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Marsh KJ, Bearhop S, Harrison XA. Linking microbiome temporal dynamics to host ecology in the wild. Trends Microbiol 2024:S0966-842X(24)00132-X. [PMID: 38797653 DOI: 10.1016/j.tim.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024]
Abstract
Ignoring the dynamic nature of microbial communities risks underestimating the power of microbes to impact the health of their hosts. Microbiomes are thought to be important for host fitness, yet the coarse temporal scale and population-level focus of many studies precludes the ability to investigate the importance of among-individual variation in stability and identify the ecological contexts in which this variation matters. Here we briefly summarise current knowledge of temporal dynamics in wild host-associated microbial communities. We then discuss the implications of among-individual variation in microbiota stability and suggest analytical approaches for understanding these patterns. One major requirement is for future studies to conduct individual-level longitudinal analyses, with some systems already well set up for answering these questions.
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Affiliation(s)
- Kirsty J Marsh
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK.
| | - Stuart Bearhop
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK
| | - Xavier A Harrison
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK.
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2
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Williams CE, Brown AE, Williams CL. The role of diet and host species in shaping the seasonal dynamics of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad156. [PMID: 38070877 PMCID: PMC10750813 DOI: 10.1093/femsec/fiad156] [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: 02/21/2023] [Revised: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023] Open
Abstract
The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.
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Affiliation(s)
- Claire E Williams
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Ashli E Brown
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS State, MS 39762, United States
| | - Candace L Williams
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS State, MS 39762, United States
- Beckman Center for Conservation Science, San Diego Zoo Wildlife Alliance, San Diego, CA 92027, United States
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3
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Yan M, Xu C, Li C, Feng Y, Duan J, Zhao K, Wu D, Li G, Yang S, Han X, Xie Y, Huang Y, Yu X, Wu J, Zou L. Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure. ENVIRONMENTAL RESEARCH 2023; 235:116662. [PMID: 37453509 DOI: 10.1016/j.envres.2023.116662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/02/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.
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Affiliation(s)
- Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Yongqi Feng
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Juntang Duan
- Shanghai Wild Animal Park, Shanghai, 201399, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Guo Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Xinfeng Han
- College of Veterinary Science, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yue Xie
- College of Veterinary Science, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiawei Wu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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4
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Yao Y, Zhao W, Xiang G, Lv R, Dong Y, Yan H, Li M. Bamboo Plant Part Preference Affects the Nutrients Digestibility and Intestinal Microbiota of Geriatric Giant Pandas. Animals (Basel) 2023; 13:ani13050844. [PMID: 36899701 PMCID: PMC10000146 DOI: 10.3390/ani13050844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Bamboo part preference plays a critical role in influencing the nutrient utilization and gastrointestinal microbiota composition of captive giant pandas. However, the effects of bamboo part consumption on the nutrient digestibility and gut microbiome of geriatric giant pandas remain unknown. A total of 11 adult and 11 aged captive giant pandas were provided with bamboo shoots or bamboo leaves in the respective single-bamboo-part consumption period, and the nutrient digestibility and fecal microbiota of both adult and aged giant pandas in each period were evaluated. Bamboo shoot ingestion increased the crude protein digestibility and decreased the crude fiber digestibility of both age groups. The fecal microbiome of the bamboo shoot-fed giant pandas exhibited greater alpha diversity indices and significantly different beta diversity index than the bamboo leaf-fed counterparts regardless of age. Bamboo shoot feeding significantly changed the relative abundance of predominant taxa at both phylum and genus levels in adult and geriatric giant pandas. Bamboo shoot-enriched genera were positively correlated with crude protein digestibility and negatively correlated with crude fiber digestibility. Taken together, these results suggest that bamboo part consumption dominates over age in affecting the nutrient digestibility and gut microbiota composition of giant pandas.
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Affiliation(s)
- Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
| | - Wenjia Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Guilin Xiang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Ruiqing Lv
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
| | - Yanpeng Dong
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
| | - Honglin Yan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Correspondence: (H.Y.); (M.L.)
| | - Mingxi Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Correspondence: (H.Y.); (M.L.)
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Tan Y, Wang J, He Y, Yu X, Chen S, Penttinen P, Liu S, Yang Y, Zhao K, Zou L. Organic Fertilizers Shape Soil Microbial Communities and Increase Soil Amino Acid Metabolites Content in a Blueberry Orchard. MICROBIAL ECOLOGY 2023; 85:232-246. [PMID: 35064809 DOI: 10.1007/s00248-022-01960-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The decline in soil nutrients is becoming a major concern of soil degradation. The possibility of using organic waste as a soil additive to increase nutrients and essential components is significant in soil quality protection and waste management. The aim of this study was to investigate the effects of composted spent mushroom substrate (MS), giant panda feces (PF), and cattle manure (CM) as organic fertilizers in soil microbial communities and metabolites in blueberry orchard in China, which were measured by using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Altogether, 45.66% of the bacterial operational taxonomic units (OTUs) and 9.08% of the fungal OTUs were detected in all treatments. Principal coordinates analysis demonstrated that the bacterial and fungal communities in MS and PF treatments were similar, whereas the communities in the not-organic fertilized control (CK) were significantly different from those in the organic fertilizer treatments. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant bacterial phyla, and Basidiomycota, Ascomycota, and Mortierellomycota the dominant fungal phyla. Redundancy analysis indicated that pH and available potassium were the main factors determining the composition of microbial communities. The fungal genera Postia, Cephalotrichum, and Thermomyces increased in organic fertilizer treatments, and likely promoted the degradation of organic fertilizers into low molecular-weight metabolites (e.g., amino acids). PCA and PLS-DA models showed that the metabolites in CK were different from those in the other three treatments, and those in CM were clearly different from those in MS and PF. Co-occurrence network analysis showed that several taxa correlated positively with amino acid contents. The results of this study provide new insights into organic waste reutilization and new directions for further studies.
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Affiliation(s)
- Yulan Tan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Wang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yongguo He
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan, 611830, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Petri Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu Sichuan, 611130, China.
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District, Chengdu Sichuan, 611130, China.
