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Tamao Kitaori
- Department of Obstetrics and Gynecology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Yasuhiko Ozaki
- Department of Obstetrics and Gynecology, Nagoya City University West Medical Center, Nagoya 462-8508, Japan
| | - Mayumi Sugiura-Ogasawara
- Department of Obstetrics and Gynecology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
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Safika S, Indrawati A, Afiff U, Hastuti YT, Zureni Z, Jati AP. First Study on profiling of gut microbiome in wild and captive Sumatran orangutans ( Pongo abelii). Vet World 2023; 16:717-727. [PMID: 37235163 PMCID: PMC10206964 DOI: 10.14202/vetworld.2023.717-727] [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: 11/08/2022] [Accepted: 02/27/2023] [Indexed: 05/28/2023] Open
Abstract
Background and Aim Orangutans are an "umbrella species" for conserving tropical forests in Sumatra and Kalimantan. There are remarkable changes between the gut microbiomes of wild and captive Sumatran orangutans. This study aimed to profile gut microbiota of wild and captive Sumatran orangutans. Materials and Methods Nine fecal samples collected from wild orangutans and nine fecal samples collected from captive orangutans were divided into three replicates. Each replicate randomly combined three pieces and were analyzed on the Illumina platform. A bioinformatics study of 16S rRNA according to Qiime2 (Version 2021.4) and microbiome profiling analysis was conducted. Results The relative abundance of different microbial taxa varied significantly between wild and captive Sumatran orangutans. Among the operational taxonomic units, various proportions of Firmicutes, Proteobacteria, Bacteroidetes, Euryarchaeota, Acidobacteria, Actinobacteria and Verrucomicrobia predominated. Solobacterium was found only in 19% of captive orangutans. Methanobrevibacter was identified to be prevalent among wild orangutans (16%). Analysis of the core microbiome from the combined wild and captive data revealed seven species as cores. According to linear discriminant analysis effect size, Micrococcus luteus, Bacteroidescaccae, Lachnospiraceae bacterium, Ruthenibacterium lactatiformans, Haemophilus haemolyticus, and Chishuiella spp. were microbiome biomarkers in captive orangutans, whereas Roseburia inulinivorans, Collinsella aerofaciens, Oscillibacter spp., and Eubacterium hallii were microbiome biomarkers in wild orangutans. Conclusion There were differences in the microbiome biomarkers of wild and captive Sumatran orangutans. This study is important for understanding the role of gut bacteria in the health of Sumatran orangutans.
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Affiliation(s)
- Safika Safika
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Agustin Indrawati
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Usamah Afiff
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | | | - Zureni Zureni
- Class II Agricultural Quarantine Center Medan, Indonesia
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10
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Modifying the diets of captive proboscis monkeys in a temperate zoo to reduce weight loss and renal disease. Primates 2023; 64:123-141. [PMID: 36357633 DOI: 10.1007/s10329-022-01031-y] [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: 02/15/2022] [Accepted: 10/12/2022] [Indexed: 11/12/2022]
Abstract
In animal husbandry, diets should help in maintaining a healthy body condition, support reproduction, and promote species-specific longevity. It is recommended to feed folivorous primates kept in zoos a high-fiber diet, i.e., leaves, although satisfying such a requirement is challenging in temperate regions because it is difficult to obtain fresh leaves, especially in autumn and winter. As equally important for their appropriate treatment, it is valuable to provide details of clinical reports of medical problems and pathological findings, although such clinical reports are rather limited. Therefore, in foregut-fermenting proboscis monkeys (Nasalis larvatus), we (1) described the individual clinical reports of renal disease and weight loss at the Yokohama Zoological Gardens in Japan, (2) determined the nutritional profile of the diets supplied to these animals because other potential triggers for their renal disease and weight loss could be excluded, (3) modified the diet regimen to minimize weight loss and the development of hypercalcemia and hypophosphatemia, and (4) assessed the effects of such dietary modification by comparing the body weight and the Ca and P concentrations and the Ca/P ratios in the blood before and after diet modification with a comparison of these measurements between zoo and free-ranging individuals. Based on the nutritional profile of the diets, we concluded that the reported cases of renal failure might be caused by consumption of leaves with a Ca/P ratio far above the appropriate level in autumn and winter. Additionally, the dietary modification of minerals and metabolizable energy achieved certain beneficial effects on zoo-kept proboscis monkeys.
