1
|
Łopucki R, Sajnaga E, Kalwasińska A, Klich D, Kitowski I, Stępień-Pyśniak D, Christensen H. Green spaces contribute to structural resilience of the gut microbiota in urban mammals. Sci Rep 2024; 14:15508. [PMID: 38969657 PMCID: PMC11226671 DOI: 10.1038/s41598-024-66209-4] [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: 03/03/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024] Open
Abstract
The gut microbiome of wild animals is subject to various environmental influences, including those associated with human-induced alterations to the environment. We investigated how the gut microbiota of a synurbic rodent species, the striped field mouse (Apodemus agrarius), change in cities of varying sizes, seeking the urban microbiota signature for this species. Fecal samples for analysis were collected from animals living in non-urbanized areas and green spaces of different-sized cities (Poland). Metagenomic 16S rRNA gene sequencing and further bioinformatics analyses were conducted. Significant differences in the composition of gut microbiomes among the studied populations were found. However, the observed changes were dependent on local habitat conditions, without strong evidence of a correlation with the size of the urbanized area. The results suggest that ecological detachment from a more natural, non-urban environment does not automatically lead to the development of an "urban microbiome" model in the studied rodent. The exposure to the natural environment in green spaces may serve as a catalyst for microbiome transformations, providing a previously underestimated contribution to the maintenance of native gut microbial communities in urban mammals.
Collapse
Affiliation(s)
- Rafał Łopucki
- Department of Biomedicine and Environmental Research, The John Paul II Catholic University of Lublin, Konstantynów 1J, 20-708, Lublin, Poland.
| | - Ewa Sajnaga
- Department of Biomedicine and Environmental Research, The John Paul II Catholic University of Lublin, Konstantynów 1J, 20-708, Lublin, Poland
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Daniel Klich
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences (SGGW), Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Ignacy Kitowski
- University College of Applied Sciences in Chełm, Pocztowa 54, 22-100, Chełm, Poland
| | - Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-612, Lublin, Poland
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| |
Collapse
|
2
|
Gani M, Mohd-Ridwan AR, Sitam FT, Kamarudin Z, Selamat SS, Awang NMZ, Karuppannan KV, Md-Zain BM. Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling. World J Microbiol Biotechnol 2024; 40:111. [PMID: 38416247 DOI: 10.1007/s11274-023-03868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 02/29/2024]
Abstract
The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.
Collapse
Affiliation(s)
- Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Zubaidah Kamarudin
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Siti Suzana Selamat
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Nik Mohd Zamani Awang
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
Collapse
Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, 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
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Mo F, Li Y, Liu Z, Zheng J, Huang Z. Captivity restructures the gut microbiota of François' langurs ( Trachypithecus francoisi). Front Microbiol 2023; 14:1166688. [PMID: 37250037 PMCID: PMC10218129 DOI: 10.3389/fmicb.2023.1166688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Gut microbiota is crucial to primate survival. Data on the gut microbiota of captive and wild animals can provide a physiological and ecological basis for the conservation of rare and endangered species. To study the effect of captivity on the gut microbiota, we examine the difference in the gut microbiota composition between captive and wild Francois' langurs (Trachypithecus francoisi), using 16S rRNA sequencing technology. The results showed that the composition of the gut microbiota of captive and wild langurs was characterized by Firmicutes (51.93 ± 10.07% vs. 76.15 ± 8.37%) and Bacteroidetes (32.43 ± 10.00% vs. 4.82 ± 1.41%) at the phylum level and was characterized by Oscillospiraceae (15.80 ± 5.19% vs. 30.21 ± 4.87%) at the family level. The alpha diversity of gut microbiota in captive langurs was higher than those in wild, such as the Shannon index (4.45 ± 0.33 vs. 3.98 ± 0.19, P < 0.001) and invSimpson index (35.11 ± 15.63 vs. 19.02 ± 4.87, P < 0.001). Principal coordinates analysis (PCoA) results showed significant differences in the composition of gut microbiota between captive and wild langurs at both the phylum and family levels (weight UniFrac algorithm, phylum level: R2 = 0.748, P = 0.001; family level: R2 = 0.685, P = 0.001). The relative abundance of Firmicutes (51.93 ± 10.07%) in captive langurs was lower than that of wild langurs (76.15 ± 8.37%), and the relative abundance of Bacteroidetes (32.43 ± 10.00%) in captive langurs was higher than that of wild (4.82 ± 1.41%). Our study concludes that dietary composition could be a crucial determinant in shaping the gut microbiota of langurs because more fiber-rich foods used by the wild langurs could increase the abundance of Firmicutes, and more simple carbohydrate-rich foods consumed by the captive langurs increase the abundance of Bacteroidetes. We highlight the importance of captivity on the gut microbiota and the need to consider the gut microbiota in animal provision.
