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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.
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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.
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Khairulmunir M, Gani M, Karuppannan KV, Mohd-Ridwan AR, Md-Zain BM. High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger ( Pantheratigrisjacksoni) during fasting. Biodivers Data J 2023; 11:e104757. [PMID: 37711366 PMCID: PMC10498273 DOI: 10.3897/bdj.11.e104757] [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: 04/09/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota SamarahanMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
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3
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Rymer TL, Pillay N. The effects of antibiotics and illness on gut microbial composition in the fawn-footed mosaic-tailed rat (Melomys cervinipes). PLoS One 2023; 18:e0281533. [PMID: 36827295 PMCID: PMC9956021 DOI: 10.1371/journal.pone.0281533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/25/2023] [Indexed: 02/25/2023] Open
Abstract
The gut microbiota are critical for maintaining the health and physiological function of individuals. However, illness and treatment with antibiotics can disrupt bacterial community composition, the consequences of which are largely unknown in wild animals. In this study, we described and quantified the changes in bacterial community composition in response to illness and treatment with antibiotics in a native Australian rodent, the fawn-footed mosaic-tailed rat (Melomys cervinipes). We collected faecal samples during an undiagnosed illness outbreak in a captive colony of animals, and again at least one year later, and quantified the microbiome at each time point using 16s ribosomal rRNA gene sequencing. Gut bacterial composition was quantified at different taxonomic levels, up to family. Gut bacterial composition changed between time periods, indicating that illness, treatment with antibiotics, or a combination affects bacterial communities. While some bacterial groups increased in abundance, others decreased, suggesting differential effects and possible co-adapted and synergistic interactions. Our findings provide a greater understanding of the dynamic nature of the gut microbiome of a native Australian rodent species and provides insights into the management and ethical well-being of animals kept under captive conditions.
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Affiliation(s)
- Tasmin L. Rymer
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
- Centre for Tropical Environmental and Sustainability Sciences, James Cook University, Queensland, Australia
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Neville Pillay
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Zhang J, Long X, Liao Q, Chai J, Zhang T, Chen L, He H, Yuan Y, Wan K, Wang J, Liu A. Distinct Gut Microbiome Induced by Different Feeding Regimes in Weaned Piglets. Genes (Basel) 2022; 14:49. [PMID: 36672790 PMCID: PMC9858795 DOI: 10.3390/genes14010049] [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: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
It is well accepted that the gut microbiota of breast-fed (BF) and formula-fed (FF) infants are significantly different. However, there is still a limited number of studies comparing the gut microbiota of BF and FF piglets, despite increasing numbers of FF piglets in the modern pig industry. The present study identified the differences in gut microbiota composition between BF- and FF-weaned Rongchang piglets at 30 days old, using pair-end sequencing on the Illumina HiSeq 2500 platform. The BF piglets had lower microbiota diversities than FF piglets (p < 0.05), and the community structures were well clustered as a result of each feeding pattern. Firmicutes and Bacteroidetes represented the most dominant phyla, and Ruminococcus, Prevotella, and Gemmiger were prominent genera in all piglets. Ruminococcus, Prevotella, Oscillospira, Eubacterium, Gemmiger, Dorea, and Lactobacillus populations were significantly higher, while Treponema and Coprococcus were significantly lower in BF piglets compared to FF piglets (p < 0.05). The metabolism pathways in the BF piglets were significantly different from FF piglets, which included carbohydrate and amino acid metabolism (p < 0.05). In addition, the top 10 abundance of microbiota were more or less significantly associated with the two phenotypes (p < 0.05). Collectively, these findings provide probable explanations for the importance of BF in neonates and support a theoretical basis for feeding regimes in indigenous Chinese piglets.