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Suo P, Wang K, Yu H, Fu X, An L, Bhowmick B, Zhang J, Han Q. Seasonal Variation of Midgut Bacterial Diversity in Culex quinquefasciatus Populations in Haikou City, Hainan Province, China. BIOLOGY 2022; 11:biology11081166. [PMID: 36009794 PMCID: PMC9405131 DOI: 10.3390/biology11081166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Mosquito midgut microbiota has become an interesting field in mosquito vector biology, as it has been shown to form an integral part of the mosquito life history. But less is known about seasonal variation of midgut bacterial diversity of Culex quinquefasciatus. Our results illustrate that the Bacteroidetes (Bacterial Phyla) communities have been well observed in autumn and winter seasons, suggesting that this might participate in the nutritional supply of adult mosquitoes when temperatures drop. This discovery provides a new perspective for the control of Cx. quinquefasciatus to reduce the transmission of diseases. There is much sufficiently practical significance to reduce the density of Cx. quinquefasciatus in autumn and winter when their activities are weakened, which is of absolute benefit to human beings and the natural environment. Abstract Culex quinquefasciatus, one of the most significant mosquito vectors in the world, is widespread in most parts of southern China. A variety of diseases including Bancroft’s filariasis, West Nile disease, and St. Louis encephalitis could be transmitted by the vector. Mosquitoes have been shown to host diverse bacterial communities that vary depending on environmental factors such as temperature and rainfall. In this work, 16S rDNA sequencing was used to analyze the seasonal variation of midgut bacterial diversity of Cx. Quinquefasciatus in Haikou City, Hainan Province, China. Proteobacteria was the dominant phylum, accounting for 79.7% (autumn), 73% (winter), 80.4% (spring), and 84.5% (summer). The abundance of Bacteroidetes in autumn and winter was higher than in others. Interestingly, Epsilonbacteraeota, which only exists in autumn and winter, was discovered accidentally in the midgut. We speculated that this might participate in the nutritional supply of adult mosquitoes when temperatures drop. Wolbachia is the most abundant in autumn, accounting for 31.6% of bacteria. The content of Pantoea was highest in the summer group, which might be related to the enhancement of the ability of mosquitoes as temperatures increased. Pseudomonas is carried out as the highest level in winter. On the contrary, in spring and summer, the genus in highest abundance is Enterobacter. Acinetobacter enriches in the spring when it turns from cold to hot. By studying the diversity of midgut bacteria of Cx. quinquefasciatus, we can further understand the co-evolution of mosquitoes and their symbiotic microbes. This is necessary to discuss the seasonal variation of microorganisms and ultimately provide a new perspective for the control of Cx. quinquefasciatus to reduce the spread of the diseases which have notably vital practical significance for the effective prevention of Cx. quinquefasciatus.
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Affiliation(s)
- Penghui Suo
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
| | - Kaixuan Wang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
| | - Hongxiao Yu
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
| | - Xiuhao Fu
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
| | - Liping An
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
| | - Biswajit Bhowmick
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
| | - Jiachao Zhang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China;
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China; (P.S.); (K.W.); (H.Y.); (X.F.); (L.A.); (B.B.)
- One Health Institute, Hainan University, Haikou 570228, China
- Correspondence:
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7
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Zhan M, Wang A, Yao Y, Zhou Y, Zhang S, Fu X, Zhou J, Pei E, Wang L. An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures. Front Microbiol 2022; 13:926515. [PMID: 35958139 PMCID: PMC9363027 DOI: 10.3389/fmicb.2022.926515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/04/2022] [Indexed: 11/14/2022] Open
Abstract
The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | | | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
- *Correspondence: Lei Wang,
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8
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Marsh KJ, Raulo AM, Brouard M, Troitsky T, English HM, Allen B, Raval R, Venkatesan S, Pedersen AB, Webster JP, Knowles SCL. Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations. Front Microbiol 2022; 13:809735. [PMID: 35547129 PMCID: PMC9083407 DOI: 10.3389/fmicb.2022.809735] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/08/2022] [Indexed: 12/03/2022] Open
Abstract
The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.
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Affiliation(s)
- Kirsty J Marsh
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Cornwall, United Kingdom
| | - Aura M Raulo
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc Brouard
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Tanya Troitsky
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Holly M English
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Bryony Allen
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Rohan Raval
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Saudamini Venkatesan
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy B Pedersen
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Sarah C L Knowles
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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9
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Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study. Microorganisms 2022; 10:microorganisms10050978. [PMID: 35630422 PMCID: PMC9146640 DOI: 10.3390/microorganisms10050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Giant pandas feed almost exclusively on bamboo but miss lignocellulose-degrading genes. Their gut microbiome may contribute to their nutrition; however, the limited access to pandas makes experimentation difficult. In vitro incubation of dung samples is used to infer gut microbiome activity. In pandas, such tests indicated that green leaves are largely fermented to ethanol at neutral pH and yellow pith to lactate at acidic pH. Pandas may feed on either green leaves or yellow pith within the same day, and it is unclear how pH, dung sample, fermentation products and supplied bamboo relate to one another. Additionally, the gut microbiome contribution to solid bamboo digestion must be appropriately assessed. Here, gut microbiomes derived from dung samples with mixed colors were used to ferment green leaves, also by artificially adjusting the initial pH. Gut microbiomes digestion of solid lignocellulose accounted for 30–40% of the detected final fermentation products. At pH 6.5, mixed-color dung samples had the same fermentation profile as green dung samples (mainly alcohols), while adjusting the initial pH to 4.5 resulted in the profile of yellow dung samples (mainly lactate). Metaproteomics confirmed that gut microbiomes attacked hemicellulose, and that the panda’s alpha amylase was the predominant enzyme (up to 75%).
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10
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Martínez‐Romero E, Aguirre‐Noyola JL, Bustamante‐Brito R, González‐Román P, Hernández‐Oaxaca D, Higareda‐Alvear V, Montes‐Carreto LM, Martínez‐Romero JC, Rosenblueth M, Servín‐Garcidueñas LE. We and herbivores eat endophytes. Microb Biotechnol 2021; 14:1282-1299. [PMID: 33320440 PMCID: PMC8313258 DOI: 10.1111/1751-7915.13688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.