Collapse
Affiliation(s)
- Fengxiang Mo
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zheng Liu
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Jingjin Zheng
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhonghao Huang
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| |
Collapse
|
7
|
He T, Lee W, Hanya G. In vitro digestion and fermentation of Japanese macaque (Macaca fuscata) food: The influence of food type and particle size. Am J Primatol 2023; 85:e23470. [PMID: 36725317 DOI: 10.1002/ajp.23470] [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: 09/07/2022] [Revised: 12/19/2022] [Accepted: 01/14/2023] [Indexed: 02/03/2023]
Abstract
Chewing is critical for herbivores to obtain nutrients. Measuring digesta particle size as the outcome of chewing can improve our understanding of the relationship between food and digestion. Previous studies of feeds of domestic animals have shown that smaller digesta particle size leads to more efficient digestion. Increased digesta particle size-either due to animal factors (e.g., a senile dentition) or to feed factors (e.g., fracture resistance) could be a sign of an animal experiencing compromised nutritional intake. However, for some primates that are dietary generalists, digesta particle size has been shown to increase when consuming preferred foods, which raises doubts about the role of chewing in digesting such foods. This uncertainty makes it difficult to understand the connection between diet, chewing, and digestion through digesta particle size in dietary generalists. In this study, using five typical food items from the Japanese macaque (Macaca fuscata) diet, we conducted in vitro digestibility and fermentation assays to explore the effects of particle size on enzymatic and microbial digestion. For the fermentation assays, we used feces from captive Japanese macaques as inoculum. Among the five food items, we found that particle size has a stronger influence on the digestibility of seeds and mature leaves compared to young leaves and pulp. The influence of particle size on the fermentation rate was stronger in pulp and seeds compared to that in leaves. The differences in physical structure, texture, digestion barriers, and soluble components may play important roles in such differences. These results support the hypothesis that reducing food particle size is less important for consuming fruits than for consuming leaves. The limited effects of particle size on digesting fruits suggest that the two fruits examined in this study are cost-effective concerning food processing and chewing.
Collapse
Affiliation(s)
- Tianmeng He
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Wanyi Lee
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| |
Collapse
|
8
|
Kuthyar S, Watson K, Huang S, Brent LJN, Platt M, Horvath J, Gonzalez-Martinez J, Martínez M, Godoy-Vitorino F, Knight R, Dominguez-Bello MG, Amato KR. Limited microbiome differences in captive and semi-wild primate populations consuming similar diets. FEMS Microbiol Ecol 2022; 98:fiac098. [PMID: 36047944 PMCID: PMC9528791 DOI: 10.1093/femsec/fiac098] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Gut microbial communities are shaped by a myriad of extrinsic factors, including diet and the environment. Although distinct human populations consistently exhibit different gut microbiome compositions, variation in diet and environmental factors are almost always coupled, making it difficult to disentangle their relative contributions to shaping the gut microbiota. Data from discrete animal populations with similar diets can help reduce confounds. Here, we assessed the gut microbiota of free-ranging and captive rhesus macaques with at least 80% diet similarity to test the hypothesis that hosts in difference environments will have different gut microbiomes despite a shared diet. Although we found that location was a significant predictor of gut microbial composition, the magnitude of observed differences was relatively small. These patterns suggest that a shared diet may limit the typical influence of environmental microbial exposure on the gut microbiota.
