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Liukkonen M, Muriel J, Martínez-Padilla J, Nord A, Pakanen VM, Rosivall B, Tilgar V, van Oers K, Grond K, Ruuskanen S. Seasonal and environmental factors contribute to the variation in the gut microbiome: A large-scale study of a small bird. J Anim Ecol 2024. [PMID: 39041321 DOI: 10.1111/1365-2656.14153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
Environmental variation can shape the gut microbiome, but broad/large-scale data on among and within-population heterogeneity in the gut microbiome and the associated environmental factors of wild populations is lacking. Furthermore, previous studies have limited taxonomical coverage, and knowledge about wild avian gut microbiomes is still scarce. We investigated large-scale environmental variation in the gut microbiome of wild adult great tits across the species' European distribution range. We collected fecal samples to represent the gut microbiome and used the 16S rRNA gene sequencing to characterize the bacterial gut microbiome. Our results show that gut microbiome diversity is higher during winter and that there are compositional differences between winter and summer gut microbiomes. During winter, individuals inhabiting mixed forest habitat show higher gut microbiome diversity, whereas there was no similar association during summer. Also, temperature was found to be a small contributor to compositional differences in the gut microbiome. We did not find significant differences in the gut microbiome among populations, nor any association between latitude, rainfall and the gut microbiome. The results suggest that there is a seasonal change in wild avian gut microbiomes, but that there are still many unknown factors that shape the gut microbiome of wild bird populations.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jaime Muriel
- Department of Biology, University of Turku, Turku, Finland
| | - Jesús Martínez-Padilla
- Department of Biodiversity Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (IPE-CSIC), Jaca, Spain
| | - Andreas Nord
- Department of Biology, Lund University, Lund, Sweden
| | | | - Balázs Rosivall
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Vallo Tilgar
- Department of Zoology, Tartu University, Tartu, Estonia
| | - Kees van Oers
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Biology, University of Turku, Turku, Finland
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Wang Y, Zhai J, Tang B, Dong Y, Sun S, He S, Zhao W, Lancuo Z, Jia Q, Wang W. Metagenomic comparison of gut communities between wild and captive Himalayan griffons. Front Vet Sci 2024; 11:1403932. [PMID: 38784654 PMCID: PMC11112026 DOI: 10.3389/fvets.2024.1403932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. Methods In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Results Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). Discussion In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.
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Affiliation(s)
- You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yonggang Dong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Shengzhen Sun
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Qiangqiang Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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Zhang Y, He X, Mo X, Wu H, Zhao D. Similarities and differences: species and diet impact gut microbiota of captive pheasants. PeerJ 2024; 12:e16979. [PMID: 38560462 PMCID: PMC10979745 DOI: 10.7717/peerj.16979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/29/2024] [Indexed: 04/04/2024] Open
Abstract
The fecal microbiota plays an important role in maintaining animal health and is closely related to host life activities. In recent years, there have been an increasing number of studies on the fecal microbiota from birds. An exploration of the effects of species and living environments on the composition of gut microbiota will provide better protection for wildlife. In this study, non-injury sampling and 16S rDNA high-throughput sequencing were used to investigate the bacterial composition and diversity of the fecal microbiota in silver pheasants (Lophura nycthemera) and golden pheasants (Chrysolophus pictus) from Tianjin Zoo and Beijing Wildlife Park. The results showed that the abundance of Firmicutes was the highest in all fecal samples. At the genus level, Bacteroides was the common dominant bacteria, while there were some differences in other dominant bacteria genera. There were significant differences in fecal microbial composition between the golden pheasants from Tianjin Zoo and Beijing Wildlife Park. The metabolic analysis and functional prediction suggested that the gut microbiota composition and host metabolism were influenced by dietary interventions and living conditions. The results of this study provide the basis for further research of intestinal microbial of L. nycthemera and C. pictus, and valuable insights for conservation of related species.
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Affiliation(s)
- Yushuo Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xin He
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xiuhong Mo
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
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Wu Y, Wang H, Gao Z, Wang H, Zou H. Comparison of the Intestinal Bacterial Communities between Captive and Semi-Free-Range Red-Crowned Cranes ( Grus japonensis) before Reintroduction in Zhalong National Nature Reserve, China. Animals (Basel) 2023; 14:3. [PMID: 38200734 PMCID: PMC10778468 DOI: 10.3390/ani14010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/03/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
The wild populations of red-crowned cranes (Grus japonensis) in west China are gradually decreasing, necessitating the optimization of reintroduction measures. This study used 16S rRNA high-throughput sequencing technology to compare the gut microbiota communities of cranes living in two modes (captive and semi-free-range) before their reintroduction in Zhalong National Nature Reserve, Heilongjiang Province, China. The results showed that Proteobacteria (74.39%) and Firmicutes (25.29%) were the dominant gut bacterial phyla inhabiting these cranes. Significant differences were found in the gut microbiota community composition between semi-free-range and captive cranes (p < 0.01). Psychrobacter, Sporosarcina, and Lactococcus were significantly enriched in captive cranes (p < 0.05), while Pseudomonadaceae_Pseudomonas, Pantoea, Lysobacter, and Enterobacteriaceae_Pseudomonas were more abundant in semi-free-range cranes (p < 0.05). The functions and community structure of gut microbiota were affected by feeding patterns (p < 0.05). The metabolic pathways of ethylbenzene degradation, PPAR signaling pathway, betalain biosynthesis, systemic lupus erythematosus, and shigellosis were up-regulated in semi-free-range cranes (p < 0.05).
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Affiliation(s)
- Yining Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
| | - Huan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
| | - Zhongyan Gao
- Management Bureau of Heilongjiang Zhalong National Reserve, Qiqihar 161005, China;
| | - He Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
| | - Hongfei Zou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.W.); (H.W.); (H.W.)
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Chalifour BN, Elder LE, Li J. Diversity of gut microbiome in Rocky Mountainsnail across its native range. PLoS One 2023; 18:e0290292. [PMID: 38011083 PMCID: PMC10681204 DOI: 10.1371/journal.pone.0290292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/07/2023] [Indexed: 11/29/2023] Open
Abstract
The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.
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Affiliation(s)
- Bridget N. Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Leanne E. Elder
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
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He Y, Zhang M, Dai C, Yu L. Comparison of the Gut Microbial Communities of Domestic and Wild Mallards ( Anas platyrhynchos) Based on High-Throughput Sequencing Technology. Animals (Basel) 2023; 13:2956. [PMID: 37760356 PMCID: PMC10525502 DOI: 10.3390/ani13182956] [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: 08/07/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.
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Affiliation(s)
- Yaoyin He
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Minghui Zhang
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China;
| | - Lijiang Yu
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
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Pacheco-Torres I, Hernández-Sánchez D, García-De la Peña C, Tarango-Arámbula LA, Crosby-Galván MM, Sánchez-Santillán P. Analysis of the Intestinal and Faecal Bacterial Microbiota of the Cervidae Family Using 16S Next-Generation Sequencing: A Review. Microorganisms 2023; 11:1860. [PMID: 37513032 PMCID: PMC10386072 DOI: 10.3390/microorganisms11071860] [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: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
The Cervidae family has a wide distribution due to its adaptation to numerous ecological environments, which allows it to develop a diverse microbial community in its digestive tract. Recently, research has focused on the taxonomic composition and functionality of the intestinal and faecal microbiota of different cervid species worldwide, as well as their microbial diversity and variation under different associated factors such as age, sex, diet, distribution, and seasonal variation. In addition, there is special interest in knowing how cervids act as reservoirs of zoonotic pathogenic microorganisms, which represent a threat to public health. This review provides a synthesis of the growing field of microbiota determination in cervids worldwide, focusing on intestinal and faecal samples using 16S next-generation sequencing. It also documents factors influencing microbial diversity and composition, the microorganisms reported as pathogenic/zoonotic, and the perspectives regarding the conservation of these species. Knowing the interactions between bacteria and cervid health can drive management and conservation strategies for these species and help develop an understanding of their evolutionary history and the interaction with emerging disease-causing microorganisms.