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11
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Matsuda I. Following the trail of the elusive proboscis monkey in Borneo. Ecol Res 2022. [DOI: 10.1111/1440-1703.12343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ikki Matsuda
- Chubu University Academy of Emerging Sciences Kasugai‐shi Japan
- Chubu Institute for Advanced Studies, Chubu University Kasugai‐shi Japan
- Wildlife Research Center of Kyoto University Kyoto Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS Kota Kinabalu Malaysia
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12
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Malik H, Ratovonamana YR, Rakotondranary SJ, Ganzhorn JU, Sommer S. Anthropogenic Disturbance Impacts Gut Microbiome Homeostasis in a Malagasy Primate. Front Microbiol 2022; 13:911275. [PMID: 35801106 PMCID: PMC9253676 DOI: 10.3389/fmicb.2022.911275] [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: 04/02/2022] [Accepted: 05/19/2022] [Indexed: 12/05/2022] Open
Abstract
Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of gray-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species marked by a reduction in bacterial diversity and a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria (i.e., members of the Bacteroidaceae family) together with a slight increase in disease-associated bacteria (i.e., members of the Veillonellaceae family), and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to pathogen resistance and host health, such negative alterations in the gut microbiome of mouse lemurs inhabiting anthropogenically disturbed habitats might render them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.
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Affiliation(s)
- Hina Malik
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Yedidya R Ratovonamana
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
- Département Biologie Animale, Faculté des Sciences, Université d' Antananarivo, Antananarivo, Madagascar
| | - Solofomalala Jacques Rakotondranary
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
- Département Biologie Animale, Faculté des Sciences, Université d' Antananarivo, Antananarivo, Madagascar
| | - Jörg U Ganzhorn
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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13
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Matsuda I, Hashimoto C, Ihobe H, Yumoto T, Baranga D, Clauss M, Hummel J. Dietary Choices of a Foregut-Fermenting Primate, Colobus guereza: A Comprehensive Approach Including Leaf Chemical and Mechanical Properties, Digestibility and Abundance. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.795015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Free-ranging animals make dietary choices that affect their nutritional status and, ultimately, their health and fitness. We investigated food selection by a leaf-eating foregut-fermenting primate, the guereza (Colobus guereza), using multiple criteria, including chemical and mechanical properties, in vitro digestibility and leaf abundance, on the basis of 30 consecutive months of behavioral observations (4308 h in total) of a family group in the Kalinzu Forest, Uganda, as well as vegetation surveys. We noted that leaf toughness may be a proximate cue for the chemical properties of plant foods, especially for protein, which is an important selection factor used by primates. We also found that the in vitro digestibility of plant foods was greatly influenced by the concentrations of fiber and secondary compounds. At a broad level, none of the studied factors, including leaf chemical and mechanical properties, digestibility and abundance, affected whether guerezas consumed specific leaf items. At a more detailed level, however, protein content, digestibility and toughness were related to the percentage of foraging effort that guerezas devoted to specific items in our study site.