Collapse
Affiliation(s)
- Sahana Kuthyar
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
- Division of Biological Sciences, University of California San Diego 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Karli Watson
- Institute of Cognitive Science, University of Colorado Boulder 1777 Exposition Drive Boulder, CO, 80309, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter Stocker Rd, Exeter EX4 4PY, United Kingdom
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd Philadelphia, PA, 19104, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, 425 S. University Ave Philadelphia, PA, 19104-6018, USA
- Department of Marketing, Wharton School of Business, University of Pennsylvania, 3620 Locust Walk, Philadelphia, PA, USA 19104, PA, USA
| | - Julie Horvath
- Research and Collections, North Carolina Museum of Natural Sciences, 11 W Jones St, Raleigh, NC, 27601, USA
- Biological and Biomedical Sciences Department, North Carolina Central University, 1801 Fayetteville St, Durham, NC, 27707, USA
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Campus Box 90383 Durham, NC, 27708, USA
- Department of Biological Sciences, North Carolina State University, 3510 Thomas Hall Campus Box 7614 Raleigh, NC, USA 27695, USA
| | - Janis Gonzalez-Martinez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Melween Martínez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, Medical Sciences Campus, PO BOX 365067 San Juan, PR 00936-5067, Puerto Rico
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
- Department of Computer Sciences and Engineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, USA 08901, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA 1810, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
| |
Collapse
|
9
|
First Descriptive Analysis of the Faecal Microbiota of Wild and Anthropized Barbary Macaques (Macaca sylvanus) in the Region of Bejaia, Northeast Algeria. BIOLOGY 2022; 11:biology11020187. [PMID: 35205054 PMCID: PMC8869477 DOI: 10.3390/biology11020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 11/18/2022]
Abstract
Simple Summary The gut microbiota is very important for animal physiology and health. It has been demonstrated that the gut microbiota composition of several primate species is influenced by a variety of anthropogenic factors. However, these aspects are not documented for the gut microbiota of the endangered wild Barbary macaque. This study is the first to characterize the faecal microbiota of the species and investigate the impact on it of tourist food provisioning by comparing two groups of Barbary macaques: a tourist-provisioned group and a wild-feeding group. Our results revealed the presence of 209 bacterial genera from 17 phyla in the faecal microbiota of Barbary macaques. Firmicutes was the most abundant bacterial phylum, followed by Bacteroidetes and Verrucomicrobia. The tourism activity was associated with a significant alteration of this profile, probably due to tourist provisioning issues. Increasing risks of obesity and illness call for special management measures to reduce the provisioning rate in tourist areas. Abstract Previous research has revealed the gut microbiota profile of several primate species, as well as the impact of a variety of anthropogenic factors, such as tourist food supply, on these bacterial communities. However, there is no information on the gut microbiota of the endangered wild Barbary macaque (Macaca sylvanus). The present study is the first to characterize the faecal microbiota of this species, as well as to investigate the impact of tourist food provisioning on it. A total of 12 faecal samples were collected in two groups of M. sylvanus in the region of Bejaia in Algeria. The first group—a tourist-provisioned one—was located in the tourist area of the Gouraya National Park and the second group—a wild-feeding one—was located in the proximity of the village of Mezouara in the forest of Akfadou. After DNA extraction, the faecal microbiota composition was analysed using 16S rDNA sequencing. Statistical tests were performed to compare alpha diversity and beta diversity between the two groups. Non-metric multidimensional scaling analysis (NMDS) was applied to visualize biodiversity between groups. Behaviour monitoring was also conducted to assess the time allocated to the consumption of anthropogenic food by the tourist-provisioned group. Our results revealed the presence of 209 bacterial genera from 17 phyla in the faecal microbiota of Barbary macaques. Firmicutes was the most abundant bacterial phylum, followed by Bacteroidetes and Verrucomicrobia. On the other hand, the comparison between the faecal microbiota of the two study groups showed that tourism activity was associated with a significant change on the faecal microbiota of M.sylvanus, probably due to diet alteration (with 60% of feeding time allocated to the consumption of anthropogenic food). The potentially low-fibre diet at the tourist site adversely influenced the proliferation of bacterial genera found in abundance in the wild group such as Ruminococcaceae. Such an alteration of the faecal microbiota can have negative impacts on the health status of these animals by increasing the risk of obesity and illness and calls for special management measures to reduce the provisioning rate in tourist areas.