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Affiliation(s)
| | | | | | | | | | - Paulino Sánchez-Santillán
- Faculty of Veterinary Medicine and Zootechnics No. 2, Autonomous University of Guerrero, Cuajinicuilapa 41940, Mexico
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Xu W, Xu N, Zhang Q, Tang K, Zhu Y, Chen R, Zhao X, Ye W, Lu C, Liu H. Association between diet and the gut microbiome of young captive red-crowned cranes (Grus japonensis). BMC Vet Res 2023; 19:80. [PMID: 37391732 DOI: 10.1186/s12917-023-03636-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/23/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Exploring the association of diet and indoor and outdoor environments on the gut microbiome of red-crowned cranes. We investigated the microbiome profile of the 24 fecal samples collected from nine cranes from day 1 to 35. Differences in the gut microbiome composition were compared across diet and environments. RESULTS A total of 2,883 operational taxonomic units (OTUs) were detected, with 438 species-specific OTUs and 106 OTUs common to the gut microbiomes of four groups. The abundance of Dietzia and Clostridium XI increased significantly when the red-crowned cranes were initially fed live mealworms. Skermanella and Deinococcus increased after the red-crowned cranes were fed fruits and vegetables and placed outdoors. Thirty-three level II pathway categories were predicted. Our study revealed the mechanism by which the gut microbiota of red-crowned cranes responds to dietary and environmental changes, laying a foundation for future breeding, nutritional and physiological studies of this species. CONCLUSIONS The gut microbiome of red-crowned cranes could adapt to changes in diet and environment, but the proportion of live mealworms in captive red-crowned cranes can be appropriately reduced at the initial feeding stage, reducing the negative impact of high-protein and high-fat foods on the gut microbiome and growth and development.
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Affiliation(s)
- Wei Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Nan Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Qingzheng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610042, China
| | - Ying Zhu
- Institute of Qinghai Tibetan Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Rong Chen
- Nanjing Hongshan Forest Zoo, Nanjing, 210028, China
| | - Xinyi Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Wentao Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Changhu Lu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Hongyi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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Shang Y, Zhong H, Liu G, Wang X, Wu X, Wei Q, Shi L, Zhang H. Characteristics of Microbiota in Different Segments of the Digestive Tract of Lycodon rufozonatus. Animals (Basel) 2023; 13:ani13040731. [PMID: 36830518 PMCID: PMC9952230 DOI: 10.3390/ani13040731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of Lycodon rufozonatus. Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the L. rufozonatus gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.
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Affiliation(s)
- Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Huaming Zhong
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China
| | - Gang Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence:
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Gao Z, Song H, Dong H, Ji X, Lei Z, Tian Y, Wu Y, Zou H. Comparative analysis of intestinal flora between rare wild red-crowned crane and white-naped crane. Front Microbiol 2022; 13:1007884. [DOI: 10.3389/fmicb.2022.1007884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
IntroductionAnimal intestines are extremely rich in microbial ecosystems. Numerous studies in different fields, such as epidemiology and histology, have revealed that gut microorganisms considerably mediate the survival and reproduction of animals. However, gut microbiology studies of homogeneously distributed wild cranes are still rare. This study aimed to understand the structural composition of the gut microbial community of wild cranes and elucidate the potential roles of the microorganisms.MethodsWe used high-throughput sequencing to analyze the gut microbial community structure of wild cranes in the Zhalong Nature Reserve.ResultsA total of 1,965,683 valid tags and 5248 OTUs were obtained from 32 fecal samples. Twenty-six bacteria phyla and 523 genera were annotated from the intestinal tract of the red-crowned crane. Twenty-five bacteria phyla and 625 genera were annotated from the intestine of the white-naped crane. Firmicutes, Proteobacteria, and Bacteroidetes are the dominant bacterial phyla in the intestinal tract of red-crowned cranes, while Catellicoccus, Lactobacillus, Neisseria, and Streptococcus were the dominant genera. The dominant bacterial phyla in the intestinal tract of white-naped cranes were Firmicutes, Proteobacteria, Bacteroidetes, Epsilonbacteraeota, Actinobacteria, and Fusobacteria. However, the dominant genera were Catellicoccus, Lactobacillus, Neisseria, Campylobacter, Streptococcus, Anaerobiospirillum, Romboutsia, Turicibacter, Haemophilus, and Lautropia. Firmicutes had significantly higher relative abundance in the intestine of the red-crowned than white-naped cranes (P < 0.05). However, the relative abundance of Actinobacteria and Bacteroidetes was significantly higher (P < 0.05) in the intestines of white-naped than red-crowned cranes. The diversity of the intestinal flora between the two crane species was significantly different (P < 0.05). Besides, the alpha diversity of the intestinal flora was higher for white-naped than red-crowned cranes. Eight of the 41 functional pathways differed in the gut of both crane species (P < 0.05).DiscussionBoth species live in the same area and have similar feeding and behavioral characteristics. Therefore, host differences are possibly the main factors influencing the structural and functional differences in the composition of the gut microbial community. This study provides important reference data for constructing a crane gut microbial assessment system. The findings have implications for studying deeper relationships between crane gut microbes and genetics, nutrition, immunity, and disease.
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Effect of diet on gut microbiota diversity in mandarin ducks (Aix galericulata) revealed by Illumina high-throughput sequencing. Arch Microbiol 2022; 204:725. [DOI: 10.1007/s00203-022-03333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Engel K, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota. MICROBIOME 2022; 10:202. [PMID: 36434663 PMCID: PMC9700942 DOI: 10.1186/s40168-022-01401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social environment and host selection throughout host ontogeny remains understudied, particularly in avian species. We conducted conspecific and heterospecific cross-fostering experiments in zebra finches (Taeniopygia guttata) and Bengalese finches (Lonchura striata domestica) under controlled conditions and repeatedly sampled the faecal microbiota of these birds over the first 3 months of life. We thus documented the development of the gut microbiota and characterised the relative impacts of the early social environment and host selection due to species-specific characteristics and individual genetic backgrounds across ontogeny by using 16S ribosomal RNA gene sequencing. RESULTS The taxonomic composition and community structure of the gut microbiota changed across ontogenetic stages; juvenile zebra finches exhibited higher alpha diversity than adults at the post-breeding stage. Furthermore, in early development, the microbial communities of juveniles raised by conspecific and heterospecific foster parents resembled those of their foster family, emphasising the importance of the social environment. In later stages, the social environment continued to influence the gut microbiota, but host selection increased in importance. CONCLUSIONS We provided a baseline description of the developmental succession of gut microbiota in zebra finches and Bengalese finches, which is a necessary first step for understanding the impact of the early gut microbiota on host fitness. Furthermore, for the first time in avian species, we showed that the relative strengths of the two forces that shape the establishment and maintenance of the gut microbiota (i.e. host selection and dispersal from the social environment) change during development, with host selection increasing in importance. This finding should be considered when experimentally manipulating the early-life gut microbiota. Our findings also provide new insights into the mechanisms of host selection. Video Abstract.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany.
