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Liu S, Imad S, Hussain S, Xiao S, Yu X, Cao H. Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs. BMC Microbiol 2024; 24:34. [PMID: 38262927 PMCID: PMC10804495 DOI: 10.1186/s12866-023-03150-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Frogs are critical economic animals essential to agricultural ecosystem equilibrium. However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings. While frog-associated microbiota contribute to elemental cycling and immunity, the effects of frog sex and health on gut bacteria remain understudied, and the relationship between frog habitat and soil microbes is unclear. We aimed to determine how frog sex, health status and habitat influence symbiotic bacteria and community assembly mechanism to provide guidance for sustainable frog farming and conservation. RESULTS We employed 16S rRNA sequencing to investigate gut microbiota differences in relation to frog sex and health status. We also compared symbiotic communities in frog-aggregation, native and soybean soil on the farm. Results showed that gut bacterial β-diversity and taxonomy were markedly influenced by frog sex and health. Healthy frogs had more robust gut bacterial metabolism than frogs infected with MID. Cooccurrence network analysis revealed that healthy female frogs had more complex microbial network structure than males; however, diseased males showed the greatest network complexity. The assembly mechanism of gut bacteria in male frogs was dominated by deterministic processes, whereas in female frogs it was dominated by stochastic processes. Among symbiotic bacteria in frog habitat soils, deterministic processes predominantly shaped the community assembly of soybean soil. In particular, soybean soil was enriched in pathogens and nitrogen functions, whereas frog-aggregation soil was markedly increased in sulphur respiration and hydrocarbon degradation. CONCLUSION Our study reveals that sex mainly alters the interaction network and assembly mechanism of frog intestinal bacteria; MID infection significantly inhibits the metabolic functions of intestinal bacteria. Furthermore, diverse frog habitat soils could shape more symbiotic bacteria to benefit frog farming. Our findings provide new horizons for symbiotic bacteria among frogs, which could contribute to sustainable agriculture and ecological balance.
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Affiliation(s)
- Senlin Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Sewar Imad
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | | | - Xiaowei Yu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China.
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Santos B, Martins FMS, Sabino-Pinto J, Licata F, Crottini A. Skin and gut microbiomes of tadpoles vary differently with host and water environment: a short-term experiment using 16S metabarcoding. Sci Rep 2023; 13:16321. [PMID: 37770544 PMCID: PMC10539280 DOI: 10.1038/s41598-023-43340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 09/30/2023] Open
Abstract
The host-microbiome community is influenced by several host and environmental factors. In order to disentangle the individual effects of host and environment, we performed a laboratory experiment to assess the effects of the exposure to different water sources on the skin and gut microbiome of two amphibian species (Pelophylax perezi and Bufo spinosus). We observed that the bacterial communities greatly varied with water environment and host identity. Tadpoles of B. spinosus collected from a waterbody with poorer bacterial diversity exhibited a more diverse skin and gut microbiome after exposed to a richer water source. Tadpoles of P. perezi, originally collected from a richer water environment, exhibited less marked alterations in diversity patterns independently of the water source but showed alterations in gut composition. These results highlight that environment alterations, such as the water source, combined with the host effect, impact the microbiome of amphibian species in different ways; the population history (e.g., previous water environment and habitat) of the host species may also influence future alterations on tadpole microbiome.
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Affiliation(s)
- Bárbara Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Filipa M S Martins
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Joana Sabino-Pinto
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Fulvio Licata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
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Villatoro-Castañeda M, Forsburg ZR, Ortiz W, Fritts SR, Gabor CR, Carlos-Shanley C. Exposure to Roundup and Antibiotics Alters Gut Microbial Communities, Growth, and Behavior in Rana berlandieri Tadpoles. BIOLOGY 2023; 12:1171. [PMID: 37759571 PMCID: PMC10525943 DOI: 10.3390/biology12091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
The gut microbiome is important for digestion, host fitness, and defense against pathogens, which provides a tool for host health assessment. Amphibians and their microbiomes are highly susceptible to pollutants including antibiotics. We explored the role of an unmanipulated gut microbiome on tadpole fitness and phenotype by comparing tadpoles of Rana berlandieri in a control group (1) with tadpoles exposed to: (2) Roundup® (glyphosate active ingredient), (3) antibiotic cocktail (enrofloxacin, sulfamethazine, trimethoprim, streptomycin, and penicillin), and (4) a combination of Roundup and antibiotics. Tadpoles in the antibiotic and combination treatments had the smallest dorsal body area and were the least active compared to control and Roundup-exposed tadpoles, which were less active than control tadpoles. The gut microbial community significantly changed across treatments at the alpha, beta, and core bacterial levels. However, we did not find significant differences between the antibiotic- and combination-exposed tadpoles, suggesting that antibiotic alone was enough to suppress growth, change behavior, and alter the gut microbiome composition. Here, we demonstrate that the gut microbial communities of tadpoles are sensitive to environmental pollutants, namely Roundup and antibiotics, which may have consequences for host phenotype and fitness via altered behavior and growth.
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Affiliation(s)
- Melissa Villatoro-Castañeda
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Zachery R. Forsburg
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
- Archbold Biological Station, 123 Main Dr., Venus, FL 33960, USA
| | - Whitney Ortiz
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Sarah R. Fritts
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Caitlin R. Gabor
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Camila Carlos-Shanley
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
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Shi Q, Li Y, Deng S, Zhang H, Jiang H, Shen L, Pan T, Hong P, Wu H, Shu Y. The succession of gut microbiota in the concave-eared torrent frog ( Odorrana tormota) throughout developmental history. Ecol Evol 2023; 13:e10094. [PMID: 37214611 PMCID: PMC10199338 DOI: 10.1002/ece3.10094] [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: 03/13/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
The gut microbiota of amphibians plays a crucial role in maintaining health and adapting to various developmental stages. The composition of gut microbial community is influenced by the phylogeny, habitat, diet, and developmental stage of the host. The present study analyzed the microbiota in the intestine of O. tormota at 11 developmental stages (from the tadpole at Gosner stage 24 to the 3-year-old adult) using high-throughput 16S rRNA sequencing. Alpha diversity index analysis of the microbiota revealed that the index decreased from tadpole at Gosner stage 24 to adult frog stage, remained stable during the adult frog stages, but increased significantly at the early metamorphosis and hibernation preparation stages. The gut microbiota structure is similar in adult frogs but differs significantly in other developmental stages. Furthermore, the dominant phyla of gut microbiota in tadpoles were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, whereas those in adult frogs were Proteobacteria, Firmicutes, Bacteroidetes, and Verrucomicrobia. Host and environmental factors jointly affected the gut microbial diversity and community composition of O. tormota, but developmental stage, feeding habit, and habitat type had a more significant influence. The microbial community in the gut varies with the developmental stage of the host and constantly adapts to the survival requirements of the host. These findings advance our understanding of the evolutionary mechanism of amphibian gut microbiota in maintaining health homeostasis and adaptation.