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Affiliation(s)
- Jie Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Xi Long
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Qinfeng Liao
- College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing 404155, China
| | - Jie Chai
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Tinghuan Zhang
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Li Chen
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Hang He
- College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing 404155, China
| | - Yancong Yuan
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Kun Wan
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Anfang Liu
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
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5
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Chiang E, Deblois CL, Carey HV, Suen G. Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Anim Microbiome 2022; 4:1. [PMID: 34980290 PMCID: PMC8722175 DOI: 10.1186/s42523-021-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. RESULTS Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. CONCLUSIONS This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
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Affiliation(s)
- Edna Chiang
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Courtney L. Deblois
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hannah V. Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Garret Suen
- Present Address: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
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Diaz J, Reese AT. Possibilities and limits for using the gut microbiome to improve captive animal health. Anim Microbiome 2021; 3:89. [PMID: 34965885 PMCID: PMC8715647 DOI: 10.1186/s42523-021-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022] Open
Abstract
Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.
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Affiliation(s)
- Jessica Diaz
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Aspen T Reese
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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8
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Skeen HR, Cooper NW, Hackett SJ, Bates JM, Marra PP. Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird. Mol Ecol 2021; 30:5900-5916. [PMID: 34580952 DOI: 10.1111/mec.16170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 01/04/2023]
Abstract
Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.
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Affiliation(s)
- Heather R Skeen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Nathan W Cooper
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - John M Bates
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Peter P Marra
- Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
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9
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Special Issue: Wildlife Microbiology. Microorganisms 2021; 9:microorganisms9091968. [PMID: 34576861 PMCID: PMC8469691 DOI: 10.3390/microorganisms9091968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
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Sawaswong V, Praianantathavorn K, Chanchaem P, Khamwut A, Kemthong T, Hamada Y, Malaivijitnond S, Payungporn S. Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand. Sci Rep 2021; 11:14280. [PMID: 34253790 PMCID: PMC8275770 DOI: 10.1038/s41598-021-93779-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques’ natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.
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Affiliation(s)
- Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.,Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ariya Khamwut
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand. .,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand. .,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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11
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Betts EL, Hoque S, Torbe L, Bailey JR, Ryan H, Toller K, Breakell V, Carpenter AI, Diana A, Matechou E, Gentekaki E, Tsaousis AD. Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles. BIOLOGY 2021; 10:457. [PMID: 34067374 PMCID: PMC8224621 DOI: 10.3390/biology10060457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022]
Abstract
(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.
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Affiliation(s)
- Emma L. Betts
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Sumaiya Hoque
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Lucy Torbe
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Jessica R. Bailey
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
| | - Hazel Ryan
- Wildwood Trust, Herne Common, Herne Bay CT6 7LQ, UK; (H.R.); (K.T.); (V.B.)
| | - Karen Toller
- Wildwood Trust, Herne Common, Herne Bay CT6 7LQ, UK; (H.R.); (K.T.); (V.B.)
| | - Vicki Breakell
- Wildwood Trust, Herne Common, Herne Bay CT6 7LQ, UK; (H.R.); (K.T.); (V.B.)
| | - Angus I. Carpenter
- School of Animal, Rural and Environmental Sciences, Brackenhurst Campus, Nottingham Trent University, Nottinghamshire NG1 4FQ, UK;
| | - Alex Diana
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury CT2 7NJ, UK; (A.D.); (E.M.)
| | - Eleni Matechou
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury CT2 7NJ, UK; (A.D.); (E.M.)
| | - Eleni Gentekaki
- School of Science and Human Gut Microbiome for Health Research Unit, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Anastasios D. Tsaousis
- Laboratory of Molecular and Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (E.L.B.); (S.H.); (L.T.); (J.R.B.)