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Affiliation(s)
| | | | | | - Pilar González‐Román
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
| | | | | | | | | | - Mónica Rosenblueth
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
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11
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Zhan M, Wang L, Xie C, Fu X, Zhang S, Wang A, Zhou Y, Xu C, Zhang H. Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism. Front Microbiol 2020; 11:551038. [PMID: 33072012 PMCID: PMC7537565 DOI: 10.3389/fmicb.2020.551038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation to a bamboo diet is an essential process for giant panda growth, and gut microbes play an important role in the digestion of the polysaccharides in bamboo. The dietary transition in giant panda cubs is particularly complex, but it is an ideal period in which to study the effects of gut microbes on polysaccharide use because their main food changes from milk to bamboo (together with some bamboo shoot and coarse pastry). Here, we used 16S rDNA and internal transcribed spacer 1 (ITS1) DNA sequencing and metagenomic sequencing analysis to investigate the succession of the gut microbial structure in feces sampled from twin giant panda cubs during the completely dietary transition and determine the abundances of polysaccharide-metabolizing genes and their corresponding microbes to better understand the degradation of bamboo polysaccharides. Successive changes in the gut microbial diversity and structure were apparent in the growth of pandas during dietary shift process. Microbial diversity increased after the introduction of supplementary foods and then varied in a complex way for 1.5–2 years as bamboo and complex food components were introduced. They then stabilized after 2 years, when the cubs consumed a specialized bamboo diet. The microbes had more potential to metabolize the cellulose in bamboo than the hemicellulose, providing genes encoding cellulase systems corresponding to glycoside hydrolases (GHs; such as GH1, GH3, GH5, GH8, GH9, GH74, and GH94). The cellulose-metabolizing species (or genes) of gut bacteria was more abundant than that of gut fungi. Although cellulose-metabolizing species did not predominate in the gut bacterial community, microbial interactions allowed the giant pandas to achieve the necessary dietary shift and ultimately adapt to a bamboo diet.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Chunyu Xie
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Hemin Zhang
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
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12
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Jin L, Wu D, Li C, Zhang A, Xiong Y, Wei R, Zhang G, Yang S, Deng W, Li T, Li B, Pan X, Zhang Z, Huang Y, Zhang H, He Y, Zou L. Bamboo nutrients and microbiome affect gut microbiome of giant panda. Symbiosis 2020. [DOI: 10.1007/s13199-020-00673-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Cabana F, Yusof O, Kawi J, Li D, Huang Y, Wang P, Tay T. Seasonal diet switching in captive giant pandas. URSUS 2020. [DOI: 10.2192/ursus-d-17-00023.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Francis Cabana
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826
| | - Omar Yusof
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826
| | - Josephine Kawi
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826
| | - Desheng Li
- China Conservation and Research Centre for the Giant Panda (CCRCGP), 1275 Xiongmao Ave, Chengua, Chendu, Sichuan, China, 610016
| | - Yan Huang
- China Conservation and Research Centre for the Giant Panda (CCRCGP), 1275 Xiongmao Ave, Chengua, Chendu, Sichuan, China, 610016
| | | | - Trisha Tay
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826
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14
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Scoma A, Khor WC, Coma M, Heyer R, Props R, Schoelynck J, Bouts T, Benndorf D, Li D, Zhang H, Rabaey K. Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate. Front Microbiol 2020; 11:530. [PMID: 32300339 PMCID: PMC7145396 DOI: 10.3389/fmicb.2020.00530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/11/2020] [Indexed: 01/31/2023] Open
Abstract
The giant panda is known worldwide for having successfully moved to a diet almost exclusively based on bamboo. Provided that no lignocellulose-degrading enzyme was detected in panda's genome, bamboo digestion is believed to depend on its gut microbiome. However, pandas retain the digestive system of a carnivore, with retention times of maximum 12 h. Cultivation of their unique gut microbiome under controlled laboratory conditions may be a valid tool to understand giant pandas' dietary habits, and provide valuable insights about what component of lignocellulose may be metabolized. Here, we collected gut microbiomes from fresh fecal samples of a giant panda (either entirely green or yellow stools) and supplied them with green leaves or yellow pith (i.e., the peeled stem). Microbial community composition was substrate dependent, and resulted in markedly different fermentation profiles, with yellow pith fermented to lactate and green leaves to lactate, acetate and ethanol, the latter to strikingly high concentrations (∼3%, v:v, within 3.5 h). Microbial metaproteins pointed to hemicellulose rather than cellulose degradation. The alpha-amylase from the giant panda (E.C. 3.2.1.1) was the predominant identified metaprotein, particularly in reactors inoculated with pellets derived from fecal samples (up to 60%). Gut microbiomes assemblage was most prominently impacted by the change in substrate (either leaf or pith). Removal of soluble organics from inocula to force lignocellulose degradation significantly enriched Bacteroides (in green leaf) and Escherichia/Shigella (in yellow pith). Overall, different substrates (either leaf or pith) markedly shaped gut microbiome assemblies and fermentation profiles. The biochemical profile of fermentation products may be an underestimated factor contributing to explain the peculiar dietary behavior of giant pandas, and should be implemented in large scale studies together with short-term lab-scale cultivation of gut microbiomes.