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Affiliation(s)
- Qingkai Shi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Yue Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Shuaitao Deng
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Shanghai Wildlife and Protected Natural Areas Research CenterShanghaiChina
| | - Huijuan Zhang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Huiling Jiang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Liang Shen
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Tao Pan
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Pei Hong
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Hailong Wu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Yilin Shu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
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Zhang L, Yang Z, Yang F, Wang G, Zeng M, Zhang Z, Yang M, Wang Z, Li Z. Gut microbiota of two invasive fishes respond differently to temperature. Front Microbiol 2023; 14:1087777. [PMID: 37056740 PMCID: PMC10088563 DOI: 10.3389/fmicb.2023.1087777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Temperature variation structures the composition and diversity of gut microbiomes in ectothermic animals, key regulators of host physiology, with potential benefit to host or lead to converse results (i.e., negative). So, the significance of either effect may largely depend on the length of time exposed to extreme temperatures and how rapidly the gut microbiota can be altered by change in temperature. However, the temporal effects of temperature on gut microbiota have rarely been clarified. To understand this issue, we exposed two juvenile fishes (Cyprinus carpio and Micropterus salmoides), which both ranked among the 100 worst invasive alien species in the world, to increased environmental temperature and sampled of the gut microbiota at multiple time points after exposure so as to determine when differences in these communities become detectable. Further, how temperature affects the composition and function of microbiota was examined by comparing predicted metagenomic profiles of gut microbiota between treatment groups at the final time point of the experiment. The gut microbiota of C. carpio was more plastic than those of M. salmoides. Specifically, communities of C. carpio were greatly altered by increased temperature within 1 week, while communities of M. salmoides exhibit no significant changes. Further, we identified 10 predicted bacterial functional pathways in C. carpio that were temperature-dependent, while none functional pathways in M. salmoides was found to be temperature-dependent. Thus, the gut microbiota of C. carpio was more sensitive to temperature changes and their functional pathways were significantly changed after temperature treatment. These results showed the gut microbiota of the two invasive fishes differ in response to temperature change, which may indicate that they differ in colonization modes. Broadly, we have confirmed that the increased short-term fluctuations in temperatures are always expected to alter the gut microbiota of ectothermic vertebrates when facing global climate change.
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Affiliation(s)
- Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
- Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem and The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province, Xinxiang, China
- *Correspondence: Lixia Zhang,
| | - Zi Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Fan Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Gege Wang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ming Zeng
- Jigongshan National Nature Reserve, Xinyang, China
| | | | - Mengxiao Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, China
| | - Zhibing Li
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
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Sawada K, Kadowaki S. Change in the Guild Structure of a Snake Community in Japan over 30 Years. CURRENT HERPETOLOGY 2023. [DOI: 10.5358/hsj.42.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Kiyoto Sawada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ten-nodai 1–1–1, Tsukuba, Ibaraki 305–8572, JAPAN
| | - Seishi Kadowaki
- Tsukuba Experimental Forest, Mountain Science Center, University of Tsukuba, Ten-nodai 1–1–1, Tsukuba Ibaraki 305–8572, JAPAN
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7
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Holmes IA, Grundler MC. Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community. Mol Ecol 2023; 32:258-274. [PMID: 36221927 PMCID: PMC9797449 DOI: 10.1111/mec.16733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022]
Abstract
While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.
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Affiliation(s)
- Iris A. Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Michael C. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
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Gut Bacterial Communities Vary across Habitats and Their Diversity Increases with Increasing Glucocorticoids in Toad Tadpoles. DIVERSITY 2022. [DOI: 10.3390/d15010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The gut microbiome is important for host health and can be influenced by environmental and hormonal changes. We studied the interactions between anthropogenic land use, glucocorticoid hormones, and gut bacterial communities in common toads (Bufo bufo). We sampled tadpoles from ponds of three habitat types (natural, agricultural, and urban ponds), examined gut microbiome composition using amplicon sequencing of the 16S rRNA gene, and measured the associated stress physiology using water-borne hormones. Tadpoles from different habitat types significantly differed in bacterial composition. However, bacterial richness, Shannon diversity, and Firmicutes to Bacteroidota ratio did not vary with habitat type. In contrast with other studies, we found a positive correlation between baseline corticosterone release rate and bacterial diversity. Stress response and negative feedback were not significantly correlated with bacterial diversity. These results suggest that, despite alterations in the composition of intestinal bacterial communities due to land-use change, common toad tadpoles in anthropogenic habitats may maintain their physiological health in terms of the “gut-brain axis”.
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Zhao N, Ma Z, Jiang Y, Shi Y, Xie Y, Wang Y, Wu S, Liu S, Wang S. Geographical patterns of Fejervarya limnocharis gut microbiota by latitude along mainland China’s coastline. Front Microbiol 2022; 13:1062302. [DOI: 10.3389/fmicb.2022.1062302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
The gut microbiota affects many aspects of host biology and plays key roles in the coevolutionary association with its host. Geographical gradients may play a certain role on gut microbiota variation in the natural environment. However, the distribution pattern of amphibian gut microbiota in the latitudinal gradient remains largely unexplored. Here, we sampled six natural populations of Fejervarya limnocharis along the eastern coastline of mainland China (spanning 20°–30° N = 1,300 km) using 16S rRNA amplicon sequencing to characterize the gut microbiota. First of all, a significant correlation between gut microbial diversity and latitude was observed in our research system. Second, we discovered that latitude influenced the composition of the gut microbiota of F. limnocharis. Finally, we detected that geographical distance could not determine gut microbiota composition in F. limnocharis. These results indicate that latitude can play an important role in shaping the gut microbial diversity of amphibian. Our study offers the first evidence that gut microbial diversity of amphibian presents a latitudinal pattern and highlights the need for increased numbers of individuals to be sampled during microbiome studies in wild populations along environmental gradients.