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14
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Specialised digestive adaptations within the hindgut of a colobine monkey. Innovation (N Y) 2022; 3:100207. [PMID: 35243466 PMCID: PMC8857510 DOI: 10.1016/j.xinn.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
In mammal herbivores, fiber digestion usually occurs predominantly in either the foregut or the hindgut. Reports of mechanisms showing synergistic function in both gut regions for the digestion of fiber and other nutrients in wild mammals are rare because it requires integrative study of anatomy, physiology, and gut microbiome. Colobine monkeys (Colobinae) are folivorous, with high-fiber foods fermented primarily in their foreguts. A few colobine species live in temperate regions, so obtaining energy from fiber during the winter is essential. However, the mechanisms enabling this remain largely unknown. We hypothesized that such species possess specialized mechanisms to enhance fiber digestion in the hindgut and studied microbial and morphological digestive adaptations of golden snub-nosed monkeys (GSMs), Rhinopithecus roxellana. which is a temperate forest colobine from central China that experiences high-thermal-energy demands while restricted to a fibrous, low-energy winter diet. We tested for synergistic foregut and hindgut fiber digestion using comparisons of morphology, microbiome composition and function, and digestive efficiency. We found that the GSM colon has a significantly greater volume than that of other foregut-fermenting colobines. The microbiomes of the foregut and hindgut differed significantly in composition and abundance. However, while digestive efficiency and the expression of microbial gene functions for fiber digestion were higher in the foregut than in the hindgut, both gut regions were dominated by microbial taxa producing enzymes to enable active digestion of complex carbohydrates. Our data suggest that both the GSM foregut and hindgut facilitate fiber digestion and that an enlarged colon is likely an adaptation to accommodate high throughput of fiber-rich food during winter. How folivores extract adequate nutrition from their ultra-high-fiber diets remains unclear We studied the morphology, microbiome and digestive efficiency of gut for R. roxellana (GSM) Both fore- and hind-gut regions of GSM play important function of digesting complex carbohydrates An enlarged colon of GSM likely accommodates a high throughput of fiber-rich food during winter
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15
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Zeng Y, Pu Y, Niu L, Deng J, Zeng D, Amato K, Li Y, Zhou Y, Lin Y, Wang J, Wu L, Chen B, Pan K, Jing B, Ni X. Comparison of gastrointestinal microbiota in golden snub-nosed monkey (Rhinopithecus roxellanae), green monkey (Chlorocebus aethiops sabaeus), and ring-tailed lemur (Lemur catta) by high throughput sequencing. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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16
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Hoshino S, Seino S, Funahashi T, Hoshino T, Clauss M, Matsuda I, Yayota M. Apparent diet digestibility of captive colobines in relation to stomach types with special reference to fibre digestion. PLoS One 2021; 16:e0256548. [PMID: 34543310 PMCID: PMC8452005 DOI: 10.1371/journal.pone.0256548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Colobine monkeys are known for the anatomical complexity of their stomachs, making them distinct within the primate order. Amongst foregut fermenters, they appear peculiar because of the occurrence of two different stomach types, having either three (‘tripartite’) or four (‘quadripartite’, adding the praesaccus) chambers. The functional differences between tri and quadripartite stomachs largely remain to be explained. In this study, we aim to compare the apparent digestibility (aD) in tripartite and quadripartite colobines. Hence, we measured the aD in two colobine species, Nasalis larvatus (quadripartite) and Trachypithecus cristatus (tripartite), in two zoos. We also included existing colobine literature data on the aD and analysed whether the aD of fibre components is different between the stomach types to test the hypothesis of whether quadripartite colobines show higher aD of fibre components than tripartite colobines did. Our captive N. larvatus specimen had a more distinctively varying nutrient intake across seasons with a larger seasonal variation in aD than that of a pair of T. cristatus, which mostly consumed commercial foods with a lower proportion of browse and less seasonal variation. We observed higher aD of dry matter (DM), neutral detergent fibre (NDF) and acid detergent fibre (ADF) in the N. larvatus specimen, suggesting a higher gut capacity of N. larvatus provided by the additional praesaccus forestomach chamber. Based on the analysis of literature data for aD, we also found that quadripartite species achieved higher fibre digestibility at similar dietary fibre levels compared with tripartite species, supporting the hypothesis that the additional gut capacity offered by the praesaccus facilitates a longer retention and hence more thorough microbial fermentation of plant fibre.