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Institute for Bio- and Geosciences, Research Center Jülich, Jülich, Germany
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kathrin Engel
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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Grieves LA, Bottini CLJ, Gloor GB, MacDougall-Shackleton EA. Uropygial gland microbiota differ between free-living and captive songbirds. Sci Rep 2022; 12:18283. [PMID: 36316352 PMCID: PMC9622905 DOI: 10.1038/s41598-022-22425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Symbiotic microbes can affect host behavior and fitness. Gut microbiota have received the most study, with less attention to other important microbial communities like those of scent-producing glands such as mammalian anal glands and the avian uropygial gland. However, mounting evidence suggests that microbes inhabiting scent-producing glands play an important role in animal behavior by contributing to variation in chemical signals. Free-living and captive conditions typically differ in social environment, food diversity and availability, disease exposure, and other factors-all of which can translate into differences in gut microbiota. However, whether extrinsic factors such as captivity alter microbial communities in scent glands remains an open question. We compared the uropygial gland microbiota of free-living and captive song sparrows (Melospiza melodia) and tested for an effect of dietary manipulations on the gland microbiota of captive birds. As predicted, the uropygial gland microbiota was significantly different between free-living and captive birds. Surprisingly, microbial diversity was higher in captive than free-living birds, and we found no effect of dietary treatments on captive bird microbiota. Identifying the specific factors responsible for microbial differences among groups and determining whether changes in symbiotic microbiota alter behavior and fitness are important next steps in this field.
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Affiliation(s)
- L. A. Grieves
- grid.39381.300000 0004 1936 8884Department of Biology, The University of Western Ontario, 1151 Richmond St., London, ON N6A 5B7 Canada ,grid.25073.330000 0004 1936 8227Present Address: Department of Biology, McMaster University, 1280 Main St. W, Hamilton, ON L8S 3L8 Canada
| | - C. L. J. Bottini
- grid.39381.300000 0004 1936 8884Department of Biology, The University of Western Ontario, 1151 Richmond St., London, ON N6A 5B7 Canada
| | - G. B. Gloor
- grid.39381.300000 0004 1936 8884Department of Biochemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A 5C1 Canada
| | - E. A. MacDougall-Shackleton
- grid.39381.300000 0004 1936 8884Department of Biology, The University of Western Ontario, 1151 Richmond St., London, ON N6A 5B7 Canada
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Zhang K, Wang X, Gong X, Sui J. Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity. Front Microbiol 2022; 13:858592. [PMID: 35794924 PMCID: PMC9251364 DOI: 10.3389/fmicb.2022.858592] [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: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.
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Tang S, Li Y, Huang C, Yan S, Li Y, Chen Z, Wu Z. Comparison of Gut Microbiota Diversity Between Captive and Wild Tokay Gecko (Gekko gecko). Front Microbiol 2022; 13:897923. [PMID: 35783386 PMCID: PMC9248866 DOI: 10.3389/fmicb.2022.897923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
Captive animals and wild animals may exhibit different characteristics due to the heterogeneity of their living environments. The gut microbiota play an important role in the digestion and absorption, energy metabolism, immune regulation, and physiological health of the host. However, information about the gut microbiota of captive and wild Gekko gecko is currently limited. To determine the difference in gut microbiota community composition, diversity, and structure between captive and wild geckos, we used the Illumina miseq platform to conduct high-throughput sequencing and bioinformatics analysis of the v3–v4 hypervariable region of 16S rRNA in 54 gecko samples. Our results showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant gut microbiota phyla of the gecko. The dominant genera comprised mainly Pseudomonas, Burkholderia-caballeronia-paraburkholderia, Ralstonia, Romboutsia, and Bacteroides. Captive geckos had significantly higher alpha diversity and potential pathogenic bacteria than wild populations. Moreover, significant differences in beta diversity of gut microbiota were observed between two populations. Functional prediction analysis showed that the relative abundance of functional pathways of wild geckos was more higher in metabolism, genetic information processing and organismal system function than those in captive geckos. Total length significantly affected gut microbial community (R2 = 0.4527, p = 0.001) and explained 10.45% of the total variation for gut microbial community variance between two groups. These results may be related to differences in diet and living environment between two populations, suggesting that the management of captive populations should mimic wild environments to the greatest extent possible to reduce the impact on their gut microbiota.
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Affiliation(s)
- Sanqi Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Chengming Huang
- Key Laboratory of Animal Ecology and Conservation, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shufa Yan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Yongtai Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Zening Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- Zening Chen,
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- *Correspondence: Zhengjun Wu,
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Zhao X, Ye W, Xu W, Xu N, Zheng J, Chen R, Liu H. Changes in the Diversity and Composition of Gut Microbiota of Red-Crowned Cranes (Grus japonensis) after Avian Influenza Vaccine and Anthelmintic Treatment. Animals (Basel) 2022; 12:ani12091183. [PMID: 35565609 PMCID: PMC9099658 DOI: 10.3390/ani12091183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 01/27/2023] Open
Abstract
Gut microbiota homeostasis is important for host health and well-being; however, drugs may affect the composition and function of the gut microbiota. Red-crowned cranes are a vulnerable species. Treatment of red-crowned cranes with avian influenza vaccines and anthelmintics has played pivotal roles in therapeutic management in zoos. To investigate the changes in the diversity and composition of gut microbiota after the avian influenza vaccine and anthelmintic treatment, we used 16S rRNA sequencing to obtain and compare the bacterial community composition before and after the treatment. The alpha diversity of the gut microbiota of red-crowned cranes decreased on the day of the treatment and then fluctuated over time. The composition of gut microbiota tended to be similar in the short term after the treatment, as supported by the beta diversity hierarchical cluster analysis. Only 3, 8, and 72 operational taxonomic units (OTUs) of the three individuals were shared among the five groups before and after treatment. The relative abundance of Firmicutes significantly increased to 99.04% ± 0.28% on the day of the treatment, in which the relative abundance of Lactobacillus was 93.33% ± 5.85%. KEGG pathways analysis indicated that the main function of the gut microbiota is involved in metabolism, and the present study indicates that the gut microbiota of red-crowned cranes is resilient to the avian influenza vaccine and anthelmintic, even disordered in the short term, and could recover over time. More individual experimentation and functional potential in metabolism are needed in the future to support animal disease control and optimal management in the zoo.
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Affiliation(s)
- Xinyi Zhao
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (W.Y.); (W.X.); (N.X.); (J.Z.)
| | - Wentao Ye
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (W.Y.); (W.X.); (N.X.); (J.Z.)
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (W.Y.); (W.X.); (N.X.); (J.Z.)
| | - Nan Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (W.Y.); (W.X.); (N.X.); (J.Z.)
| | - Jiajun Zheng
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (W.Y.); (W.X.); (N.X.); (J.Z.)
| | - Rong Chen
- Nanjing Hongshan Forest Zoo, Nanjing 210028, China;
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (W.Y.); (W.X.); (N.X.); (J.Z.)
- Correspondence:
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Chen X, Huang L, Cheng L, Hu B, Liu H, Hu J, Hu S, Han C, He H, Kang B, Xu H, Wang J, Li L. Effects of floor- and net-rearing systems on intestinal growth and microbial diversity in the ceca of ducks. BMC Microbiol 2022; 22:76. [PMID: 35296244 PMCID: PMC8925166 DOI: 10.1186/s12866-022-02478-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/19/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Rearing systems can affect livestock production directly, but whether they have effects on intestinal growth states and ceca microorganisms in ducks is largely unclear. The current study used Nonghua ducks to estimate the effects of rearing systems on the intestines by evaluating differences in intestinal growth indices and cecal microorganisms between ducks in the floor-rearing system (FRS) and net-rearing system (NRS). RESULTS The values of relative weight (RW), relative length (RL) and RW/RL of the duodenum, jejunum, ileum and ceca in the FRS were significantly higher than those in the NRS during weeks 4, 8 and 13 (p < 0.05). A total of 157 genera were identified from ducks under the two systems, and the dominant microorganisms in both treatments were Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria at the phylum level. The distribution of microorganisms in the ceca of the two treatments showed significant separation during the three time periods, and the value of the Simpson index in the FRS was significantly higher than that in the NRS at 13 weeks (p < 0.05). Five differential microorganisms and 25 differential metabolic pathways were found in the ceca at week 4, seven differential microorganisms and 25 differential metabolic pathways were found in the ceca at week 8, and four differential microorganisms and two differential metabolic pathways were found in the ceca at week 13. CONCLUSIONS The rearing system influences duck intestinal development and microorganisms. The FRS group had higher intestinal RL, RW and RW/RL and obviously separated ceca microorganisms compared to those of the NRS group. The differential metabolic pathways of cecal microorganisms decreased with increasing age, and the abundance of translation pathways was higher in the NRS group at week 13, while cofactor and vitamin metabolism were more abundant in the FRS group.