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Qin W, Li S, Wu N, Wen Z, Xie J, Ma H, Zhang S. Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group. Animals (Basel) 2022; 12:ani12141777. [PMID: 35883324 PMCID: PMC9312300 DOI: 10.3390/ani12141777] [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: 06/03/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary This study examined the differences and similarities in gut microbial diversity and ecological assembly processes of Datong yaks, including domestic males and females and wild males, which were fed together on the Qinghai-Tibet Plateau in a mixed group. The results revealed that mixed grouping could influence the gut microbiota of these three groups of yaks and improve the gut microbial diversity of domestic females. The findings of this study can help to understand the effects of mixed grouping on the gut microbiota of livestock on the Qinghai-Tibet Plateau and improve the production of Datong yaks. Abstract The Datong yak (Bos grunniens) is the first artificial breed of yaks in the world and has played an important role in the improvement of domestic yak quality on the Qinghai-Tibet Plateau. The Datong yak breeding farm in the Qinghai province of China is the main place for the breeding and feeding of Datong yaks. It hosts domestic Datong yaks and wild male yaks, mainly in mixed groups. Different managements have different effects on livestock. The gut microbiota is closely related to the health and immunity of Datong yaks, and mixed grouping can affect the composition and diversity of the gut microbiota of Datong yaks. To reveal the effects of mixed grouping on the gut microbiota of Datong yaks and wild yaks and identify the main dominant factors, we compared the gut microbial diversities of domestic males and females and wild males based on 16S rRNA V3–V4 regions using fresh fecal samples. The data showed significant differences in the gut microbial diversity of these three groups, and the α-diversity was the highest in wild males. Different factors influence the gut microbiota, and the main influencing factors were different in different groups, including sex differences, host genetics, and physical interactions. We also compared ecological assembly processes in the three groups. The results showed that mixed grouping contributed to the improvement of gut microbial diversity in domestic females. Our study provides effective and feasible suggestions for the feeding and management of the Datong yaks.
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Affiliation(s)
- Wen Qin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Shuang Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
| | - Nan Wu
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (N.W.); (Z.W.)
| | - Zhouxuan Wen
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (N.W.); (Z.W.)
| | - Jiuxiang Xie
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China;
| | - Hongyi Ma
- Forestry and Grassland Comprehensive Service Center of Yushu Prefecture, Yushu 815000, China;
| | - Shoudong Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, School of Life Sciences, Fudan University, Shanghai 200433, China
- Global Flyway Ecology, Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9700 CC Groningen, The Netherlands
- Correspondence:
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Chen Z, Chen J, Liu Y, Zhang J, Chen X, Qu Y. Comparative study on gut microbiota in three Anura frogs from a mountain stream. Ecol Evol 2022; 12:e8854. [PMID: 35475186 PMCID: PMC9021931 DOI: 10.1002/ece3.8854] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 12/25/2022] Open
Abstract
Composition and diversity in gut microbiota are impacted by a wide variety of factors. The similarity of gut microbiota in related or sympatric species has been gaining recent traction. Here, 16S rRNA gene sequencing technology was employed to study the gut microbiota of three sympatric frog species, namely Odorrana tormota, O. graminea, and Amolops wuyiensis. In these three frog species, the most abundant phylum was Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, and Firmicutes. The most abundant family was Burkholderiaceae in three species. The most dominant genera were Burkholderia, Caballeronia, and Paraburkholderia with the highest relative abundance in O. tormota, O. graminea, and A. wuyiensis, respectively. No differences were observed in alpha diversity indexes among the three frog species. However, bacterial similarity of gut microbiota was significantly different between O. tormota and A. wuyiensis and between O. graminea and A. wuyiensis. Metabolism‐related gene function was predominantly enriched in the gut microbiota of the three evaluated frog species. From these findings, that the relative abundance of the gut microbiota and predicted gene functions differed in three species, we conclude that there were significant differences in the gut microbiota of the three species. Similar alpha diversity and interspecific bacterial similarity in the gut might be related to bacterial transmission among the three Anura frogs evaluated in this study.
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Affiliation(s)
- Zhuo Chen
- College of Life Sciences Henan Normal University Xinxiang Henan China
- The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province Xinxiang Henan China
| | - Jun‐Qiong Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing Jiangsu China
| | - Yao Liu
- College of Life Sciences Henan Normal University Xinxiang Henan China
- The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province Xinxiang Henan China
| | - Jie Zhang
- College of Fisheries Henan Normal University Xinxiang Henan China
| | - Xiao‐Hong Chen
- College of Life Sciences Henan Normal University Xinxiang Henan China
- The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province Xinxiang Henan China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing Jiangsu China
| | - Yan‐Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing Jiangsu China
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Chimetto Tonon LA, Rua C, Crnkovic CM, Bernardi DI, Pires Junior OR, Haddad CFB, Pedrosa CSG, Souza LRQ, Rehen SK, de Azevedo GPR, Thompson CC, Thompson FL, Berlinck RGS. Microbiome associated with the tetrodotoxin-bearing anuran Brachycephalus pitanga. Toxicon 2021; 203:139-146. [PMID: 34653444 DOI: 10.1016/j.toxicon.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/15/2022]
Abstract
The genus Brachycephalus includes small species of aposematic anurans known as microendemic, occurring in the mountains of the Atlantic Forest. Brachycephalus ephippium, B. nodoterga and B. pernix have been reported to contain the neurotoxin tetrodotoxin in skin and viscera. The biological conservation of several Brachycephalus species is currently threatened by climate change, deforestation, and the pandemic caused by the fungus Batrachochytrium dendrobatidis (Bd). Despite the well-known importance of amphibians' associated bacteria in the defensive role against pathogens, there is still a poor understanding of amphibian microbiome composition. The present study investigated the composition of B. pitanga microbial community and the presence of TTX in the host and in cultures of bacterial isolates, using a combination of metagenomics, bacterial culture isolation, mass spectrometry and metabolomic analyses. Results of culture-dependent and -independent analyses characterized the microbial communities associated with the skin and viscera of B. pitanga. Mass spectrometry analysis indicated the presence of TTX in host tissues, while bacterial production of TTX was not observed under the experimental conditions used in this investigation. This is the first report confirming the occurrence of TTX in B. pitanga.