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Affiliation(s)
- Satoru Hoshino
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
- Zoo Biology Research Center, Gifu University, Gifu, Japan
| | - Satoru Seino
- Preservation and Research Center, City of Yokohama, Yokohama, Japan
| | | | | | - Marcus Clauss
- Vetsuisse Faculty, Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zürich, Zürich, Switzerland
| | - Ikki Matsuda
- Japan Monkey Centre, Inuyama, Aichi, Japan
- Chubu University Academy of Emerging Sciences, Kasugai-shi, Aichi, Japan
- Wildlife Research Center of Kyoto University, Sakyo, Kyoto, Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Masato Yayota
- Zoo Biology Research Center, Gifu University, Gifu, Japan
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- * E-mail:
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17
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Suzuki-Hashido N, Tsuchida S, Hayakawa T, Sakamoto M, Azumano A, Seino S, Matsuda I, Ohkuma M, Ushida K. Lactobacillus nasalidis sp. nov., isolated from the forestomach of a captive proboscis monkey ( Nasalis larvatus). Int J Syst Evol Microbiol 2021; 71. [PMID: 33906706 DOI: 10.1099/ijsem.0.004787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains (YZ01T, YZ02 and YZ03) of Gram-stain-positive, facultatively anaerobic rods were isolated from the forestomach contents collected from a captive male proboscis monkey (Nasalis larvatus) at Yokohama Zoo in Japan. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belonged to the genus Lactobacillus. Based on the sequence similarity of the 16S rRNA gene, Lactobacillus delbrueckii subsp. indicus JCM 15610T was the closest phylogenetic neighbour to YZ01T. Sequence analyses of two partial concatenated housekeeping genes, the RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS) also indicated that the novel strains belonged to the genus Lactobacillus. The average nucleotide identity and digital DNA-DNA hybridization (dDDH) between L. delbrueckii subsp. indicus and YZ01T were 85.9 and 31.4 %, respectively. The phylogenetic tree based on the whole genomic data of strains YZ01T, YZ02 and YZ03 suggested that these three strains formed a single monophyletic cluster in the genus Lactobacillus, indicating that it belonged to a new species. The DNA G+C content of strain YZ01T was 51.6 mol%. The major fatty acids were C16 : 0 and C18 : 1 ω9c. Therefore, based on phylogenetic, phenotypic and physiological evidence, strains YZ01T, YZ02 and YZ03 represent a novel species of the genus Lactobacillus, for which the name Lactobacillus nasalidis sp. nov. is proposed with the type strain YZ01T (=JCM 33769T=DSM 110539T).
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Affiliation(s)
- Nami Suzuki-Hashido
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-0083, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan
| | - Takashi Hayakawa
- Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810 Hokkaido, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Satoru Seino
- Present address: Preservation and Research Center, City of Yokohama, Yokohama, Kanagawa, 241-0804, Japan.,Yokohama Zoo Zoorasia, Yokohama, Kanagawa, 241-0001, Japan
| | - Ikki Matsuda
- Wildlife Research Center, Kyoto University, Sakyo-ku, Kyoto, 606-8203, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan.,Institute for Tropical Biology and Conservation, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.,Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan
| | | | - Kazunari Ushida
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan
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18
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Lee W, Hayakawa T, Kurihara Y, Hanzawa M, Sawada A, Kaneko A, Morimitsu Y, Natsume T, Aisu S, Ito T, Honda T, Hanya G. Stomach and colonic microbiome of wild Japanese macaques. Am J Primatol 2021; 83:e23242. [PMID: 33566369 DOI: 10.1002/ajp.23242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 01/18/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022]
Abstract
Within the gastrointestinal tract, the physiochemical microenvironments are highly diversified among the different stages of food digestion. Accordingly, gut microbiome composition and function vary at different gut sites. In this study, we examine and compare the compositional and functional potential between the stomach and colonic microbiome of wild Japanese macaques (Macaca fuscata yakui) living in the evergreen forest of Yakushima Island. We find a significantly lower microbial diversity in the stomach than in the colon, possibly due to the stomach's acidic and aerobic environment, which is suboptimal for microbial survival. According to past studies, the microbial taxa enriched in the stomach are aero- and acid-tolerant. By functional prediction through PICRUSt2, we reveal that the stomach microbiome is more enriched in pathways relating to the metabolism of simple sugars. On the contrary, the colonic microbiota is more enriched with fiber-degrading microbes, such as those from Lachnospiracea, Ruminococcaceae, and Prevotella. Our study shows a clear difference in the microbiome between the stomach and colon of Japanese macaques in both composition and function. This study provides a preliminary look at the alpha diversity and taxonomic composition within the stomach microbiome of Japanese macaques, a hindgut-fermenting nonhuman primate.