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Affiliation(s)
- Alberto Scoma
- Center for Microbial Ecology and Technology, University of Ghent, Ghent, Belgium.,Department of Bioscience, Microbiology Section, Aarhus University, Aarhus C, Denmark.,Department of Engineering, Biological and Chemical Engineering, Aarhus University, Aarhus N, Denmark
| | - Way Cern Khor
- Center for Microbial Ecology and Technology, University of Ghent, Ghent, Belgium
| | - Marta Coma
- Center for Microbial Ecology and Technology, University of Ghent, Ghent, Belgium
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University of Magdeburg, Magdeburg, Germany
| | - Ruben Props
- Center for Microbial Ecology and Technology, University of Ghent, Ghent, Belgium
| | | | - Tim Bouts
- Pairi Daiza Foundation, Brugelette, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University of Magdeburg, Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Desheng Li
- China Conservation and Research Centre for Giant Panda, Dujiangyan City, China
| | - Hemin Zhang
- China Conservation and Research Centre for Giant Panda, Dujiangyan City, China
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology, University of Ghent, Ghent, Belgium
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15
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Gao H, Chi X, Li G, Qin W, Song P, Jiang F, Liu D, Zhang J, Zhou X, Li S, Zhang T. Gut microbial diversity and stabilizing functions enhance the plateau adaptability of Tibetan wild ass (Equus kiang). Microbiologyopen 2020; 9:1150-1161. [PMID: 32157819 PMCID: PMC7294314 DOI: 10.1002/mbo3.1025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/20/2022] Open
Abstract
Interactions between gut microbiota not only regulate physical health, but also form a vital bridge between the environment and the host, thus helping the host to better adapt to the environment. The improvement of modern molecular sequencing techniques enables in‐depth investigations of the gut microbiota of vertebrate herbivores without harming them. By sequencing the 16S rRNA V4‐V5 region of the gut microbiota of both the captive and wild kiang in winter and summer, the diversity and function of the microbiota could be compared. The reasons for observed differences were discussed. The results showed that the dominant phyla of the kiang were Bacteroidetes and Firmicutes, and the structure and abundance of the gut microbiota differed significantly between seasons and environments. However, the relatively stable function of the gut microbiota supplies the host with increased adaptability to the environment. The diversity of the intestinal flora of the kiang is relatively low in captivity, which increases their risk to catch diseases to some extent. Therefore, importance should be attached to the impact of captivity on wildlife.
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Affiliation(s)
- Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangwen Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangying Li
- Qinghai Provincial Environmental Protection Department, Xining, China
| | - Wen Qin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Daoxin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Shengqing Li
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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16
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Tang J, Wang C, Zhang H, Zhao J, Guo W, Mishra S, Kong F, Zeng B, Ning R, Li D, Yang J, Yang M, Zhang M, Ni Q, Li Y, Li Y. Gut microbiota in reintroduction of giant panda. Ecol Evol 2020; 10:1012-1028. [PMID: 32015861 PMCID: PMC6988533 DOI: 10.1002/ece3.5963] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 01/21/2023] Open
Abstract
Reintroduction is a key approach in the conservation of endangered species. In recent decades, many reintroduction projects have been conducted for conservation purposes, but the rate of success has been low. Given the important role of gut microbiota in health and diseases, we questioned whether gut microbiota would play a crucial role in giant panda's wild-training process. The wild procedure is when captive-born babies live with their mothers in a wilderness enclosure and learn wilderness survival skills from their mothers. During the wild-training process, the baby pandas undergo wilderness survival tests and regular physical examinations. Based on their performance through these tests, the top subjects (age 2-3 years old) are released into the wild while the others are translocated to captivity. After release, we tracked one released panda (Zhangxiang) and collected its fecal samples for 5 months (January 16, 2013 to March 29 2014). Here, we analyzed the Illumina HiSeq sequencing data (V4 region of 16S rRNA gene) from captive pandas (n = 24), wild-training baby pandas (n = 8) of which 6 were released and 2 were unreleased, wild-training mother pandas (n = 8), one released panda (Zhangxiang), and wild giant pandas (n = 18). Our results showed that the gut microbiota of wild-training pandas is significantly different from that of wild pandas but similar to that of captive ones. The gut microbiota of the released panda Zhangxiang gradually changed to become similar to those of wild pandas after release. In addition, we identified several bacteria that were enriched in the released baby pandas before release, compared with the unreleased baby pandas. These bacteria include several known gut-health related beneficial taxa such as Roseburia, Coprococcus, Sutterella, Dorea, and Ruminococcus. Therefore, our results suggest that certain members of the gut microbiota may be important in panda reintroduction.
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Affiliation(s)
- Jingsi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Chengdong Wang
- China Conservation and Research Center for the Giant PandaYa'anSichuanChina
| | - Hemin Zhang
- China Conservation and Research Center for the Giant PandaYa'anSichuanChina
| | - Jiangchao Zhao
- Department of Animal ScienceDivision of AgricultureUniversity of ArkansasFayettevilleARUSA
| | - Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Desheng Li
- China Conservation and Research Center for the Giant PandaYa'anSichuanChina
| | - Jiandong Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduSichuanChina
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17
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Trevelline BK, Fontaine SS, Hartup BK, Kohl KD. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc Biol Sci 2019; 286:20182448. [PMID: 30963956 PMCID: PMC6364583 DOI: 10.1098/rspb.2018.2448] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers the effects, both direct and indirect, of anthropogenic disturbances on wildlife physiology and health. A recent surge in research has revealed that host-associated microbiota-the archaeal, bacterial, fungal and viral communities residing on and inside organisms-profoundly influence animal health, and that these microbial communities can be drastically altered by anthropogenic activities. Therefore, conservation practitioners should consider the disruption of host-associated microbial diversity as a serious threat to wildlife populations. Despite the tremendous potential for microbiome research to improve conservation outcomes, few efforts have been made to truly integrate these fields. In this review, we call for the microbial renaissance of conservation biology, where biodiversity of host-associated microbiota is recognized as an essential component of wildlife management practices. Using evidence from the existing literature, we will examine the known effects of anthropogenic activities on the diversity of host-associated microbial communities and integrate approaches for maintaining microbial diversity to successfully achieve conservation objectives.