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Affiliation(s)
- Xuefei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Liansi Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Lumin Cheng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Bo Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Bo Kang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Hengyong Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan People’s Republic of China
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Weinhold A. Bowel Movement: Integrating Host Mobility and Microbial Transmission Across Host Taxa. Front Microbiol 2022; 13:826364. [PMID: 35242121 PMCID: PMC8886138 DOI: 10.3389/fmicb.2022.826364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 11/22/2022] Open
Abstract
The gut microbiota of animals displays a high degree of plasticity with respect to environmental or dietary adaptations and is shaped by factors like social interactions, diet diversity or the local environment. But the contribution of these drivers varies across host taxa and our ability to explain microbiome variability within wild populations remains limited. Terrestrial animals have divergent mobility ranges and can either crawl, walk or fly, from a couple of centimeters toward thousands of kilometers. Animal movement has been little regarded in host microbiota frameworks, though it can directly influence major drivers of the host microbiota: (1) Aggregation movement can enhance social transmissions, (2) foraging movement can extend range of diet diversity, and (3) dispersal movement determines the local environment of a host. Here, I would like to outline how movement behaviors of different host taxa matter for microbial acquisition across mammals, birds as well as insects. Host movement can have contrasting effects and either reduce or enlarge spatial scale. Increased dispersal movement could dissolve local effects of sampling location, while aggregation could enhance inter-host transmissions and uniformity among social groups. Host movement can also extend the boundaries of microbial dispersal limitations and connect habitat patches across plant-pollinator networks, while the microbiota of wild populations could converge toward a uniform pattern when mobility is interrupted in captivity or laboratory settings. Hence, the implementation of host movement would be a valuable addition to the metacommunity concept, to comprehend microbial dispersal within and across trophic levels.
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Affiliation(s)
- Arne Weinhold
- Faculty of Biology, Cellular and Organismic Networks, Ludwig-Maximilians-Universität München, Munich, Germany
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Obrochta S, Savo Sardaro ML, Amato KR, Murray MH. Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.742369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology. For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness. However, the microbiome is an understudied aspect of avian ecology, particularly in the context of migration and urbanization in wild birds. For this study, we hypothesized that, within urban birds, migrants would exhibit greater microbial diversity and inter-individual variation in microbiome composition than residents because they are exposed to more diverse habitats. We focused on Canada geese (Branta canadensis), one of many migratory species that exhibit increasingly more year-round residency in cities. We used 16S rRNA gene amplicon sequencing to quantify microbiome taxonomic composition in fecal samples from 32 GPS-tracked Canada geese, 22 of which were year-round residents of the Chicago area and 10 of which were migrants. Similar to recent studies on wild species feeding near human habitation, urban resident geese had higher gut microbial diversity than migrants. They also had increased inter-individual variation in microbiome composition and, on average, lower relative abundances of bacteria in the phylum Firmicutes, and the genera Terrisporobacter, Turicibacter, and Cellulosilyticum, which all have metabolic functions that may aid in goose digestion. Therefore, the gut microbiome of resident geese may provide fewer potential health benefits. These patterns may be a result of anthropogenic influences on aspects of resident goose ecology, such as diet, as well the influence of migration on migrant goose ecology and biology. Overall, our results suggest that reduced migration for urban-adapted wildlife species may have important consequences for physiology and health.
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Chiang E, Deblois CL, Carey HV, Suen G. Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Anim Microbiome 2022; 4:1. [PMID: 34980290 PMCID: PMC8722175 DOI: 10.1186/s42523-021-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. RESULTS Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. CONCLUSIONS This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
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Affiliation(s)
- Edna Chiang
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Courtney L. Deblois
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hannah V. Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Garret Suen
- Present Address: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
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22
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Diaz J, Reese AT. Possibilities and limits for using the gut microbiome to improve captive animal health. Anim Microbiome 2021; 3:89. [PMID: 34965885 PMCID: PMC8715647 DOI: 10.1186/s42523-021-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022] Open
Abstract
Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.
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Affiliation(s)
- Jessica Diaz
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Aspen T Reese
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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23
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Structural changes in the gut microbiota community of the black-necked crane (Grus nigricollis) in the wintering period. Arch Microbiol 2021; 203:6203-6214. [PMID: 34561717 DOI: 10.1007/s00203-021-02587-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022]
Abstract
During overwintering of black-necked cranes (Grus nigricollis), the composition and function of the gut microbiota changes are of considerable interest for understanding its environmental adaption mechanism. In this study, we characterized the structure of the gut microbiota from the black-necked crane in the Dashanbao wintering area, and compared the early-winter (November) microbiota to the late-winter (March of the next year) microbiota. The results showed that the gut microbiota diversity of black-necked crane in the early-overwintering stage was higher than that in the late-overwintering stage, but it did not reach a significant level. Gut microbiota taxonomic composition analysis showed that relative abundance of Bacteroidota increased significantly, and showed decreased Firmicutes to Bacteroidota ratio at the phylum level, meanwhile, the abundance of Lactobacillus decreased significantly at the genus level. Explain gut microbiota between the early- and late-wintering showed some differences in microbiota richness but maintained a relatively conservative microbiota structure. PICRUSt2 method was used to predict and analyze the KEGG functional abundance of 16S rDNA sequences of bacteria, it was found that the changes in gut microbiota composition increased the abundance of bacteria associated with amino acid biosynthesis and acid metabolism in the late stage of overwintering. This work provides basic data for black-necked crane gut microbiota study, which might further contribute to their protection.
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24
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Liu K, Yang J, Yuan H. Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau. J Evol Biol 2021; 34:1514-1530. [PMID: 34473899 DOI: 10.1111/jeb.13924] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/05/2021] [Accepted: 08/30/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities that inhabit the host's intestine influence many aspects of the host's health and bear the adaptive potential to alterations in harsh environments and diets. The Qinghai-Tibet Plateau represents one of the harshest environments in the world. Preliminary progress has been made in identifying the communities of gut microbes in Indigenous Tibetans and non-human animals. However, due to the complexity of microbial communities, the effects of gut microbes on the host's health and high-plateau adaptation remain unexplained. Herein, we review the latest progress in identifying factors affecting the gut microbiota of native Tibetans and non-human animals and highlight the complex interactions between the gut microbiota, health and highland adaptation, which provides a basis for exploring the correlations between the gut microbiota and clinical indexes in native highland residents and travellers, as well as developing microbiota-based strategies to mitigate health risks for tourists and treatments for mountain sickness during high-altitude travel in the future.