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Affiliation(s)
- Luciane A Chimetto Tonon
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
| | - Cintia Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Camila M Crnkovic
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil; Departamento de Tecnologia Bioquímico-Farmacêutica (FBT), Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Osmindo R Pires Junior
- Laboratório de Toxinologia, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | | | | | - Stevens K Rehen
- Instituto D'Or de Pesquisa e Ensino (IDOR), RJ, Brazil; Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Gustavo P R de Azevedo
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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Taxonomy, not locality, influences the cloacal microbiota of two nearctic colubrids: a preliminary analysis. Mol Biol Rep 2021; 48:6435-6442. [PMID: 34403035 DOI: 10.1007/s11033-021-06645-x] [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: 05/22/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The gut microbiota is an emerging frontier in wildlife research and its importance to vertebrate health and physiology is becoming ever more apparent. Reptiles, in particular snakes, have not received the same attention given to other vertebrates and the composition of their wild gut microbiome remains understudied. The primary goal of this work was to describe the cloacal microbiota of two Colubrids, the Eastern Gartersnake (Thamnophis sirtalis sirtalis) and the Northern Watersnake (Nerodia sipedon sipedon), and if their cloacal microbiota differed as well as if it did between a wetland and upland population of the former species. METHODS AND RESULTS We utilized next-generation sequencing of cloacal swabs-a non-destructive proxy for the gut microbiota. The cloacal microbiome of Eastern Gartersnakes (N = 9) was like those of other snakes being comprised of Proteobacteria, Bacteroidetes, and Firmicutes, while that of Northern Watersnakes (N = 6) was dominated by Tenericutes. Seven microbial operational taxonomic units (OTUs), all members of Proteobacteria, were shared among all individuals and were indicative of a core microbiome in Eastern Gartersnakes, but these OTUs were not particularly relevant to Northern Watersnakes. The latter had greater OTU richness than did Eastern Gartersnakes, and habitat did not have any apparent effect on the microbial community composition in Eastern Gartersnakes. CONCLUSIONS Our findings suggest host taxonomy to be a determining factor in the cloacal microbiota of snakes and that Tenericutes are associated with aquatic habitats. This is the first report to examine the cloacal microbiome of these species and provides a useful foundation for future work to build upon.
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Song X, Zhang J, Song J, Zhai Y. Decisive Effects of Life Stage on the Gut Microbiota Discrepancy Between Two Wild Populations of Hibernating Asiatic Toads ( Bufo gargarizans). Front Microbiol 2021; 12:665849. [PMID: 34413833 PMCID: PMC8369469 DOI: 10.3389/fmicb.2021.665849] [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: 02/09/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Until now, the effects of driving factors on the gut microbiota of amphibians are still mostly confounded. Due to a long-term fasting, hibernating amphibians are ideal experimental materials to explore this question. In this study, we characterized the small intestine microbiota of adult hibernating Asiatic toads (Bufo gargarizans) collected from two geographical populations using 16S rRNA amplicon sequencing technique and evaluated the effects of non-dietary factors (e.g., sex and host genetic background). Proteobacteria (0.9196 ± 0.0892) was characterized as the most dominant phylum in the small gut microbiota of hibernating Asiatic toads, among which five core OTUs were identified and three were classified into Pseudomonas. In view of the coincidence between the dominant KEGG pathways (such as the two-component system) and Pseudomonas, Pseudomonas appeared to be a key adaptor for small gut microbiota during hibernation. Furthermore, we detected a greater discrepancy of gut microbiota between geographical populations than between sexes. Both sex and host genetic background showed a minor effect on the gut microbiota variation. Finally, life stage was determined to be the decisive factor driving the gut microbiota discrepancy between populations. However, a large proportion of the gut microbiota variation (∼70%) could not be explained by the measured deterministic factors (i.e., sex, location, body length, and routine blood indices). Therefore, other factors and/or stochastic processes may play key roles in shaping gut bacterial community of hibernating amphibians.
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Affiliation(s)
- Xiaowei Song
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jingwei Zhang
- Hospital of Xinyang Normal University, Xinyang Normal University, Xinyang, China
| | - Jinghan Song
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yuanyuan Zhai
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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15
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Li Q, Li N, Liu H, Du Y, He H, Zhang L, Liu Y. Estrogen-decreased hsa_circ_0001649 promotes stromal cell invasion in endometriosis. Reproduction 2021; 160:511-519. [PMID: 32698139 PMCID: PMC7497355 DOI: 10.1530/rep-19-0540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/06/2020] [Indexed: 01/25/2023]
Abstract
Endometriosis (EMs) is an estrogen (E2)-dependent inflammatory disorder. Although EMs is considered a benign disease, it presents with malignant characteristics, such as migration and invasion. An increasing number of studies have shown that aberrantly expressed circular RNAs (circRNAs) play an essential role in disease development and progression. However, the mechanisms by which circRNAs exert their pathological effects in EMs remain unclear. Hsa_circ_0001649, a novel cancer-associated circRNA, has been previously reported to be downregulated in several cancer types and related to cell migration and invasion. In the present study, real-time PCR (qRT-PCR) was carried out to measure hsa_circ_0001649 levels in human tissues, human primary endometrial stromal cells (ESCs) and a human endometrial stromal cell line (ThESCs). Matrix metalloproteinase 9 (MMP9) levels in ESCs and ThESCs were assessed by qRT-PCR and Western blotting, and the migration and invasion capacities of ThESCs were evaluated by transwell assay. As a result, hsa_circ_0001649 expression was significantly decreased in ectopic and eutopic endometrial samples compared with that in normal endometrial samples. E2 decreased hsa_circ_0001649 expression but increased MMP9 expression in ESCs and ThESCs. Furthermore, ThESCs were more invasive under E2 stimulation. However, these effects disappeared when ICI or hsa_circ_0001649 transfection was used. Collectively, our findings reveal that decreased hsa_circ_0001649 expression plays a role in E2-increased MMP9 expression through E2 receptors (ERs), which have critical functions in EMs.