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Affiliation(s)
- Brian K. Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha S. Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barry K. Hartup
- Department of Conservation Medicine, International Crane Foundation, Baraboo, WI, USA
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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18
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Hu X, Liu G, Li Y, Wei Y, Lin S, Liu S, Zheng Y, Hu D. High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer ( Moschus berezovskii). Front Microbiol 2018; 9:1674. [PMID: 30093891 PMCID: PMC6070636 DOI: 10.3389/fmicb.2018.01674] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023] Open
Abstract
The gut microbiota plays a key role in the nutritional ecology of ruminants, and host diet has a significant effect on these microbial communities. Longitudinal studies assessing variation of seasonal microbiota in animals can provide a comparative context for interpreting the adaptive significance of such changes. However, few studies have investigated the effects of seasonally-related dietary shifts on the gut microbial communities of endangered forest musk deer (FMD), and the national breeding programs need this information to promote the growth of captive populations. The present study applied bacterial 16S rRNA genes based on high-throughput sequencing to profile the fecal microbial communities of FMD across four seasons. Microbial diversity was higher in seasons with dry leaf diets (winter and spring) compared to seasons with fresh leaf diets (summer and autumn). The dominant microbial phyla were Firmicutes and Bacteroidetes, and the core bacterial taxa also comprised mostly (94.40% of shared OTUs) Firmicutes (37 taxa) and Bacteroidetes (6 taxa), which were relatively stable across different seasons. The Firmicutes-Bacteroidetes ratio declined in seasons with fresh leaf diets relative to seasons with dry leaf diets, and the dominant genera among the four seasons showed no significant variation in abundance. This work explores the seasonal variation in the microbial communities of FMD for the first time, and reveals how gut microbial community dynamics vary seasonally in accordance with differences in dietary plants (fresh and dry leaf). These results indicate that the annual cyclic reconfiguration of FMD gut microbiota could be associated with shifts in dietary nutrients, which is important information to inform captive FMD management.
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Affiliation(s)
- Xiaolong Hu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Gang Liu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Yimeng Li
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuting Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Shaobi Lin
- Zhangzhou Pien Tze Huang Pharmaceutical, Co., Ltd., Zhangzhou, China
| | - Shuqiang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yunlin Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Defu Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
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19
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Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME JOURNAL 2018; 13:576-587. [PMID: 29995839 DOI: 10.1038/s41396-018-0175-0] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/18/2018] [Accepted: 03/27/2018] [Indexed: 11/09/2022]
Abstract
Over the past decade several studies have reported that the gut microbiomes of mammals with similar dietary niches exhibit similar compositional and functional traits. However, these studies rely heavily on samples from captive individuals and often confound host phylogeny, gut morphology, and diet. To more explicitly test the influence of host dietary niche on the mammalian gut microbiome we use 16S rRNA gene amplicon sequencing and shotgun metagenomics to compare the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely related non-folivores, evenly distributed throughout the primate order and representing a range of gut morphological specializations. While folivory results in some convergent microbial traits, collectively we show that the influence of host phylogeny on both gut microbial composition and function is much stronger than that of host dietary niche. This pattern does not result from differences in host geographic location or actual dietary intake at the time of sampling, but instead appears to result from differences in host physiology. These findings indicate that mammalian gut microbiome plasticity in response to dietary shifts over both the lifespan of an individual host and the evolutionary history of a given host species is constrained by host physiological evolution. Therefore, the gut microbiome cannot be considered separately from host physiology when describing host nutritional strategies and the emergence of host dietary niches.
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20
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Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas. mSphere 2018; 3:3/3/e00229-18. [PMID: 29898983 PMCID: PMC6001608 DOI: 10.1128/msphere.00229-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/19/2018] [Indexed: 12/20/2022] Open
Abstract
The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature. Gut microbes can enhance the ability of hosts to consume secondary plant compounds and, therefore, expand the dietary niche breadth of mammalian herbivores. The giant and red pandas are bamboo-eating specialists within the mammalian order Carnivora. Bamboo contains abundant plant secondary metabolites (e.g., cyanide-containing compounds). However, Carnivora species, including the giant panda, have deficient levels of rhodanese (one of the essential cyanide detoxification enzymes) in their tissues compared with the same tissues of herbivores. Here, we make a comparative analysis of 94 gut metagenomes, including 25 from bamboo-eating pandas (19 from giant pandas and 6 from red pandas), 30 from Père David’s deer, and 39 from published data for other mammals. The bamboo-eating pandas’ gut microbiomes had some common features, such as high proportions of Pseudomonas bacteria. The results revealed that bamboo-eating pandas’ gut microbiomes were significantly enriched in putative genes coding for enzymes related to cyanide degradation (e.g., rhodanese) compared with the gut microbiomes of typical herbivorous mammals, which might have coevolved with their special bamboo diets. The enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. IMPORTANCE The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature.
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21
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Mallott EK, Amato KR, Garber PA, Malhi RS. Influence of fruit and invertebrate consumption on the gut microbiota of wild white‐faced capuchins (
Cebus capucinus
). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:576-588. [DOI: 10.1002/ajpa.23395] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/09/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Elizabeth K. Mallott
- Department of AnthropologyNorthwestern University1810 Hinman Ave, Evanston Illinois 60208
| | - Katherine R. Amato
- Department of AnthropologyNorthwestern University1810 Hinman Ave, Evanston Illinois 60208
| | - Paul A. Garber
- Department of AnthropologyUniversity of Illinois at Urbana‐Champaign109A Davenport Hall, 607 South Mathews Avenue, Urbana Illinois 61801
| | - Ripan S. Malhi
- Department of AnthropologyUniversity of Illinois at Urbana‐Champaign109A Davenport Hall, 607 South Mathews Avenue, Urbana Illinois 61801
- Carl R Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐Champaign1206 West Gregory Drive, Urbana Illinois 61801
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Williams CL, Caraballo-Rodríguez AM, Allaband C, Zarrinpar A, Knight R, Gauglitz JM. Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2019.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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23
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Springer A, Fichtel C, Al‐Ghalith GA, Koch F, Amato KR, Clayton JB, Knights D, Kappeler PM. Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas ( Propithecus verreauxi). Ecol Evol 2017; 7:5732-5745. [PMID: 28808547 PMCID: PMC5551086 DOI: 10.1002/ece3.3148] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/08/2017] [Accepted: 05/17/2017] [Indexed: 12/27/2022] Open
Abstract
The intestinal microbiota plays a major role in host development, metabolism, and health. To date, few longitudinal studies have investigated the causes and consequences of microbiota variation in wildlife, although such studies provide a comparative context for interpreting the adaptive significance of findings from studies on humans or captive animals. Here, we investigate the impact of seasonality, diet, group membership, sex, age, and reproductive state on gut microbiota composition in a wild population of group-living, frugi-folivorous primates, Verreaux's sifakas (Propithecus verreauxi). We repeatedly sampled 32 individually recognizable animals from eight adjacent groups over the course of two different climatic seasons. We used high-throughput sequencing of the 16S rRNA gene to determine the microbiota composition of 187 fecal samples. We demonstrate a clear pattern of seasonal variation in the intestinal microbiota, especially affecting the Firmicutes-Bacteroidetes ratio, which may be driven by seasonal differences in diet. The relative abundances of certain polysaccharide-fermenting taxa, for example, Lachnospiraceae, were correlated with fruit and fiber consumption. Additionally, group membership influenced microbiota composition independent of season, but further studies are needed to determine whether this pattern is driven by group divergences in diet, social contacts, or genetic factors. In accordance with findings in other wild mammals and primates with seasonally fluctuating food availability, we demonstrate seasonal variation in the microbiota of wild Verreaux's sifakas, which may be driven by food availability. This study adds to mounting evidence that variation in the intestinal microbiota may play an important role in the ability of primates to cope with seasonal variation in food availability.