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Affiliation(s)
- Wanyi Lee
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan.,Japan Monkey Centre, Inuyama, Aichi, Japan
| | - Yosuke Kurihara
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan.,Center for Education and Research in Field Sciences, Faculty of Agriculture, Shizuoka University, Hamamatsu, Japan
| | - Maho Hanzawa
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Akiko Sawada
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan.,Academy of Emerging Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Akihisa Kaneko
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoshiki Morimitsu
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | | | - Seitaro Aisu
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Tsuyoshi Ito
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Takeaki Honda
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Goro Hanya
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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19
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Hanya G, Tackmann J, Sawada A, Lee W, Pokharel SS, de Castro Maciel VG, Toge A, Kuroki K, Otsuka R, Mabuchi R, Liu J, Hatakeyama M, Yamasaki E, von Mering C, Shimizu-Inatsugi R, Hayakawa T, Shimizu KK, Ushida K. Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses. MICROBIAL ECOLOGY 2020; 80:459-474. [PMID: 32328670 DOI: 10.1007/s00248-020-01515-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.
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Affiliation(s)
- Goro Hanya
- Primate Research Institute, Kyoto University, Inuyama, Japan.
| | - Janko Tackmann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Akiko Sawada
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Chubu University Academy of Emerging Sciences, Kasugai, Japan
| | - Wanyi Lee
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | | | - Akito Toge
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Kota Kuroki
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Ryoma Otsuka
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan
| | - Ryoma Mabuchi
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Jie Liu
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Eri Yamasaki
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Takashi Hayakawa
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Japan
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20
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Hanya G. Gut microbiota composition of Japanese macaques associates with extent of human encroachment. Am J Primatol 2019; 81:e23072. [PMID: 31788810 DOI: 10.1002/ajp.23072] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/29/2019] [Accepted: 11/10/2019] [Indexed: 12/28/2022]
Abstract
In recent decades, human-wildlife interaction and associated anthropogenic food provisioning has been increasing and becoming more severe due to fast population growth and urban development. Noting the role of the gut microbiome in host physiology like nutrition and health, it is thus essential to understand how human-wildlife interactions and availability of anthropogenic food in habitats can affect an animal's gut microbiome. This study, therefore, set out to examine the gut microbiota of Japanese macaques (Macaca fuscata) with varying accessibility to anthropogenic food and the possibility of using gut microbiota as indicator for macaques' reliance on anthropogenic food. Using 16S ribosomal RNA gene sequencing, we described the microbial composition of Japanese macaques experiencing different types of human disturbance and anthropogenic food availability-captive, provisioned, crop-raiding, and wild. In terms of alpha diversity, our results showed that observed richness of gut microbiota did not differ significantly between disturbance types but among collection sites, whereas Shannon diversity index differed by both disturbance types and sites. In terms of beta diversity, captive populations harbored the most distinctive gut microbial composition, and had the greatest difference compared with wild populations. Whereas for provisioned and crop-raiding groups, the macaques exhibited intermediate microbiota between wild and captive. We identified several potential bacterial taxa at different taxonomic ranks whose abundance potentially could help in assessing macaques' accessibility to anthropogenic food. This study revealed the flexibility of the gut microbiome of Japanese macaques and provided possible indices based on the gut microbiome profile in assessing macaques' accessibility to/reliance on anthropogenic foods.