Collapse
|
10
|
Grassotti TT, Kothe CI, Prichula J, Mohellibi N, Mann MB, Wagner PGC, Campos FS, Campos AAS, Frazzon J, Frazzon APG. Fecal bacterial communities of wild black capuchin monkeys ( Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100048. [PMID: 34841339 PMCID: PMC8610302 DOI: 10.1016/j.crmicr.2021.100048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/19/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria ( χ ¯ = 80.54%), followed by Firmicutes ( χ ¯ = 12.14%), Actinobacteria ( χ ¯ = 4.60%), and Bacteriodetes ( χ ¯ = 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates.
Collapse
Key Words
- FROGS, Find Rapidly OTUs with Galaxy Solution
- FastQC, Fast Quality Control
- Fecal microbiota
- HTS, high-throughput sequencing
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MultiQC, Multi Quality Control
- OTUs, Operational Taxonomic Units
- PGMTM, Personal Genome Machine
- PICRUSt2, Phylogenetic Investigation of Communities by Reconstruction of Unobserved State
- Primate conservation
- Proteobacteria
- Robust capuchins
- SCS, Santa Cruz do Sul
- SSC, São Sebastião do Caí
- SSU, Small Subunit rRNA gene
- Wild south Brazilian primates
Collapse
Affiliation(s)
- Tiela Trapp Grassotti
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Janira Prichula
- Department of Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, RS, Brazil
| | - Nacer Mohellibi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Michele Bertoni Mann
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Fabricio Souza Campos
- Laboratory of Bioinformatics and Biotechnology, Campus de Gurupi, Federal University of Tocantins, Gurupi, TO, Brazil; Federal University of Tocantins, Federal University of Tocantins, Palmas, TO, Brazil
| | | | - Jeverson Frazzon
- Biochemistry and Molecular Biology of Microorganisms Laboratory, Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Paula Guedes Frazzon
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
11
|
Linking gut microbiome with the feeding behavior of the Arunachal macaque (Macaca munzala). Sci Rep 2021; 11:21926. [PMID: 34754005 PMCID: PMC8578487 DOI: 10.1038/s41598-021-01316-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022] Open
Abstract
Exploring the gut microbiome is an emerging tool for monitoring wildlife health and physiological conditions which often sustained under the variety of stresses and challenges. We analyzed gut microbiome of Arunachal macaque (Macaca munzala) of two disjunct populations from Arunachal Pradesh, India, to validate whether the geography or the feeding habits plays a principal role in shaping the gut microbiome in natural populations. We observed geography has a mere effect but feeding habits (i.e. feeding upon the leftover food and crop-raiding) significantly influenced the gut microbiome composition. The phylum Proteobacteria found to be enriched in leftover feeding group while phylum Bacteroidetes was differentially abundant in crop-raiding group. We observed predominant phyla Firmicutes followed by Proteobacteria and Bacteroidetes with the dominant classes represented by the Clostridia. Interestingly, one individual with known diarrheal/metabolic disorder exhibited complete dominance of the order Bacillales and showed 100% sequence similarity with genus Solibacillus. We raise concern that shift in diet of macaques may compel them to expose for various human diseases as two macaques feeding upon the leftover food exhibited dysbiotic gut microbiome. The present study provides the pragmatic evidences of how the alteration of food resources can harm the physiological condition of the macaques in wild and raises alarm to the forest officials/managers in strategise planting of natural food resources and monitor anthropogenic activities in the distribution of Arunachal macaques.