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Affiliation(s)
- Andrea Springer
- Behavioral Ecology and Sociobiology UnitGerman Primate CenterGöttingenGermany
- Institute for Parasitology, Centre for Infection MedicineUniversity of Veterinary Medicine HannoverHanoverGermany
- Present address:
Institute for ParasitologyCentre for Infection MedicineUniversity of Veterinary Medicine HannoverHanoverGermany
| | - Claudia Fichtel
- Behavioral Ecology and Sociobiology UnitGerman Primate CenterGöttingenGermany
| | - Gabriel A. Al‐Ghalith
- Biomedical Informatics and Computational BiologyUniversity of MinnesotaMinneapolisMNUSA
| | - Flávia Koch
- Behavioral Ecology and Sociobiology UnitGerman Primate CenterGöttingenGermany
- Department of PsychologyUniversity of LethbridgeLethbridgeABCanada
| | | | - Jonathan B. Clayton
- Department of Veterinary and Biomedical SciencesUniversity of MinnesotaSaint PaulMNUSA
- GreenViet Biodiversity Conservation CenterSon Tra District, DanangVietnam
| | - Dan Knights
- Biotechnology InstituteUniversity of MinnesotaSaint PaulMNUSA
- Computer Science and EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter M. Kappeler
- Behavioral Ecology and Sociobiology UnitGerman Primate CenterGöttingenGermany
- Department of Sociobiology/AnthropologyUniversity of GöttingenGöttingenGermany
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Knott KK, Christian AL, Falcone JF, Vance CK, Bauer LL, Fahey GC, Kouba AJ. Phenological changes in bamboo carbohydrates explain the preference for culm over leaves by giant pandas (Ailuropoda melanoleuca) during spring. PLoS One 2017; 12:e0177582. [PMID: 28614359 PMCID: PMC5470666 DOI: 10.1371/journal.pone.0177582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 04/28/2017] [Indexed: 11/29/2022] Open
Abstract
Seasonal changes in the foodscape force herbivores to select different plant species or plant parts to meet nutritional requirements. We examined whether the search for calorie-rich carbohydrates explained giant panda’s selection for bamboo culm over leaves during spring. Leaves and culms were collected from four Phyllostachys bamboos (P. aurea, P. aureosulcata, P. glauca, and P. nuda) once per month over 18–27 months. Monthly changes in annual plant part nutrients were examined, and compared to seasonal foraging behaviors of captive giant pandas. Although total fiber was greater (p<0.0001) in culm (85.6 ± 0.5%) than leaves (55.3 ± 0.4%) throughout the year, culm fiber was at its lowest in spring (79–85%) when culm selection by giant pandas exceeded 70% of their overall diet. Culm starch also was greatest (p = 0.044) during spring (5.5 ± 1.1%) and 2.5-fold the percentage of starch in leaves (2.2 ± 0.6%). The free sugars in spring culm consisted of a high proportion of glucose (35%) and fructose (47%), whereas sucrose made up 42% of the total free sugar content of spring leaves. Bound sugars in culm consisted of 60% glucose and 38% xylose likely representative of hemicellulose. The concentrations of bound sugars (hemicelluloses) in spring culms (543.7 ± 13.0 mg/g) was greater (p<0.001) than in leaves (373.0 ± 14.8 mg/g). These data help explain a long-standing question in giant panda foraging ecology: why consume the plant part with the lowest protein and fat during the energetically intensive spring breeding season? Giant pandas likely prefer spring culm that contains abundant mono- and polysaccharides made more bioavailable as a result of reduced fiber content. These data suggest that phenological changes in bamboo plant part nutrition drive foraging decisions by giant pandas.
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Affiliation(s)
- Katrina K. Knott
- Conservation and Research Department, Memphis Zoological Society, Memphis, Tennessee, United States of America
- * E-mail:
| | - Amelia L. Christian
- Conservation and Research Department, Memphis Zoological Society, Memphis, Tennessee, United States of America
- Department of Animal Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Josephine F. Falcone
- Conservation and Research Department, Memphis Zoological Society, Memphis, Tennessee, United States of America
| | - Carrie K. Vance
- Biochemistry, Molecular Biology, Entomology, and Plant Pathology Department, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Laura L. Bauer
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - George C. Fahey
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Andrew J. Kouba
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Mississippi State, Mississippi, United States of America
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25
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Williams CL, Dill-McFarland KA, Vandewege MW, Sparks DL, Willard ST, Kouba AJ, Suen G, Brown AE. Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca). Front Microbiol 2016; 7:661. [PMID: 27199976 PMCID: PMC4858621 DOI: 10.3389/fmicb.2016.00661] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 01/19/2023] Open
Abstract
Dietary shifts can result in changes to the gastrointestinal tract (GIT) microbiota, leading to negative outcomes for the host, including inflammation. Giant pandas (Ailuropoda melanoleuca) are physiologically classified as carnivores; however, they consume an herbivorous diet with dramatic seasonal dietary shifts and episodes of chronic GIT distress with symptoms including abdominal pain, loss of appetite and the excretion of mucous stools (mucoids). These episodes adversely affect the overall nutritional and health status of giant pandas. Here, we examined the fecal microbiota of two giant pandas’ non-mucoid and mucoid stools and compared these to samples from a previous winter season that had historically few mucoid episodes. To identify the microbiota present, we isolated and sequenced the 16S rRNA using next-generation sequencing. Mucoids occurred following a seasonal feeding switch from predominately bamboo culm (stalk) to leaves. All fecal samples displayed low diversity and were dominated by bacteria in the phyla Firmicutes and to a lesser extent, Proteobacteria. Fecal samples immediately prior to mucoid episodes had lower microbial diversity as compared to mucoids. Mucoids were mostly comprised of common mucosal-associated taxa including Streptococcus and Leuconostoc species, and exhibited increased abundance for bacteria in the family Pasteurellaceae. Taken together, these findings indicate that mucoids may represent an expulsion of the mucosal lining that is driven by changes in diet. We suggest that these occurrences serve to reset their GIT microbiota following changes in bamboo part preference, as giant pandas have retained a carnivorous GIT anatomy while shifting to an herbivorous diet.