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Affiliation(s)
- Wanyi Lee
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Japan Monkey Centre, Inuyama, Aichi, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Goro Hanya
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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Clayton JB, Shields-Cutler RR, Hoops SL, Al-Ghalith GA, Sha JC, Johnson TJ, Knights D. Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). Am J Primatol 2019; 81:e22977. [PMID: 30997937 PMCID: PMC6800578 DOI: 10.1002/ajp.22977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022]
Abstract
The mammalian order primates contains wide species diversity. Members of the subfamily Colobinae are unique amongst extant primates in that their gastrointestinal systems more closely resemble those of ruminants than other members of the primate order. In the growing literature surrounding nonhuman primate microbiomes, analysis of microbial communities has been limited to the hindgut, since few studies have captured data on other gut sites, including the foregut of colobine primates. In this study, we used the red-shanked douc (Pygathrix nemaeus) as a model for colobine primates to study the relationship between gastrointestinal bacterial community structure and gut site within and between subjects. We analyzed fecal and pregastric stomach content samples, representative of the hindgut and foregut respectively, using 16S recombinant DNA (rDNA) sequencing and identified microbiota using closed-reference operational taxonomic unit (OTU) picking against the GreenGenes database. Our results show divergent bacterial communities clearly distinguish the foregut and hindgut microbiomes. We found higher bacterial biodiversity and a higher Firmicutes:Bacteroides ratio in the hindgut as opposed to the foregut. These gut sites showed strong associations with bacterial function. Specifically, energy metabolism was upregulated in the hindgut, whereas detoxification was increased in the foregut. Our results suggest a red-shanked douc's foregut microbiome is no more concordant with its own hindgut than it is with any other red-shanked douc's hindgut microbiome, thus reinforcing the notion that the bacterial communities of the foregut and hindgut are distinctly unique. OPEN PRACTICES: This article has been awarded Open Materials and Open Data badges. All materials and data are publicly accessible via the IRIS Repository at https://www.iris-database.org/iris/app/home/detail?id=york:934328. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Jonathan B. Clayton
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union St SE, Minneapolis, MN 55455, USA
- GreenViet Biodiversity Conservation Center, K39/21 Thanh Vinh Street, Son Tra District, Danang, Vietnam
- Primate Microbiome Project, 6-124 MCB, 420 Washington Ave SE, Minneapolis, MN 55455, USA
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Robin R. Shields-Cutler
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
- Department of Biology, Macalester College, 1600 Grand Ave, St. Paul, MN 55105, USA
| | - Susan L. Hoops
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Gabriel A. Al-Ghalith
- Bioinformatics and Computational Biology, 200 Union St SE, University of Minnesota, Minneapolis, MN 55455, USA
| | - John C.M. Sha
- School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Timothy J. Johnson
- Primate Microbiome Project, 6-124 MCB, 420 Washington Ave SE, Minneapolis, MN 55455, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
- University of Minnesota, Mid-Central Research and Outreach Center, Willmar, Minnesota, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union St SE, Minneapolis, MN 55455, USA
- Primate Microbiome Project, 6-124 MCB, 420 Washington Ave SE, Minneapolis, MN 55455, USA
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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Matsuda I, Espinosa-Gómez FC, Ortmann S, Sha JC, Osman I, Nijboer J, Schwarm A, Ikeda T, Clauss M. Retention marker excretion suggests incomplete digesta mixing across the order primates. Physiol Behav 2019; 208:112558. [DOI: 10.1016/j.physbeh.2019.112558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 01/31/2023]
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Hale VL, Tan CL, Niu K, Yang Y, Zhang Q, Knight R, Amato KR. Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi. Am J Primatol 2019; 81:e22989. [PMID: 31106872 DOI: 10.1002/ajp.22989] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/14/2019] [Accepted: 04/21/2019] [Indexed: 12/30/2022]