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Affiliation(s)
- Qi Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hengwei Liu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yu Du
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haitang He
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Santos B, Bletz MC, Sabino-Pinto J, Cocca W, Fidy JFS, Freeman KL, Kuenzel S, Ndriantsoa S, Noel J, Rakotonanahary T, Vences M, Crottini A. Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species. PeerJ 2021; 9:e11532. [PMID: 34249488 PMCID: PMC8247705 DOI: 10.7717/peerj.11532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/07/2021] [Indexed: 12/19/2022] Open
Abstract
Biological invasions are on the rise, with each invader carrying a plethora of associated microbes. These microbes play important, yet poorly understood, ecological roles that can include assisting the hosts in colonization and adaptation processes or as possible pathogens. Understanding how these communities differ in an invasion scenario may help to understand the host's resilience and adaptability. The Asian common toad, Duttaphrynus melanostictus is an invasive amphibian, which has recently established in Madagascar and is expected to pose numerous threats to the native ecosystems. We characterized the skin and gut bacterial communities of D. melanostictus in Toamasina (Eastern Madagascar), and compared them to those of a co-occurring native frog species, Ptychadena mascareniensis, at three sites where the toad arrived in different years. Microbial composition did not vary among sites, showing that D. melanostictus keeps a stable community across its expansion but significant differences were observed between these two amphibians. Moreover, D. melanostictus had richer and more diverse communities and also harboured a high percentage of total unique taxa (skin: 80%; gut: 52%). These differences may reflect the combination of multiple host-associated factors including microhabitat selection, skin features and dietary preferences.
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Affiliation(s)
- Bárbara Santos
- Cibio, Research Centre in Biodiversity and Genetic Resources, InBio, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Portugal, Porto, Portugal
| | - Molly C Bletz
- Department of Biology, University of Massachussetts Boston, Boston, MA, USA
| | - Joana Sabino-Pinto
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, Germany, Braunschweig, Germany
| | - Walter Cocca
- Cibio, Research Centre in Biodiversity and Genetic Resources, InBio, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Portugal, Porto, Portugal
| | | | - Karen Lm Freeman
- Madagascar Fauna and Flora Group, BP 442, 501 Toamasina, Madagascar, Toamasina, Madagascar
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Germany, Plön, Germany
| | - Serge Ndriantsoa
- Amphibian Survival Alliance c/o Durrell Wildlife Conservation Trust, Madagascar Programme, Lot II Y 49 J 12 Ampasanimalo, BP 8511 101 Antananarivo, Madagascar, Antananarivo, Madagascar
| | - Jean Noel
- Madagascar Fauna and Flora Group, BP 442, 501 Toamasina, Madagascar, Toamasina, Madagascar
| | - Tsanta Rakotonanahary
- Amphibian Survival Alliance c/o Durrell Wildlife Conservation Trust, Madagascar Programme, Lot II Y 49 J 12 Ampasanimalo, BP 8511 101 Antananarivo, Madagascar, Antananarivo, Madagascar
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, Germany, Braunschweig, Germany
| | - Angelica Crottini
- Cibio, Research Centre in Biodiversity and Genetic Resources, InBio, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Portugal, Porto, Portugal
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Seasonal Variation in Gut Microbiota Related to Diet in Fejervarya limnocharis. ANIMALS : AN OPEN ACCESS JOURNAL FROM MDPI 2021; 11:ani11051393. [PMID: 34068415 PMCID: PMC8153623 DOI: 10.3390/ani11051393] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022]
Abstract
Organisms adapt to environmental fluctuations by varying their morphology and structural, physiological, and biochemical characteristics. Gut microbiome, varying rapidly in response to environmental shifts, has been proposed as a strategy for adapting to the fluctuating environment (e.g., new dietary niches). Here, we explored the adaptive mechanism of frog intestinal microbes in response to environmental changes. We collected 170 Fejervarya limnocharis during different seasons (spring, summer, autumn, and pre-hibernation) to study the compositional and functional divergence of gut microbiota and analysed the effects of seasonal feeding habits and body condition on intestinal microorganisms using 16S rRNA high-throughput sequencing, Tax4Fun function prediction analysis, and bioinformatics analysis. The results showed no significant dietary difference in various seasons and between males and females. However, a significantly positive correlation was detected between dietary diversity and food niche width. Host condition (body size, body mass, and body condition) also revealed seasonal changes. The frogs were colonised by 71 bacterial phyla and dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stenotrophomonas was the most abundant genus in the Proteobacteria. The composition, diversity, and function of intestinal microorganisms in different seasons were significantly different. Significant differences were observed in composition and function but not in the microbial diversity between sexes. Furthermore, seasonal foods and body mass were significantly correlated with gut microbial composition. Our results suggest that gut microbiomes of F. limnocharis vary seasonally in response to diet under fluctuating environments.
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Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable ( Martes zibellina) Guts. Animals (Basel) 2021; 11:ani11030865. [PMID: 33803658 PMCID: PMC8002971 DOI: 10.3390/ani11030865] [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: 02/18/2021] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.
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The Oral Bacterial Community in Melanophryniscus admirabilis (Admirable Red-Belly Toads): Implications for Conservation. Microorganisms 2021; 9:microorganisms9020220. [PMID: 33499099 PMCID: PMC7912307 DOI: 10.3390/microorganisms9020220] [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: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad’s adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species.
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Kuthyar S, Kowalewski MM, Roellig DM, Mallott EK, Zeng Y, Gillespie TR, Amato KR. Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria. Ecol Evol 2021; 11:45-57. [PMID: 33437414 PMCID: PMC7790644 DOI: 10.1002/ece3.6910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/27/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.