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Affiliation(s)
- Candace L Williams
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State UniversityMississippi State, Mississippi, MS, USA
| | | | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Mississippi State, Mississippi, MS, USA
| | - Darrell L Sparks
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Mississippi State Chemical LaboratoryMississippi State, Mississippi, MS, USA
| | - Scott T Willard
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Mississippi State, Mississippi, MS, USA
| | - Andrew J Kouba
- Department of Conservation and Research, Memphis Zoological Society Memphis, TN, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Ashli E Brown
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Mississippi State Chemical LaboratoryMississippi State, Mississippi, MS, USA
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26
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Peng Z, Zeng D, Wang Q, Niu L, Ni X, Zou F, Yang M, Sun H, Zhou Y, Liu Q, Yin Z, Pan K, Jing B. Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca). World J Microbiol Biotechnol 2016; 32:79. [PMID: 27038949 DOI: 10.1007/s11274-016-2034-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 02/14/2016] [Indexed: 01/19/2023]
Abstract
It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics (p < 0.05), but not significant compared to the subadults (p > 0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults (p < 0.05), while other bacterial groups and species detected did not significantly differ among the three age groups (p > 0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition.
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Affiliation(s)
- Zhirong Peng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Zeng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Qiang Wang
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Fuqin Zou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingyue Yang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Hao Sun
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qian Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
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27
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Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia 2015; 180:717-33. [DOI: 10.1007/s00442-015-3507-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/02/2015] [Indexed: 01/01/2023]
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28
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The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations. mBio 2015; 6:e00022-15. [PMID: 25991678 PMCID: PMC4442137 DOI: 10.1128/mbio.00022-15] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The giant panda evolved from omnivorous bears. It lives on a bamboo-dominated diet at present, but it still retains a typical carnivorous digestive system and is genetically deficient in cellulose-digesting enzymes. To find out whether this endangered mammalian species, like other herbivores, has successfully developed a gut microbiota adapted to its fiber-rich diet, we conducted a 16S rRNA gene-based large-scale structural profiling of the giant panda fecal microbiota. Forty-five captive individuals were sampled in spring, summer, and late autumn within 1 year. Significant intraindividual variations in the diversity and structure of gut microbiota across seasons were observed in this population, which were even greater than the variations between individuals. Compared with published data sets involving 124 gut microbiota profiles from 54 mammalian species, these giant pandas, together with 9 captive and 7 wild individuals investigated previously, showed extremely low gut microbiota diversity and an overall structure that diverged from those of nonpanda herbivores but converged with those of carnivorous and omnivorous bears. The giant panda did not harbor putative cellulose-degrading phylotypes such as Ruminococcaceae and Bacteroides bacteria that are typically enriched in other herbivores, but instead, its microbiota was dominated by Escherichia/Shigella and Streptococcus bacteria. Members of the class Clostridia were common and abundant in the giant panda gut microbiota, but most of the members present were absent in other herbivores and were not phylogenetically related with known cellulolytic lineages. Therefore, the giant panda appears not to have evolved a gut microbiota compatible with its newly adopted diet, which may adversely influence the coevolutionary fitness of this herbivore. The giant panda, an endangered mammalian species endemic to western China, is well known for its unique bamboo diet. Unlike other herbivores that have successfully evolved anatomically specialized digestive systems to efficiently deconstruct fibrous plant matter, the giant panda still retains a gastrointestinal tract typical of carnivores. We characterized the fecal bacterial communities from a giant panda population to determine whether this animal relies on its symbiotic gut microbiota to cope with the complex carbohydrates that dominate its diet, as is common in other herbivores. We found that the giant panda gut microbiota is low in diversity and highly variable across seasons. It also shows an overall composition typical of bears and entirely differentiated from other herbivores, with low levels of putative cellulose-digesting bacteria. The gut microbiota of this herbivore, therefore, may not have well adapted to its highly fibrous diet, suggesting a potential link with its poor digestive efficiency.
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29
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Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA, Garber PA. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). MICROBIAL ECOLOGY 2015; 69:434-43. [PMID: 25524570 DOI: 10.1007/s00248-014-0554-7] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 12/03/2014] [Indexed: 05/04/2023]
Abstract
For most mammals, including nonhuman primates, diet composition varies temporally in response to differences in food availability. Because diet influences gut microbiota composition, it is likely that the gut microbiota of wild mammals varies in response to seasonal changes in feeding patterns. Such variation may affect host digestive efficiency and, ultimately, host nutrition. In this study, we investigate the temporal variation in diet and gut microbiota composition and function in two groups (N = 13 individuals) of wild Mexican black howler monkeys (Alouatta pigra) over a 10-month period in Palenque National Park, Mexico. Temporal changes in the relative abundances of individual bacterial taxa were strongly correlated with changes in host diet. For example, the relative abundance of Ruminococcaceae was highest during periods when energy intake was lowest, and the relative abundance of Butyricicoccus was highest when young leaves and unripe fruit accounted for 68 % of the diet. Additionally, the howlers exhibited increased microbial production of energy during periods of reduced energy intake from food sources. Because we observed few changes in howler activity and ranging patterns during the course of our study, we propose that shifts in the composition and activity of the gut microbiota provided additional energy and nutrients to compensate for changes in diet. Energy and nutrient production by the gut microbiota appears to provide an effective buffer against seasonal fluctuations in energy and nutrient intake for these primates and is likely to have a similar function in other mammal species.