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12
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Gut microbiota of frugo-folivorous sifakas across environments. Anim Microbiome 2021; 3:39. [PMID: 34006323 PMCID: PMC8132362 DOI: 10.1186/s42523-021-00093-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/04/2021] [Indexed: 12/16/2022] Open
Abstract
Background Captive animals, compared to their wild counterparts, generally harbor imbalanced gut microbiota owing, in part, to their altered diets. This imbalance is particularly striking for folivores that fundamentally rely on gut microbiota for digestion, yet rarely receive sufficient dietary fiber in captivity. We examine the critically endangered Coquerel’s sifaka (Propithecus coquereli), an anatomically specialized, rather than facultative, folivore that consumes a seasonal frugo-folivorous diet in the wild, but is provisioned predominantly with seasonal foliage and orchard vegetables in captivity. Using amplicon and metagenomic sequencing applied to fecal samples collected from two wild and one captive population (each comprising multiple groups), we clarify how dietary variation underlies the perturbational effect of captivity on the structure and function of this species’ gut microbiota. Results The gut microbiota of wild sifakas varied by study population, most notably in community evenness and in the abundance of diet-associated microbes from Prevotellaeceae and Lachnospiraceae. Nevertheless, the differences among wild subjects were minor compared to those evident between wild and captive sifakas: Unusually, the consortia of captive sifakas were the most diverse, but lacked representation of endemic Bacteroidetes and metagenomic capacity for essential amino-acid biosynthesis. Instead, they were enriched for complex fiber metabolizers from the Firmicutes phylum, for archaeal methanogens, and for several metabolic pathways putatively linked to plant fiber and secondary compound metabolism. Conclusions The relatively minor differences in gut microbial structure and function between wild sifaka populations likely reflect regional and/or temporal environmental variability, whereas the major differences observed in captive conspecifics, including the loss of endemic microbes, but gain in low-abundance taxa, likely reflect imbalanced or unstable consortia. Indeed, community perturbation may not necessarily entail decreased community diversity. Moreover, signatures of greater fiber degradation indicate that captive sifakas consume a more fibrous diet compared to their wild counterparts. These results do not mirror those typically reported for folivores and herbivores, suggesting that the direction and strength of captivity-induced ‘dysbiosis’ may not be universal across species with similar feeding strategies. We propose that tailored, species-specific dietary interventions in captivity, aimed at better approximating naturally foraged diets, could functionally ‘rewild’ gut microbiota and facilitate successful management of diverse species. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00093-5.
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Moustafa MAM, Chel HM, Thu MJ, Bawm S, Htun LL, Win MM, Oo ZM, Ohsawa N, Lahdenperä M, Mohamed WMA, Ito K, Nonaka N, Nakao R, Katakura K. Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments. Sci Rep 2021; 11:741. [PMID: 33436882 PMCID: PMC7803949 DOI: 10.1038/s41598-020-80537-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.
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Affiliation(s)
- Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Hla Myet Chel
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - May June Thu
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
- Department of Food and Drug Administration, Ministry of Health and Sports, Zabu Thiri, Nay Pyi Taw, 15011, Myanmar
| | - Saw Bawm
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Mar Mar Win
- Rector Office, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Zaw Min Oo
- Department of Extraction, Myanma Timber Enterprise, Insein, Yangon, Myanmar
| | | | - Mirkka Lahdenperä
- Department of Public Health, Turku University Hospital, University of Turku, Turku, Finland
| | | | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan.
| | - Ken Katakura
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
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Guo W, Ren K, Ning R, Li C, Zhang H, Li D, Xu L, Sun F, Dai M. Fecal microbiota transplantation provides new insight into wildlife conservation. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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15
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Castle ST, Allan N, Clifford D, Aylward CM, Ramsey J, Fascetti AJ, Pesapane R, Roy A, Statham M, Sacks B, Foley J. Diet composition analysis provides new management insights for a highly specialized endangered small mammal. PLoS One 2020; 15:e0240136. [PMID: 33007017 PMCID: PMC7531790 DOI: 10.1371/journal.pone.0240136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole' nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3-8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at <1% in two marshes but none in the remaining marshes. Metabarcoding detected ten genera of plants. When considering non-Schoenoplectus targets, for which metabarcoding had poor sensitivity, saltgrass (Distichlis spicata) was the most commonly detected species, with prominent contributions from seaside arrowgrass (Triglochin concinna) and yerba mansa (Anemopsis californica) as well. Diversity of vole diets generally increased with increasing site plant diversity, but differences were not statistically significant. Confirming details about dietary behaviors is critical for informing appropriate conservation planning including habitat management and reintroduction of voles into new sites.