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Affiliation(s)
- Kui Liu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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25
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Bodawatta KH, Hird SM, Grond K, Poulsen M, Jønsson KA. Avian gut microbiomes taking flight. Trends Microbiol 2021; 30:268-280. [PMID: 34393028 DOI: 10.1016/j.tim.2021.07.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important - but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska, Anchorage, AK, USA
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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26
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Pekarsky S, Corl A, Turjeman S, Kamath PL, Getz WM, Bowie RCK, Markin Y, Nathan R. Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation. Mol Ecol 2021; 30:4723-4739. [PMID: 34260783 DOI: 10.1111/mec.16079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/14/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022]
Abstract
Human activities shape resources available to wild animals, impacting diet and probably altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS-tracking) over three periods of their migratory cycle, and by analysing the effect of artificially supplemented food provided as part of a crane-agriculture management programme. We sampled faecal droppings in Russia (nonsupplemented, premigration) and in Israel in late autumn (nonsupplemented, postmigration) and winter (supplemented and nonsupplemented, wintering). As supplemented food is typically homogenous, we predicted lower microbiota diversity and different composition in birds relying on supplementary feeding. We did not observe changes in microbial diversity with food supplementation, as diversity differed only in samples from nonsupplemented wintering sites. However, both food supplementation and season affected bacterial community composition and led to increased abundance of specific genera (mostly Firmicutes). Cranes from the nonsupplemented groups spent most of their time in agricultural fields, probably feeding on residual grain when available, while food-supplemented cranes spent most of their time at the feeding station. Thus, nonsupplemented and food-supplemented diets probably diverge only in winter, when crop rotation and depletion of anthropogenic resources may lead to a more variable diet in nonsupplemented sites. Our results support the role of diet in structuring bacterial communities and show that they undergo both seasonal and human-induced shifts. Movement analyses provide important clues regarding host diet and behaviour towards understanding how human-induced changes shape the gut microbiota in wild animals.
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Affiliation(s)
- Sasha Pekarsky
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
| | - Sondra Turjeman
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Wayne M Getz
- Department of Environmental Science, Policy & Management, University of California, Berkeley, California, USA.,School Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Yuri Markin
- Oksky State Reserve, pos. Brykin Bor, Spassky raion, Ryazanskaya oblast, Russia
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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27
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San Juan PA, Castro I, Dhami MK. Captivity reduces diversity and shifts composition of the Brown Kiwi microbiome. Anim Microbiome 2021; 3:48. [PMID: 34238378 PMCID: PMC8268595 DOI: 10.1186/s42523-021-00109-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/27/2021] [Indexed: 11/30/2022] Open
Abstract
Background Captive rearing is often critical for animals that are vulnerable to extinction in the wild. However, few studies have investigated the extent to which captivity impacts hosts and their gut microbiota, despite mounting evidence indicating that host health is affected by gut microbes. We assessed the influence of captivity on the gut microbiome of the Brown Kiwi (Apteryx mantelli), a flightless bird endemic to New Zealand. We collected wild (n = 68) and captive (n = 38) kiwi feces at seven sites on the north island of New Zealand. Results Using bacterial 16 S rRNA and fungal ITS gene profiling, we found that captivity was a significant predictor of the kiwi gut bacterial and fungal communities. Captive samples had lower microbial diversity and different composition when compared to wild samples. History of coccidiosis, a gut parasite primarily affecting captive kiwi, showed a marginally significant effect. Conclusions Our findings demonstrate captivity’s potential to shape the Brown Kiwi gut microbiome, that warrant further investigation to elucidate the effects of these differences on health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00109-0.
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Affiliation(s)
- Priscilla A San Juan
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, California, 94305, USA. .,Center for Conservation Biology, Stanford University, Stanford, California, USA.
| | - Isabel Castro
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Manpreet K Dhami
- Manaaki Whenua - Landcare Research, 54 Gerald Street, 7608, Lincoln, New Zealand.
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28
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Eliades SJ, Brown JC, Colston TJ, Fisher RN, Niukula JB, Gray K, Vadada J, Rasalato S, Siler CD. Gut microbial ecology of the Critically Endangered Fijian crested iguana ( Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes. Ecol Evol 2021; 11:4731-4743. [PMID: 33976843 PMCID: PMC8093715 DOI: 10.1002/ece3.7373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 02/01/2023] Open
Abstract
Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.
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Affiliation(s)
- Samuel J. Eliades
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Joseph C. Brown
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
- Hope Zoo Preservation FoundationKingstonJamaica
| | | | - Robert N. Fisher
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCaliforniaUSA
| | | | - Kim Gray
- San Diego Zoo Wildlife AllianceSan DiegoCaliforniaUSA
| | | | | | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahomaUSA
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29
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Couch CE, Wise BL, Scurlock BM, Rogerson JD, Fuda RK, Cole EK, Szcodronski KE, Sepulveda AJ, Hutchins PR, Cross PC. Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem. PLoS One 2021; 16:e0249521. [PMID: 33831062 PMCID: PMC8031386 DOI: 10.1371/journal.pone.0249521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 03/19/2021] [Indexed: 12/27/2022] Open
Abstract
Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of the gut microbiome for extracting and synthesizing nutrients, modulating host immunity, and many other vital host functions, but these relationships can be disrupted by dietary perturbation. The well-described interplay between diet, the microbiome, and host health in laboratory and human systems highlights the need to understand the consequences of supplemental feeding on the microbiomes of free-ranging animal populations. This study describes changes to the gut microbiomes of wild elk under different supplemental feeding regimes. We demonstrated significant cross-sectional variation between elk at different feeding locations and identified several relatively low-abundance bacterial genera that differed between fed versus unfed groups. In addition, we followed four of these populations through mid-season changes in supplemental feeding regimes and demonstrated a significant shift in microbiome composition in a single population that changed from natural forage to supplementation with alfalfa pellets. Some of the taxonomic shifts in this population mirrored changes associated with ruminal acidosis in domestic livestock. We discerned no significant changes in the population that shifted from natural forage to hay supplementation, or in the populations that changed from one type of hay to another. Our results suggest that supplementation with alfalfa pellets alters the native gut microbiome of elk, with potential implications for population health.
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Affiliation(s)
- Claire E. Couch
- Department of Fisheries & Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Benjamin L. Wise
- Wyoming Game & Fish Department, Jackson, Wyoming, United States of America
| | | | - Jared D. Rogerson
- Wyoming Game & Fish Department, Pinedale, Wyoming, United States of America
| | - Rebecca K. Fuda
- Oregon Department of Fish & Wildlife, Prineville, Oregon, United States of America
| | - Eric K. Cole
- U.S. Fish & Wildlife Service, National Elk Refuge, Jackson, Wyoming, United States of America
| | - Kimberly E. Szcodronski
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
| | - Adam J. Sepulveda
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
| | - Patrick R. Hutchins
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
| | - Paul C. Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
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30
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Wu H, Wu FT, Zhou QH, Zhao DP. Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology. Front Microbiol 2021; 12:649466. [PMID: 33841373 PMCID: PMC8027120 DOI: 10.3389/fmicb.2021.649466] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.
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Affiliation(s)
- Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China.,Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Fang-Ting Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Qi-Hai Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Da-Peng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China.,Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
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31
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Liu D, Song P, Yan J, Wang H, Cai Z, Xie J, Zhang T. Gut Microbiome Changes in Captive Plateau Zokors ( Eospalax baileyi). Evol Bioinform Online 2021; 17:1176934321996353. [PMID: 34103885 PMCID: PMC8164558 DOI: 10.1177/1176934321996353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/27/2021] [Indexed: 12/28/2022] Open
Abstract
Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor (Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference (P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.
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Affiliation(s)
- Daoxin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,Kunlun College of Qinghai University, Xining, Qinghai, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, 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, Qinghai, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyan Yan
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Haijing Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Jiuxiang Xie
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
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32
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch. Front Microbiol 2021; 12:619141. [PMID: 33679641 PMCID: PMC7933042 DOI: 10.3389/fmicb.2021.619141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A. Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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33
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The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance. mSystems 2020; 5:5/3/e00061-20. [PMID: 32457237 PMCID: PMC7253362 DOI: 10.1128/msystems.00061-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications. Human exploitation and destruction of tropical resources are currently threatening innumerable wild animal species, altering natural ecosystems and thus, food resources, with profound effects on gut microbiota. Given their conservation status and the importance to tropical ecosystems, wild nonhuman primates make excellent models to investigate the effect of human disturbance on the diversity of host-associated microbiota. Previous investigations have revealed a loss of fecal bacterial diversity in primates living in degraded compared to intact forests. However, these data are available for a limited number of species, and very limited information is available on the fungal taxa hosted by the gut. Here, we estimated the diversity and composition of gut bacterial and fungal communities in two primates living sympatrically in both human-modified and pristine forests in the Udzungwa Mountains of Tanzania. Noninvasively collected fecal samples of 12 groups of the Udzungwa red colobus (Procolobus gordonorum) (n = 89), a native and endangered primate (arboreal and predominantly leaf-eating), and five groups of the yellow baboon (Papio cynocephalus) (n = 69), a common species of least concern (ground-feeding and omnivorous), were analyzed by the V1-V3 region of the 16S rRNA gene (bacterial) and ITS1-ITS2 (fungal) sequencing. Gut bacterial diversities were associated with habitat in both species, most likely depending on their ecological niches and associated digestive physiology, dietary strategies, and locomotor behavior. In addition, fungal communities also show distinctive traits across hosts and habitat type, highlighting the importance of investigating this relatively unexplored gut component. IMPORTANCE Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.