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Affiliation(s)
- Katherine R Amato
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, 61801, USA,
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30
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Christian AL, Knott KK, Vance CK, Falcone JF, Bauer LL, Fahey GC, Willard S, Kouba AJ. Nutrient and mineral composition during shoot growth in seven species of Phyllostachys and Pseudosasa bamboo consumed by giant panda. J Anim Physiol Anim Nutr (Berl) 2015; 99:1172-83. [PMID: 25581029 DOI: 10.1111/jpn.12287] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 11/30/2014] [Indexed: 11/29/2022]
Abstract
During the annual period of bamboo shoot growth in spring, free-ranging giant pandas feed almost exclusively on the shoots while ignoring the leaves and full- height culm. Little is known about the nutritional changes that occur during bamboo shoot growth, if nutritional changes differ among species, or how these changes might influence forage selection. Our objective was to examine the nutrient and mineral composition during three phases of shoot growth (<60, 90-150 and >180 cm) for seven species of bamboo (Phyllostachys (P.) aurea, P. aureosulcata, P. bissetii, P. glauca, P. nuda, P. rubromarginata, Pseudosasa japonica) fed to captive giant pandas at the Memphis Zoo. Total dietary fiber content of bamboo shoots increased (p < 0.0001) from an overall species average of 61% dry matter (DM) at < 60 cm to 75% DM at shoot heights > 180 cm, while crude protein, fat and ash exhibited significant declines (p < 0.05). Phyllostachys nuda had the overall greatest (p = 0.007) crude protein (21% DM) and fat (4% DM) content, and lowest overall total fibre (61% DM) content compared to the other species examined. In contrast, Pseudosasa japonica had the overall lowest crude protein and fat, and relatively higher fibre content (9%, 3% and 74% respectively). Concentrations of Zn and Fe were highest in shoots <60 cm (10-50 μg/g DM) and decreased (p < 0.05) during growth in all species examined. Concentrations of Ca, Cu, Mn, Na and K varied among species and were largely unaffected by growth stage. Due to their higher concentrations of nutrients and lower fibre content in comparison to culm and leaf, bamboo shoots should be a major component of captive giant panda diets when available.
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Affiliation(s)
- A L Christian
- Conservation and Research Department, Memphis Zoological Society, Memphis, TN, USA
| | - K K Knott
- Conservation and Research Department, Memphis Zoological Society, Memphis, TN, USA
| | - C K Vance
- Conservation and Research Department, Memphis Zoological Society, Memphis, TN, USA.,Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
| | - J F Falcone
- Conservation and Research Department, Memphis Zoological Society, Memphis, TN, USA
| | - L L Bauer
- Animal Sciences Department, University of Illinois, Urbana-Champaign, IL, USA
| | - G C Fahey
- Animal Sciences Department, University of Illinois, Urbana-Champaign, IL, USA
| | - S Willard
- Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
| | - A J Kouba
- Conservation and Research Department, Memphis Zoological Society, Memphis, TN, USA
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31
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Kong F, Zhao J, Han S, Zeng B, Yang J, Si X, Yang B, Yang M, Xu H, Li Y. Characterization of the gut microbiota in the red panda (Ailurus fulgens). PLoS One 2014; 9:e87885. [PMID: 24498390 PMCID: PMC3912123 DOI: 10.1371/journal.pone.0087885] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/03/2014] [Indexed: 01/13/2023] Open
Abstract
The red panda is the only living species of the genus Ailurus. Like giant pandas, red pandas are also highly specialized to feed mainly on highly fibrous bamboo. Although several studies have focused on the gut microbiota in the giant panda, little is known about the gut microbiota of the red panda. In this study, we characterized the fecal microbiota from both wild (n = 16) and captive (n = 6) red pandas using a pyrosequecing based approach targeting the V1-V3 hypervariable regions of the 16S rRNA gene. Distinct bacterial communities were observed between the two groups based on both membership and structure. Wild red pandas maintained significantly higher community diversity, richness and evenness than captive red pandas, the communities of which were skewed and dominated by taxa associated with Firmicutes. Phylogenetic analysis of the top 50 OTUs revealed that 10 of them were related to known cellulose degraders. To the best of our knowledge, this is the first study of the gut microbiota of the red panda. Our data suggest that, similar to the giant panda, the gut microbiota in the red panda might also play important roles in the digestion of bamboo.
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Affiliation(s)
- Fanli Kong
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiangchao Zhao
- Department of Pediatrics and Communicable Disease, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Shushu Han
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiandong Yang
- Sichuan Agricultural University, College of Animal Science and Technology, Ya'an, Sichuan, China
| | - Xiaohui Si
- Sichuan Agricultural University, College of Animal Science and Technology, Ya'an, Sichuan, China
| | - Benqing Yang
- Sichuan Fengtongzhai National Nature Reserve, Baoxing, Sichuan, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huailiang Xu
- Sichuan Agricultural University, College of Animal Science and Technology, Ya'an, Sichuan, China
- * E-mail: (HX); (YL)
| | - Ying Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail: (HX); (YL)
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32
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Tun HM, Mauroo NF, Yuen CS, Ho JCW, Wong MT, Leung FCC. Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca). PLoS One 2014; 9:e79902. [PMID: 24475017 PMCID: PMC3901650 DOI: 10.1371/journal.pone.0079902] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/25/2013] [Indexed: 12/20/2022] Open
Abstract
Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis) as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.
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Affiliation(s)
- Hein Min Tun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Nathalie France Mauroo
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Hong Kong Wildlife Health Foundation, Hong Kong, Hong Kong SAR
| | - Chan San Yuen
- Clinical Laboratory, Veterinary Center, Ocean Park Corporation, Hong Kong, Hong Kong SAR
| | - John Chi Wang Ho
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Mabel Ting Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Frederick Chi-Ching Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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