Collapse
|
12
|
Thingholm LB, Bang C, Rühlemann MC, Starke A, Sicks F, Kaspari V, Jandowsky A, Frölich K, Ismer G, Bernhard A, Bombis C, Struve B, Rausch P, Franke A. Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans. BMC Microbiol 2021; 21:276. [PMID: 34635060 PMCID: PMC8504008 DOI: 10.1186/s12866-021-02337-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 368 stool samples from 38 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans. By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in westernized humans and platyrrhines, which is probably not only due to diet, but also to the social behavior and structure in these communities. Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammalian fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in westernized communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes, which promote the etiology of chronic diseases.
Collapse
Affiliation(s)
- Louise B Thingholm
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Annika Starke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Florian Sicks
- Tierpark Berlin-Friedrichsfelde GmbH, Berlin, Germany
| | - Verena Kaspari
- Tierparkvereinigung Neumuenster e.V, Neumuenster, Germany
| | | | | | | | | | - Claudia Bombis
- Tierpark Hagenbeck Gemeinnützige Gesellschaft mbH, Hamburg, Germany
| | - Barbara Struve
- Leintalzoo Schwaigern, Freudenmühle 1, 74193, Schwaigern, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany. .,University Hospital Schleswig Holstein (UKSH), Campus Kiel, Kiel, Germany.
| |
Collapse
|
13
|
Houtz JL, Sanders JG, Denice A, Moeller AH. Predictable and host-species specific humanization of the gut microbiota in captive primates. Mol Ecol 2021; 30:3677-3687. [PMID: 34013536 PMCID: PMC10039810 DOI: 10.1111/mec.15994] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Humans and nonhuman primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts' phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here, we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs' gut microbial clades based on the propensity of their lineages to be lost or replaced in captivity by lineages found in humans. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.
Collapse
Affiliation(s)
- Jennifer L. Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anthony Denice
- Project Chimps, Blue Ridge, GA, USA
- Chimpanzee Sanctuary Northwest, Cle Elum, WA, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Li Y, Chen T, Liang J, Li Y, Huang Z. Seasonal variation in the gut microbiota of rhesus macaques inhabiting limestone forests of southwest Guangxi, China. Arch Microbiol 2020; 203:787-798. [PMID: 33057745 DOI: 10.1007/s00203-020-02069-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Data on the gut microbiota of animals can provide new insights into dietary ecology of hosts, consequently assisting in understanding their adaptation strategy and evolutionary potential. We studied the gut microbiota composition and function of the wild rhesus macaques (Macaca mulatta) using 16S rRNA sequencing method. Our results revealed that the gut microbiota of the wild rhesus macaques was dominated by Firmicutes, Bacteroidetes, and Spirochaetes. Diversity and richness of gut microbiota were higher during the dry season than the rainy season. Specifically, higher proportions of Firmicutes, Tenericutes, Cyanobacteria, and unclassified bacteria at the phylum level and more Coprococcus at the genus level were detected in the dry season. Predictive functional analysis showed that pathways associated with carbohydrate metabolism and drug resistance (antimicrobial and antineoplastic) were richer in the dry season. These seasonal differences in microbiota could be due to their heavier dependence on leaf-based diet in the dry season. Additionally, macaques in limestone forests had a higher percentage of Spirochaetes, probably suggesting that the proportion of fruits in dietary composition also play an important role in the gut microbiota. We concluded that diet was strongly linked to the diversity, composition, and function of the gut microbiota in the wild groups of rhesus macaques living in the limestone forest, highlighting the importance of diet in the gut microbiota of macaques and the need to conduct further study on the adaptation strategy in response of environmental changes in the ground of gut microbiota.
Collapse
Affiliation(s)
- Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China
| | - Ting Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China
| | - Jipeng Liang
- Administration Centre of Guangxi Chongzuo White-headed Langur National Nature Reserve, Chongzuo, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China.
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, Ma J, Jiang G. Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger. Front Microbiol 2020; 11:1665. [PMID: 32793154 PMCID: PMC7393233 DOI: 10.3389/fmicb.2020.01665] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.
Collapse
Affiliation(s)
- Yao Ning
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jinzhe Qi
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Michael T Dobbins
- Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Xin Liang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jingxuan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shiyu Chen
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jianzhang Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangshun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| |
Collapse
|