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Affiliation(s)
- Sahana Kuthyar
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
| | - Martin M. Kowalewski
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
- Estación Biológica CorrientesMuseo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN‐CONICET)CorrientesArgentina
| | - Dawn M. Roellig
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention (CDC)AtlantaGAUSA
| | | | - Yan Zeng
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
| | - Thomas R. Gillespie
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
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Tong Q, Cui LY, Hu ZF, Du XP, Abid HM, Wang HB. Environmental and host factors shaping the gut microbiota diversity of brown frog Rana dybowskii. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140142. [PMID: 32615421 DOI: 10.1016/j.scitotenv.2020.140142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/18/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Symbiotic microbial communities are common in amphibians, and the composition of gut microbial communities varies with factors such as host phylogeny, life stage, ecology, and diet. However, little is known regarding how amphibians acquire their microbiota or how their growth, development, and environmental factors affect the diversity of their microbiotas. We sampled the gut microbiota during different developmental stages of brown frog Rana dybowskii, including tadpoles (T), frogs in metamorphosis (M), frogs just post-metamorphosis and after eating (F), juvenile frogs in summer (Js), adult frogs in summer (As), adult frogs in autumn (Aa), and hibernating frogs (Ah). We recorded data on the environmental (ambient temperature, fasting status, habitat, and season) and host (body mass and developmental period) factors. We investigated whether the gut microbiota diversity of R. dybowskii differs according to the host developmental stage via high-throughput Illumina sequencing and whether the gut microbiota diversity is affected by environmental and host factors. We found that alpha and beta diversity varied significantly during different developmental stages. The linear discriminant analysis effect size (LEfSe) analysis identified eight phyla exhibiting significant differences: Cyanobacteria (T group), Proteobacteria (M group), Fusobacteria (F group), Firmicutes (As group), Actinobacteria (Aa group), Verrucomicrobia (Aa group), Tenericutes (Aa group), and Bacteroidetes (Ah group). The Venn diagrams showed that 49 shared OTUs were present during all stages of development, whereas 10 OTUs were present in >90% of the samples. The environmental and host factors were significantly correlated with microbial community changes. Furthermore, the AIC-based model results suggested that development was the only variable that needed inclusion in the redundancy analysis (RDA) to explain the variance in taxa. These results have broad implications for our understanding of gut microbiota development and its associations with amphibian development and environmental factors.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China; Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Li-Yong Cui
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-Peng Du
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hayat Muhammad Abid
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
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22
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Jiménez RR, Alvarado G, Sandoval J, Sommer S. Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog. BMC Microbiol 2020; 20:292. [PMID: 32962670 PMCID: PMC7509932 DOI: 10.1186/s12866-020-01979-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be "extinct" have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd. RESULTS We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance. CONCLUSIONS Our findings support the microbial "Anna Karenina principle", in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.
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Affiliation(s)
- Randall R Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany.
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Av. Orlando Marques de Paiva 87, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - José Sandoval
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany
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23
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Tong Q, Cui LY, Du XP, Hu ZF, Bie J, Xiao JH, Wang HB, Zhang JT. Comparison of Gut Microbiota Diversity and Predicted Functions Between Healthy and Diseased Captive Rana dybowskii. Front Microbiol 2020; 11:2096. [PMID: 32983063 PMCID: PMC7490342 DOI: 10.3389/fmicb.2020.02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 08/10/2020] [Indexed: 01/26/2023] Open
Abstract
The gut microbiota plays a key role in host health, and disruptions to gut bacterial homeostasis can cause disease. However, the effect of disease on gut microbiota assembly remains unclear and gut microbiota-based predictions of health status is a promising yet poorly established field. Using Illumina high-throughput sequencing technology, we compared the gut microbiota between healthy (HA and HB) and diarrhoeic (DS) Rana dybowskii groups and analyzed the functional profiles through a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. In addition, we estimated the correlation between gut microbiota structures and predicted the functional compositions. The results showed significant differences in the phylogenetic diversity (Pd), Shannon, and observed richness (Sobs) indices between the DS and HB groups, with significant differences observed in the gut microbiota composition between the DS group and the HA and HB groups. Linear discriminant analysis (LDA) effect size (LEfSe) results revealed that Proteobacteria were significantly enriched in the DS group; Bacteroidetes were significantly enriched in the HA and HB groups; and Aeromonas, Citrobacter, Enterococcus, Hafnia-Obesumbacterium, Morganella, Lactococcus, Providencia, Vagococcus, and Staphylococcus were significantly enriched in the DS group. Venn diagrams revealed that there were many more unique genera in the DS group than the HA and HB groups. Among 102 sensitive species selected using the indicator method, 33 indicated a healthy status and 69 (e.g., Acinetobacter, Aeromonas, Legionella, Morganella, Proteus, Providencia, Staphylococcus, and Vagococcus) indicated a diseased status. There was a significant and positive association between the composition and functional composition of the gut microbiota, thus indicating low functional redundancy of the frog gut bacterial community. Rana dybowskii disease was associated with changes in the gut microbiota, which subsequently disrupted bacterial-mediated functions. The results of this study can aid in revealing the effect of the R. dybowskii gut microbiota on host health and provide a basis for elucidating the mechanism of the occurrence of R. dybowskii disease.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, China
| | - Li-Yong Cui
- Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, China
| | - Xiao-Peng Du
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Hua Xiao
- 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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24
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Cao Q, Najnine F, Han H, Wu B, Cai J. BALOs Improved Gut Microbiota Health in Postlarval Shrimp ( Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment. Front Microbiol 2020; 11:1296. [PMID: 32714290 PMCID: PMC7344170 DOI: 10.3389/fmicb.2020.01296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
Abstract
White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.
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Affiliation(s)
- Qingqing Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Farhana Najnine
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongcao Han
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Bing Wu
- Modern Analysis Centre, South China University of Technology, Guangzhou, China
| | - Junpeng Cai
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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25
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Tong Q, Du XP, Hu ZF, Cui LY, Bie J, Zhang QZ, Xiao JH, Lin Y, Wang HB. Comparison of the gut microbiota of Rana amurensis and Rana dybowskii under natural winter fasting conditions. FEMS Microbiol Lett 2020; 366:5645232. [PMID: 31778183 DOI: 10.1093/femsle/fnz241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/27/2019] [Indexed: 01/02/2023] Open
Abstract
Rana amurensis and R. dybowskii occupy similar habitats. As temperatures decrease with the onset of winter, both species migrate to ponds for hibernation. Our goal was to determine whether different species possess different intestinal microbiota under natural winter fasting conditions. We used high-throughput Illumina sequencing of 16S rRNA gene sequences to analyse the diversity of intestinal microbes in the two species. The dominant gut bacterial phyla in both species were Bacteroidetes, Proteobacteria and Firmicutes. Linear discriminant analysis (LDA) effect size revealed significant enrichment of Proteobacteria in R. amurensis and Firmicutes in R. dybowskii. There were significant differences in the gut microbiota composition between the species. The core operational taxonomic unit numbers in R. amurensis and R. dybowskii shared by the two species were 106, 100 and 36. This study indicates that the intestinal bacterial communities of the two frog species are clearly different. Phylum-level analysis showed that R. amurensis was more abundant in Proteobacteria and Verrucomicrobia than R. dybowskii was This is the first study of the composition and diversity of the gut microbiota of these two species, providing important insights for future research on the gut microbiota and the role of these bacterial communities in frogs.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Xiao-Peng Du
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Li-Yong Cui
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Qian-Zhen Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Hua Xiao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yu Lin
- Shenzhen Withsum Technology Limited, Shenzhen 518031, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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26
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Ya J, Li X, Wang L, Kou H, Wang H, Zhao H. The effects of chronic cadmium exposure on the gut of Bufo gargarizans larvae at metamorphic climax: Histopathological impairments, microbiota changes and intestinal remodeling disruption. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110523. [PMID: 32222598 DOI: 10.1016/j.ecoenv.2020.110523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
Cadmium (Cd) is carcinogenic to human and it also has adverse effects on aquatic life such as amphibian larvae. However, its influences on amphibian gut morphology and development as well as intestinal microbiota are still hardly understood. In this study, we examined the effects of chronic cadmium exposure on the gut of tadpoles at Gosner stage 42 of metamorphic climax by using Bufo gargarizans as a model species. Tadpoles were exposed to cadmium concentrations at 0, 5, 100 and 200 μg L-1 from Gosner stage 26-42. The results showed that high cadmium (100 and 200 μg L-1) exposure caused significant decrease of body length and weight but significant increase of intestinal length and weight. Moreover, severe histopathological damages were induced by high Cd exposure. In addition, microbial communities in the gut of tadpoles in high cadmium exposure groups were remarkably different from those in control group. Unexpectedly, species diversity and richness were higher in the intestinal microbiota of 200 μg L-1 cadmium exposure group. Furthermore, the abundance of prevalent phyla, families and genera of intestinal microbiota were changed by cadmium exposure. Meanwhile, cadmium exposure perturbed gut renewal functions and the relative mRNA expression of genes involved in canonical and non-canonical Wnt signaling pathway was seriously affected by high cadmium exposure. We concluded that cadmium could be harmful to tadpole health by inducing intestinal histopathological damages, gut remodeling inhibition and intestinal microbiota alterations.