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Trevelline BK, Sosa J, Hartup BK, Kohl KD. A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. Proc Biol Sci 2020; 287:20192988. [PMID: 32183630 DOI: 10.1098/rspb.2019.2988] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In numerous animal clades, the evolutionary history of host species drives patterns of gut microbial community structure, resulting in more divergent microbiota with increasing phylogenetic distance between hosts. This phenomenon, termed phylosymbiosis, has been observed in diverse evolutionary lineages, but has been difficult to detect in birds. Previous tests of phylosymbiosis among birds have been conducted using wild individuals, and thus interspecific differences in diet and environment may have masked a phylogenetic signal. Therefore, we tested for phylosymbiosis among all 15 species of cranes (family Gruidae) housed in the same captive environment and maintained on identical diets. 16S rRNA sequencing revealed that crane species harbour distinct gut microbiota. Overall, we detected marginally significant patterns of phylosymbiosis, the strength of which was increased when including the estimates of absolute microbial abundance (rather than relative abundance) derived from microbial densities determined by flow cytometry. Using this approach, we detected the statistically significant signatures of phylosymbiosis only after removing male cranes from our analysis, suggesting that using mixed-sex animal cohorts may prevent the detection of phylosymbiosis. Though weak compared with mammals (and especially insects), these results provide evidence of phylosymbiosis in birds. We discuss the potential differences between birds and mammals, such as transmission routes and host filtering, that may underlie the differences in the strength of phylosymbiosis.
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Affiliation(s)
- Brian K Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jahree Sosa
- 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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Murray MH, Lankau EW, Kidd AD, Welch CN, Ellison T, Adams HC, Lipp EK, Hernandez SM. Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird. PLoS One 2020; 15:e0220926. [PMID: 32134945 PMCID: PMC7058277 DOI: 10.1371/journal.pone.0220926] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial communities in the gastrointestinal tract influence many aspects of host health, including metabolism and susceptibility to pathogen colonization. These relationships and the environmental and individual factors that drive them are relatively unexplored for free-living wildlife. We quantified the relationships between urban habitat use, diet, and age with microbiome composition and diversity for 82 American white ibises (Eudocimus albus) captured along an urban gradient in south Florida and tested whether gut microbial diversity was associated with Salmonella enterica prevalence. Shifts in community composition were significantly associated with urban land cover and, to a lesser extent, diets higher in provisioned food. The diversity of genera was negatively associated with community composition associated with urban land cover, positively associated with age class, and negatively associated with Salmonella shedding. Our results suggest that shifts in both habitat use and diet for urban birds significantly alter gut microbial composition and diversity in ways that may influence health and pathogen susceptibility as species adapt to urban habitats.
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Affiliation(s)
- Maureen H. Murray
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
| | - Emily W. Lankau
- University of Wisconsin Department of Animal Sciences, Madison, Wisconsin, United States of America
- Ronin Institute, Montclair, New Jersey, United States of America
| | - Anjelika D. Kidd
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
| | - Catharine N. Welch
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Taylor Ellison
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Henry C. Adams
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Sonia M. Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
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Characterization of the gut microbiome of black-necked cranes (Grus nigricollis) in six wintering areas in China. Arch Microbiol 2020; 202:983-993. [PMID: 31901964 DOI: 10.1007/s00203-019-01802-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/12/2019] [Accepted: 12/21/2019] [Indexed: 12/18/2022]
Abstract
The black-necked crane (Grus nigricollis) is a vulnerable species, breeding exclusively on the high-altitude wetlands of the Qinghai-Tibet Plateau. Bird species harbor diverse communities of microorganisms within their gastrointestinal tracts, which have important roles in the health, nutrition, and physiology of birds. Hitherto, virtually nothing was known about the gut microbial communities associated with wild black-necked cranes. For the first time, this study characterized the gut microbial community compositions, diversity, and functions of black-necked cranes from six wintering areas in China using the Illumina Miseq platform. The taxonomic results revealed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the four most abundant phyla in the gut of black-necked cranes. At the genus level, 11 genera including Lactobacillus, Pseudomonas, Carnobacterium, Pantoea, Enterococcus, Erwinia, Turicibacter, Bacillus, Phenylobacterium, Sanguibacter, and Psychrobacter were dominant. The differences in the gut microbial community alpha and the beta diversities of black-necked cranes among the six wintering areas were investigated. Furthermore, the representative microbial taxa and their predicted functions in each wintering location were also determined. These data represent the first analysis of the gut microbiome of black-necked cranes, providing a baseline for further microbiological studies and a foundation for the conservation of this bird.
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Li F, Zhang X, Xie Y, Wang J. Sedimentary DNA reveals over 150 years of ecosystem change by human activities in Lake Chao, China. ENVIRONMENT INTERNATIONAL 2019; 133:105214. [PMID: 31665682 DOI: 10.1016/j.envint.2019.105214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/22/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
Understanding the extent and directionality of the impact of human activities on ecosystems is directly related to their management and protection. However, the lack of historical data limits our understanding of ecosystem changes with long-term exposure to human activities. Recently, lake sedimentary DNA (sedDNA) has become a powerful tool for revealing changes in ecosystems at the century and millennium scales. Here, we used sedDNA to reveal the dynamic of the microbial community (including bacteria and micro-eukaryotes) in Lake Chao over the past 150 years, and further explored the effects of long-term nutrient and heavy metal loads on these communities. Our data show that nutrient and heavy metal loads in Lake Chao have increased by ca. 2 to 4-fold since the 1960s. In response, the community structure, diversity, and ecological network of bacteria and micro-eukaryotes changed significantly during the 1960s, the 1980s and the 2010s. Importantly, community structure was more sensitive to human activities than diversity. We also found that the relative abundance of some taxa associated with nitrification and algal blooms (e.g., taxa in Nitrospira sp., Peridinales) has increased ca. 100-fold since the 1960s. Nutrient could better explain the variation in the bacterial community (ca. twice as much as heavy metal), while heavy metal explained micro-eukaryotes better (ca. 3 or 5-fold as much as nutrient). In particular, based on parsimonious models from distance-based linear model (distLM), we further identified that Pb is the key factor affecting the bacterial and micro-eukaryotes community in Lake Chao in addition to nutrient. Our study reveals the impacts of long-term human activities on lake ecosystems from multiple perspectives of nutrient and heavy metal loads, community structure, diversity and ecological network, these findings will contribute to the management and conservation of lakes in the future.
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Affiliation(s)
- Feilong Li
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Jizhong Wang
- Guangzhou GRG Metrology & Test (Hefei) CO., LID, Hefei 230088, PR China; School of Environment and Energy Engineering, Anhui Jianzhu University, Hefei 230601, PR China
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Guo W, Mishra S, Wang C, Zhang H, Ning R, Kong F, Zeng B, Zhao J, Li Y. Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas ( Ailuropoda melanoleuca). Genes (Basel) 2019; 10:E827. [PMID: 31635158 PMCID: PMC6826394 DOI: 10.3390/genes10100827] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from "endangered" to "vulnerable" (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild.