Abstract
Many colobine species-including the endangered Guizhou snub-nosed monkey (Rhinopithecus brelichi) are difficult to maintain in captivity and frequently exhibit gastrointestinal (GI) problems. GI problems are commonly linked to alterations in the gut microbiota, which lead us to examine the gut microbial communities of wild and captive R. brelichi. We used high-throughput sequencing of the 16S rRNA gene to compare the gut microbiota of wild (N = 7) and captive (N = 8) R. brelichi. Wild monkeys exhibited increased gut microbial diversity based on the Chao1 but not Shannon diversity metric and greater relative abundances of bacteria in the Lachnospiraceae and Ruminococcaceae families. Microbes in these families digest complex plant materials and produce butyrate, a short chain fatty acid critical to colonocyte health. Captive monkeys had greater relative abundances of Prevotella and Bacteroides species, which degrade simple sugars and carbohydrates, like those present in fruits and cornmeal, two staples of the captive R. brelichi diet. Captive monkeys also had a greater abundance of Akkermansia species, a microbe that can thrive in the face of host malnutrition. Taken together, these findings suggest that poor health in captive R. brelichi may be linked to diet and an altered gut microbiota.
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Affiliation(s)
- Vanessa L Hale
- Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Chia L Tan
- LVDI International, San Marcos, California.,Nonhuman Primate Conservation and Research Institute, Tongren University, Tongren, Guizhou, China
| | - Kefeng Niu
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Yeqin Yang
- Nonhuman Primate Conservation and Research Institute, Tongren University, Tongren, Guizhou, China
| | - Qikun Zhang
- Hangzhou KaiTai Biotechnology Co., Ltd, Hangzhou, China
| | - Rob Knight
- Pediatrics, University of California San Diego, La Jolla, California.,Computer Science and Engineering, University of California San Diego, La Jolla, California
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The feeding ecology and dietary overlap in two sympatric primate species, the long-tailed macaque (Macaca fascicularis) and dusky langur (Trachypithecus obscurus obscurus), in Malaysia. Primates 2018; 60:41-50. [PMID: 30564972 DOI: 10.1007/s10329-018-00705-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
Knowledge about the feeding ecology and dietary overlap of sympatric primates is essential for understanding how animals avoid or reduce interspecific competition. From April 2014 to March 2015, we investigated the feeding ecologies of two sympatric primates, a hindgut fermenter, the long-tailed macaque (Macaca fascicularis) and a foregut fermenter, the dusky langur (Trachypithecus obscurus obscurus), in a mixed landscape consisting of urban and agro-forested areas and forest fragments in Malaysia. We collected a total of 5570 and 4029 of feeding records for M. fascicularis and T. o. obscurus, respectively, using the 10-min scan sampling method. Food availability and seasonal changes in plant species consumed by both study groups were determined by vegetation surveys carried out across an area of 1.6 ha. A total of 113 and 130 plant species were consumed by M. fascicularis and T. o. obscurus, respectively. Leaves (51%) and fruits (40%) accounted for the majority of the feeding records in T. o. obscurus, whereas fruits (32%) and anthropogenic foods (27%) together with leaves (15%) and insects (6%) accounted for the majority of the feeding records for M. fascicularis. Throughout the year, there were 59 consumed plant species common to both species, and the dietary overlap was the highest for fruits. Although leaves were always more abundant than fruits in our study site, the amount of monthly fruit eating by the two species showed a significant correlation with that of fruit availability. Monthly fruit availability had a positive effect on overall monthly dietary overlap while flower and leaf availability had a negative effect. We showed that fruit was the preferred food resource of two sympatric species with different digestive systems. This could have implications for resource competition, interspecific competition, and niche separation, which should be investigated in more detail.
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