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Affiliation(s)
- Jing Ya
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Ling Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Honghong Kou
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongfeng Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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27
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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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28
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Jiang H, Chen W, Su L, Huang M, Lin L, Su Q, Li G, Ahmad HI, Li L, Zhang X, Li H, Chen J. Impact of host intraspecies genetic variation, diet, and age on bacterial and fungal intestinal microbiota in tigers. Microbiologyopen 2020; 9:e1050. [PMID: 32395912 PMCID: PMC7349146 DOI: 10.1002/mbo3.1050] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
The bacterial microbiota in the gut varies among species, as well as with habitat, diet, age, and other factors. Intestinal microbiota homeostasis allows a host to adjust metabolic and immune performances in response to environmental changes. Therefore, potential implications of the gut microbiota in sustaining the health of the host have gained increasing attention in the field of endangered animal conservation. However, the effect of host intraspecies genetic variation on the gut microbiota is unknown. Moreover, little is known about the complexity of the gut mycobiota. Tigers are listed as endangered species, raising worldwide concern. Potential influences of subspecies, diet, and age on the gut microbiota in tigers were investigated in this study to provide a better understanding of the response of the tiger gut microbiota to external changes. The results revealed that the impacts of the factors listed above on gut bacterial and fungal communities are versatile. Host intraspecies genetic variation significantly impacted only fungal alpha diversity of the gut microbiota. Differences in diet, on the other hand, had a significant impact on alpha diversity of the gut microbiota, but exerted different effects on beta diversity of gut bacterial and fungal communities. Host age had no significant impact on the diversity of the gut fungal communities, but significantly impacted beta diversity of gut bacterial communities. This comprehensive study of tiger gut microbiota is an essential reference for tiger conservation when considering feeding and management strategies, and will contribute to a better understanding of the mycobiota in wildlife.
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Affiliation(s)
- Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, Guangdong, China
| | - Li Su
- Guangzhou Zoo, Guangzhou, Guangdong, China
| | - Mingwei Huang
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Libo Lin
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Qiao Su
- The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guanyu Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
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29
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Zhou J, Nelson TM, Rodriguez Lopez C, Sarma RR, Zhou SJ, Rollins LA. A comparison of nonlethal sampling methods for amphibian gut microbiome analyses. Mol Ecol Resour 2020; 20:844-855. [PMID: 31990452 DOI: 10.1111/1755-0998.13139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/03/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022]
Abstract
Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.
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Affiliation(s)
- Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Tiffanie Maree Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, Qld, Australia
| | - Carlos Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Roshmi Rekha Sarma
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
| | - Shao Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
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30
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Xu LL, Chen H, Zhang M, Zhu W, Chang Q, Lu G, Chen Y, Jiang J, Zhu L. Changes in the community structure of the symbiotic microbes of wild amphibians from the eastern edge of the Tibetan Plateau. Microbiologyopen 2020; 9:e1004. [PMID: 32045512 PMCID: PMC7142363 DOI: 10.1002/mbo3.1004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/31/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Environment has a potential effect on the animal symbiotic microbiome. Here, to study the potential relationship of the symbiotic microbiomes of wild amphibians with altitude, we collected the gut and skin samples from frogs (nine species) and the environmental samples (water and soil samples) from the Leshan Mountains (altitude: 360–410 m) and Gongga Mountains (altitude: 3340–3989 m) on the eastern edge of the Tibetan Plateau. Bufo gargarizans (Bg) samples were collected from both the Leshan and Gongga mountain regions (Bg was the only species sampled on both mountains). The DNA extracted from each sample was performed high‐throughput sequencing (MiSeq) of bacterial 16S rRNA gene amplicons. High relative abundance of Caulobacteraceae and Sphingomonadaceae was found in skin samples from both Bg and the other high‐altitude amphibians (nine species combined). High relative abundance of Coxiellaceae and Mycoplasmataceae was found in gut samples from both Bg and the other high‐altitude amphibians. Furthermore, the alpha and beta diversities of skin and gut samples from Bg and the other amphibian species (nine species combined) were similar. In terms of the symbiotic microbial community, the low‐altitude samples were less diverse and more similar to each other than the high‐altitude samples were. We speculated that extreme high‐altitude environments and host phylogeny may affect the amphibian microbiome. Despite the distinct microbial community differences between the skin and gut microbiomes, some functions were similar in the Bg and combined high‐altitude samples. The Bg and high‐altitude skin samples had higher oxidative stress tolerance and biofilm formation than the low‐altitude skin samples. However, the opposite results were observed for the Bg and high‐altitude gut samples. Further study is required to determine whether these characteristics favor high‐altitude amphibian adaptation to extreme environments.