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Affiliation(s)
- Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- School of Laboratory Medicine/Sichuan Provincial EngineeringLaboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu 610500, China.
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Ya'an 611830, Sichuan, China.
| | - Hemin Zhang
- China Conservation and Research Center for the Giant Panda, Ya'an 611830, Sichuan, China.
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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Tong Q, Liu XN, Hu ZF, Ding JF, Bie J, Wang HB, Zhang JT. Effects of Captivity and Season on the Gut Microbiota of the Brown Frog ( Rana dybowskii). Front Microbiol 2019; 10:1912. [PMID: 31507549 PMCID: PMC6716059 DOI: 10.3389/fmicb.2019.01912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota of amphibians is affected by exogenous and endogenous factors. We performed a comprehensive analysis using high-throughput sequencing technology and functional predictions and observed general changes in the gut microbiota of frogs in different growth stages, seasons, and growth environments. There were no significant differences in microbial richness and diversity between juvenile and adult wild frogs, between the summer and autumn groups of captive frogs, or between wild and captive frogs. There were significant differences in the gut microbiota community structure of Rana dybowskii between the summer and autumn groups of captive frogs and between wild and captive R. dybowskii, whereas the differences between juvenile and adult wild frogs were not significant. The dominant gut bacterial phyla in frogs from both captive and wild environments included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Linear discriminant effect size (LEfSe) analysis showed that Bacteroidetes and Firmicutes were significantly enriched in captive and wild R. dybowskii, respectively linear discriminant analysis (LDA > 4). The core operational taxonomical units (OTUs) that were found in >90% of all frogs tested encompassed 15 core OTUs. The captive frogs exhibited 15 core OTUs in addition to the above overall core microbiota, whereas the wild frogs exhibited 19 core OTUs in addition to the above overall core microbiota. Predictions made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that eleven KEGG pathways, such as infectious diseases, immune system diseases, metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, metabolism of terpenoids and polyketides, neurodegenerative diseases, and transport and catabolism, were enriched in captive frogs. The relative abundance of several red-leg-syndrome-related pathogens increased significantly in captive frogs compared with that in wild frogs. To our knowledge, this is the first study on the effects of individual seasons and captivity on the gut microbiota of frogs.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-Ning Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia-Feng Ding
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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Tang W, Zhu G, Shi Q, Yang S, Ma T, Mishra SK, Wen A, Xu H, Wang Q, Jiang Y, Wu J, Xie M, Yao Y, Li D. Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions. Microbiologyopen 2019; 8:e00789. [PMID: 30848054 PMCID: PMC6612554 DOI: 10.1002/mbo3.789] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
The gut microbiota helps the host to absorb nutrients and generate immune responses that can affect host behavior, development, reproduction, and overall health. However, in most of the previous studies, microbiota was sampled mainly using feces and intestinal contents from mammals but not from wild reptiles. Here, we described the bacterial profile from five different gastrointestinal tract (GIT) segments (esophagus, stomach, small intestine, large intestine, and cloaca) of three wild Rhabdophis subminiatus using 16S rRNA V4 hypervariable amplicon sequencing. Forty-seven bacterial phyla were found in the entire GIT, of which Proteobacteria, Firmicutes, and Bacteroidetes were predominant. The results showed a significant difference in microbial diversity between the upper GIT segments (esophagus and stomach) and lower GIT segments (large intestine and cloaca). An obvious dynamic distribution of Fusobacteria and Bacteroidetes was observed, which mainly existed in the lower GIT segments. Conversely, the distribution of Tenericutes was mainly observed in the upper GIT. We also predicted the microbial functions in the different GIT segments, which showed that microbiota in each segments played an important role in higher membrane transport and carbohydrate and amino acid metabolism. Microbes in the small intestine were also mainly involved in disease-related systems, while in the large intestine, they were associated with membrane transport and carbohydrate metabolism. This is the first study to investigate the distribution of the gut microbiota and to predict the microbial function in R. subminiatus. The composition of the gut microbiota certainly reflects the diet and the living environment of the host. Furthermore, these findings provide vital evidence for the diagnosis and treatment of gut diseases in snakes and offer a direction for a model of energy budget research.
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Affiliation(s)
- Wenjiao Tang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Guangxiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qian Shi
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Shijun Yang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Shailendra Kumar Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Anxiang Wen
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Huailiang Xu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qin Wang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yanzhi Jiang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Jiayun Wu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Meng Xie
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yongfang Yao
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
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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: 191] [Impact Index Per Article: 38.2] [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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Sun C, Liu H, Zhang Y, Lu C. Comparative analysis of the gut microbiota of hornbill and toucan in captivity. Microbiologyopen 2018; 8:e00786. [PMID: 30592177 PMCID: PMC6612546 DOI: 10.1002/mbo3.786] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/25/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota plays an important role in animals and are considered microbial organs. Hornbill and toucan are birds of the same ecotypes with high appreciative value. In this study, we characterized and compared the gut microbiota of toco toucan (Ramphastos toco), great hornbill (Buceros bicornis) and wreathed hornbill (Rhyticeros undulatus) using 16S rRNA high-throughput sequencing technology, and further discussed the influence of host bird genetics on its gut microbiota. We identified 10,847 operational taxonomic units (OTUs) from the hyper-variable V4-V5 region, representing 14 phyla that were dominated by the Firmicutes, Proteobacteria, Cyanobacteria, Fusobacteria, Actinobacteria, and Bacteroidetes. Alpha diversity indices showed no significant difference among the three species (p > 0.1). However, great hornbill and toco toucan shared a high number of OTUs. Principal component analysis also revealed highly similar gut microbiotas between the two distant species. Therefore, environmental factors might dominate over host genetics in shaping the gut microbiotas of hornbill and toucan. Our study would contribute in elucidating adaptation of the hornbill and toucan to environmental change.
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Affiliation(s)
- Cheng‐He Sun
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Hong‐Yi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Yong Zhang
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Chang‐Hu Lu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
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Comparative Analysis of the Gut Microbial Composition and Meat Flavor of Two Chicken Breeds in Different Rearing Patterns. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4343196. [PMID: 30410932 PMCID: PMC6206517 DOI: 10.1155/2018/4343196] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/12/2018] [Accepted: 09/04/2018] [Indexed: 01/05/2023]
Abstract
The objective of the study is to compare the effects of free-range (FR) and cage-range (CR) breeding on gut microbiota and flavor compounds of Caoke (C) and Partridge Shank chickens (Q). A total of 120 experimental chickens were assigned to FR group and CR group; each group contain both 30 Caoke chickens and 30 Partridge Shank chickens. At 154 d old, 12 chickens of each group were selected and their cecal contents were extracted and examined for the composition of gut microbiota by illumina sequencing of the V3 region of the 16S rDNA genes, and flavor compounds were analyzed through headspace-solid-phase microextraction (HS-SPME) method. The results showed that, except for acids, the amount of flavor substances in the FR group was higher than those in the CR group, especially the content of Hexanal and D-limonene. Meanwhile, the higher concentrations of carbonyls including (E,E)-2,4-decadienal, (E)-2-decenal, (E)-2-octenal, and pentanal were in the FR chicken meat, but the differences in concentrations compared with CR were not significant. High levels of ethyl hexanoate and β-ocimene were only detected in FR groups. The Firmicutes had the highest proportion of chicken cecal microbiota, whereas the Fusobacteria was only detected in the cecal samples of Q chicken in FR group. Actinobacteria was more prevalent in FR groups than in CR groups. Meanwhile, in Q chickens, the proportions of Bacteroidetes and Proteobacteria in FR group were higher than those in CR group. Using MG-RAST Subsystem Technology, we found that some genes were associated with the formation of precursors of flavor compounds or with the metabolism and degradation of aromatic compounds. Overall, CR and FR breeding influenced the gut microbiota and flavor compounds, potentially because of the changes in diet and living conditions.