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Affiliation(s)
- Stephanie T. Castle
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Nora Allan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Deana Clifford
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Cody M. Aylward
- Department of Fish, Wildlife and Conservation Biology, University of California, Davis, CA, United States of America
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Jon Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Andrea J. Fascetti
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Risa Pesapane
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Austin Roy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Mark Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Benjamin Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
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Mittal P, Saxena R, Gupta A, Mahajan S, Sharma VK. The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Panthera Species. Front Microbiol 2020; 11:1012. [PMID: 32582053 PMCID: PMC7287027 DOI: 10.3389/fmicb.2020.01012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
Majority of metagenomic studies in the last decade have focused on revealing the gut microbiomes of humans, rodents, and ruminants; however, the gut microbiome and genic information (gene catalog) of large felids such as Panthera species are largely unknown to date. In this study, the gut bacterial, fungal, and viral metagenomic composition was assessed from three Panthera species (lion, leopard, and tiger) of Indian origin, which were consuming the same diet and belonged to the same geographical location. A non-redundant bacterial gene catalog of the Panthera gut consisting of 1,507,035 putative genes was constructed from 27 Panthera individuals, which revealed a higher abundance of purine metabolism genes correlating with their purine-rich dietary intake. Analysis with Carbohydrate Active enZyme (CAZy) and MEROPS databases identified enrichment of glycoside hydrolases (GHs), glycoside-transferases, and collagenases in the gut, which are important for nutrient acquisition from animal biomass. The bacterial, fungal, and viral community analysis provided the first comprehensive insights into the Panthera-specific microbial community. The Panthera gene catalog and the largest comparative study of the gut bacterial composition of 68 individuals of Carnivora species from different geographical locations and diet underscore the role of diet and geography in shaping the Panthera gut microbiome, which is significant for the health and conservation management of these highly endangered species.
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Affiliation(s)
- Parul Mittal
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | | | - Shruti Mahajan
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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van Leeuwen P, Mykytczuk N, Mastromonaco GF, Schulte‐Hostedde AI. Effects of captivity, diet, and relocation on the gut bacterial communities of white-footed mice. Ecol Evol 2020; 10:4677-4690. [PMID: 32551052 PMCID: PMC7297780 DOI: 10.1002/ece3.6221] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes can have important impacts on their host's survival. Captive breeding programs for endangered species include periods of captivity that can ultimately have an impact on reintroduction success. No study to date has investigated the impacts of captive diet on the gut microbiota during the relocation process of generalist species. This study simulated a captive breeding program with white-footed mice (Peromyscus leucopus) to describe the variability in gut microbial community structure and composition during captivity and relocation in their natural habitat, and compared it to wild individuals. Mice born in captivity were fed two different diets, a control with dry standardized pellets and a treatment with nonprocessed components that reflect a version of their wild diet that could be provided in captivity. The mice from the two groups were then relocated to their natural habitat. Relocated mice that had the treatment diet had more phylotypes in common with the wild-host microbiota than mice under the control diet or mice kept in captivity. These results have broad implications for our understanding of microbial community dynamics and the effects of captivity on reintroduced animals, including the potential impact on the survival of endangered species. This study demonstrates that ex situ conservation actions should consider a more holistic perspective of an animal's biology including its microbes.
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Affiliation(s)
- Pauline van Leeuwen
- Department of BiologyLaurentian UniversitySudburyONCanada
- Conservation Genetics LaboratoryUniversity of LiègeLiègeBelgium
| | - Nadia Mykytczuk
- Vale Living with Lakes CentreLaurentian UniversitySudburyONCanada
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18
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Waters JL, Ley RE. The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biol 2019; 17:83. [PMID: 31660948 PMCID: PMC6819567 DOI: 10.1186/s12915-019-0699-4] [Citation(s) in RCA: 373] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
Abstract
The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.
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Affiliation(s)
- Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tuebingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tuebingen, Germany.
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