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Abstract
The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus “Chapparvovirus”, and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.
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Reese AT, Dunn RR. Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance. mBio 2018; 9:e01294-18. [PMID: 30065092 PMCID: PMC6069118 DOI: 10.1128/mbio.01294-18] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 06/29/2018] [Indexed: 01/16/2023] Open
Abstract
The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated microbial communities (microbiomes) are poorly studied and the appropriateness of general theory is untested. Expanding diversity theory to include microbiomes is essential as diversity is a frequently cited metric of their status. Here, we review and newly analyze reports of alpha diversity for animal gut microbiomes. We demonstrate that both diet and body size affect diversity in the gut but that gut physiology (fermenter versus simple) is the most important driver. We also assess the advantages of various diversity metrics. The importance of diversity in microbiomes is often assumed but has not been tested outright. Therefore, we close by discussing how to integrate microbiomes into the field of biodiversity-ecosystem functioning to more clearly understand when and why a host supports diverse microbial communities.
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Affiliation(s)
- Aspen T Reese
- Society of Fellows, Harvard University, Cambridge, Massachusetts
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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47
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Wang W, Liu Y, Yang Y, Wang A, Sharshov K, Li Y, Cao M, Mao P, Li L. Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser. J Basic Microbiol 2018; 58:543-553. [PMID: 29668076 DOI: 10.1002/jobm.201800060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/27/2018] [Accepted: 04/02/2018] [Indexed: 12/31/2022]
Abstract
In this study, we characterized for the first time the gut microbiota of Greylag geese (Anser anser) using high-throughput 16S rRNA gene sequencing technology. The results showed that the phyla Firmicutes (78.55%), Fusobacteria (9.38%), Proteobacteria (7.55%), Bacteroidetes (1.82%), Cyanobacteria (1.44%), and Actinobacteria (0.61%) dominated the gut microbial communities in the Greylag geese. Then, the variations of gut microbial community structures and functions among the three geese species, Greylag geese, Bar-headed geese (Anser indicus), and Swan geese (Anser cygnoides), were explored. The greatest gut microbial diversity was found in Bar-headed geese group, while other two groups had the least. The dominant bacterial phyla across all samples were Firmicutes and Proteobacteria, but several characteristic bacterial phyla and genera associated with each group were also detected. At all taxonomic levels, the microbial community structure of Swan geese was different from those of Greylag geese and Bar-headed geese, whereas the latter two groups were less different. Functional KEGG categories and pathways associated with carbohydrate metabolism, energy metabolism, and amino acid metabolism were differentially expressed among different geese species. Taken together, this study could provide valuable information to the vast, and yet little explored, research field of wild birds gut microbiome.
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Affiliation(s)
- Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai Province, China
| | - Yingbao Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei Province, China
| | - Yongsheng Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai Province, China
| | - Aizhen Wang
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai Province, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, Russia
| | - Yao Li
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai Province, China
| | - Mengyao Cao
- KunLun College of Qinghai University, Xi'ning, Qinghai Province, China
| | - Puzhen Mao
- KunLun College of Qinghai University, Xi'ning, Qinghai Province, China
| | - Laixing Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai Province, China
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48
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Siriyappagouder P, Kiron V, Lokesh J, Rajeish M, Kopp M, Fernandes J. The Intestinal Mycobiota in Wild Zebrafish Comprises Mainly Dothideomycetes While Saccharomycetes Predominate in Their Laboratory-Reared Counterparts. Front Microbiol 2018; 9:387. [PMID: 29559965 PMCID: PMC5845672 DOI: 10.3389/fmicb.2018.00387] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/20/2018] [Indexed: 12/27/2022] Open
Abstract
As an integral part of the resident microbial community of fish intestinal tract, the mycobiota is expected to play important roles in health and disease resistance of the host. The composition of the diverse fungal communities, which colonize the intestine, is greatly influenced by the host, their diet and geographic origin. Studies of fungal communities are rare and the majority of previous studies have relied on culture-based methods. In particular, fungal communities in fish are also poorly characterized. The aim of this study was to provide an in-depth overview of the intestinal mycobiota in a model fish species (zebrafish, Danio rerio) and to determine differences in fungal composition between wild and captive specimens. We have profiled the intestinal mycobiota of wild-caught (Sharavati River, India), laboratory-reared (Bodø, Norway) and wild-caught-laboratory-kept (Uttara, India) zebrafish by sequencing the fungal internal transcribed spacer 2 region on the Illumina MiSeq platform. Wild fish were exposed to variable environmental factors, whereas both laboratory groups were kept in controlled conditions. There were also differences in husbandry practices at Bodø and Uttara, particularly diet. Zebrafish from Bodø were reared in the laboratory for over 10 generations, while wild-caught-laboratory-kept fish from Uttara were housed in the laboratory for only 2 months before sample collection. The intestine of zebrafish contained members of more than 15 fungal classes belonging to the phyla Ascomycota, Basidiomycota, and Zygomycota. Fungal species richness and diversity distinguished the wild-caught and laboratory-reared zebrafish communities. Wild-caught zebrafish-associated mycobiota comprised mainly Dothideomycetes in contrast to their Saccharomycetes-dominated laboratory-reared counterparts. The predominant Saccharomycetes in laboratory-reared fish belonged to the saprotrophic guild. Another characteristic feature of laboratory-reared fish was the significantly higher abundance of Cryptococcus (Tremellomycetes) compared to wild fish. This pioneer study has shed light into the differences in the intestinal fungal communities of wild-caught and laboratory-reared zebrafish and the baseline data generated will enrich our knowledge on fish mycobiota.
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Affiliation(s)
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Moger Rajeish
- College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, India
| | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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49
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Hamarová Ľ, Repel M, Javorský P, Pristaš P. Evaluation of enteromicroflora of common crane (Grus grus) as a potential reservoir of bacterial antimicrobial resistance. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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50
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Ma L, Xie Y, Han Z, Giesy JP, Zhang X. Responses of earthworms and microbial communities in their guts to Triclosan. CHEMOSPHERE 2017; 168:1194-1202. [PMID: 27810239 DOI: 10.1016/j.chemosphere.2016.10.079] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Abstract
Responses of the earthworm (Eisenia fetida) and compositions of associated microbial communities were determined after exposure to various concentrations of Triclosan (TCS) for 7 d. Concentrations of TCS were greater in intestines than in epidermis of earthworms, which suggested that earthworms accumulate TCS mainly by ingestion rather than by epidermic penetration. Exposure to TCS caused a concentration-dependent increase in activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) and in malondialdehyde (MDA) in E. fetida. Analyses of both the bacterial and eukaryotic community by next generation sequencing (NGS), demonstrated that TCS caused a concentration-dependent decrease in sensitive genera. While relative abundances of Pseudomonas, Stenotrophomonas, and Achromobacter were increased. Nine susceptible microbial groups were more sensitive to exposure to TCS, than were activities of enzymes in earthworms. Thus, rapid genomic measures of gut flora can be used as indicators to assess adverse effects of chemicals on earthworms.
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Affiliation(s)
- Lili Ma
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Collaborative Innovation Center for Regional Environmental Quality, Nanjing University, Nanjing, 210023, China
| | - Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Collaborative Innovation Center for Regional Environmental Quality, Nanjing University, Nanjing, 210023, China
| | - Zhihua Han
- Nanjing Institute of Environmental Science, MEP, Nanjing, Jiangsu, 210042, China
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Collaborative Innovation Center for Regional Environmental Quality, Nanjing University, Nanjing, 210023, China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Department of Zoology, and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA; School of Biological Sciences, University of Hong Kong, Hong Kong Special Administrative Region
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Collaborative Innovation Center for Regional Environmental Quality, Nanjing University, Nanjing, 210023, China.
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