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Affiliation(s)
- Liang Liang Xu
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Hua Chen
- Shanghai Biozeron Bioinformatics CenterShanghaiChina
| | - Mengjie Zhang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Wei Zhu
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Qing Chang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaNEUSA
| | - Youhua Chen
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Jianping Jiang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjingChina
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31
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Qin W, Song P, Lin G, Huang Y, Wang L, Zhou X, Li S, Zhang T. Gut Microbiota Plasticity Influences the Adaptability of Wild and Domestic Animals in Co-inhabited Areas. Front Microbiol 2020; 11:125. [PMID: 32117147 PMCID: PMC7018712 DOI: 10.3389/fmicb.2020.00125] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/20/2020] [Indexed: 12/23/2022] Open
Abstract
Due to the increased economic demand for livestock, the number of livestock is increasing. Because of human interference, the survival of wild animals is threatened in the face of competition, particularly in co-inhabited grazing pastures. This may lead to differences in the adaptability between wild and domestic animals, as well as nutritional deficiencies in wild animals. The gut microbiota is closely associated with host health, nutrition, and adaptability. However, the gut microbiota diversity and functions in domestic and wild animals in co-inhabited areas are unclear. To reveal the adaptability of wild and domestic animals in co-inhabited areas based on gut microbiota, we assessed the gut microbiota diversity. This study was based on the V3–V4 region of 16S rRNA and gut microbiota functions according to the metagenome analysis of fresh fecal samples in wild goitered gazelles (Gazella subgutturosa) and domestic sheep (Ovis aries) in the Qaidam Basin. The wild and domestic species showed significant differences in alpha- and beta-diversities. Specifically, the alpha-diversity was lower in goitered gazelles. We speculated that the nutritional and habitat status of the goitered gazelles were worse. The gut microbiota functions in the gazelles were enriched in metabolism and cellular processes based on the KEGG database. In summary, we reasoned that gut microbiota can improve the adaptability of goitered gazelles through energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies. These findings highlight the importance of gut microbiota diversity to improve the adaptability of goitered gazelles, laying a foundation for the conservation of wild goitered gazelles. In addition, we further provide management suggestions for domestic sheep in co-inhabited grazing pastures.
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Affiliation(s)
- Wen Qin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - YanGan Huang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | | | - Shengqing Li
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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32
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Jiménez RR, Alvarado G, Estrella J, Sommer S. Moving Beyond the Host: Unraveling the Skin Microbiome of Endangered Costa Rican Amphibians. Front Microbiol 2019; 10:2060. [PMID: 31572313 PMCID: PMC6751270 DOI: 10.3389/fmicb.2019.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/21/2019] [Indexed: 01/12/2023] Open
Abstract
Some neotropical amphibians, including a few species in Costa Rica, were presumed to be "extinct" after dramatic population declines in the late 1980s but have been rediscovered in isolated populations. Such populations seem to have evolved a resistance/tolerance to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes a deadly skin disease and is considered one of the main drivers of worldwide amphibian declines. The skin microbiome is an important component of the host's innate immune system and is associated with Bd-resistance. However, the way that the bacterial diversity of the skin microbiome confers protection against Bd in surviving species remains unclear. We studied variation in the skin microbiome and the prevalence of putatively anti-Bd bacterial taxa in four co-habiting species in the highlands of the Juan Castro Blanco National Park in Costa Rica using 16S rRNA amplicon sequencing. Lithobates vibicarius, Craugastor escoces, and Isthmohyla rivularis have recently been rediscovered, whereas Isthmohyla pseudopuma has suffered population fluctuations but has never disappeared. To investigate the life stage at which the protective skin microbiome is shaped and when shifts occur in the diversity of putatively anti-Bd bacteria, we studied the skin microbiome of tadpoles, juveniles and adults of L. vibicarius. We show that the skin bacterial composition of sympatric species and hosts with distinct Bd-infection statuses differs at the phyla, family, and genus level. We detected 94 amplicon sequence variants (ASVs) with putative anti-Bd activity pertaining to distinct bacterial taxa, e.g., Pseudomonas spp., Acinetobacter johnsonii, and Stenotrophomonas maltophilia. Bd-uninfected L. vibicarius harbored 79% more putatively anti-Bd ASVs than Bd-infected individuals. Although microbiome composition and structure differed across life stages, the diversity of putative anti-Bd bacteria was similar between pre- and post-metamorphic stages of L. vibicarius. Despite low sample size, our results support the idea that the skin microbiome is dynamic and protects against ongoing Bd presence in endangered species persisting after their presumed extinction. Our study serves as a baseline to understand the microbial patterns in species of high conservation value. Identification of microbial signatures linked to variation in disease susceptibility might, therefore, inform mitigation strategies for combating the global decline of amphibians.
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Affiliation(s)
- Randall R. Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Josimar Estrella
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Carrier TJ, Dupont S, Reitzel AM. Geographic location and food availability offer differing levels of influence on the bacterial communities associated with larval sea urchins. FEMS Microbiol Ecol 2019; 95:5526217. [PMID: 31260050 DOI: 10.1093/femsec/fiz103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/27/2019] [Indexed: 12/17/2022] Open
Abstract
Determining the factors underlying the assembly, structure, and diversity of symbiont communities remains a focal point of animal-microbiome research. Much of these efforts focus on taxonomic variation of microbiota within or between animal populations, but rarely test the proportional impacts of ecological components that may affect animal-associated microbiota. Using larvae from the sea urchin Strongylocentrotus droebachiensis from the Atlantic and Pacific Oceans, we test the hypothesis that, under natural conditions, inter-population differences in the composition of larval-associated bacterial communities are larger than intra-population variation due to a heterogeneous feeding environment. Despite significant differences in bacterial community structure within each S. droebachiensis larval population based on food availability, development, phenotype, and time, variation in OTU membership and community composition correlated more strongly with geographic location. Moreover, 20-30% of OTUs associated with larvae were specific to a single location while less than 10% were shared. Taken together, these results suggest that inter-populational variation in symbiont communities may be more pronounced than intra-populational variation, and that this difference may suggest that broad-scale ecological variables (e.g., across ocean basins) may mask smaller scale ecological variables (e.g., food availability).
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Affiliation(s)
- Tyler J Carrier
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Gothenburg, The Sven Lovén Centre for Marine Infrastructure, Kristineberg, 45178 Sweden
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
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Shu Y, Hong P, Yu Q, Wang G, Zhang J, Donde OO, Xiao B, Wu H. High-Throughput Sequencing Analysis Reveals Correlations between Host Phylogeny, Gut Microbiota, and Habitat of Wild Frogs from a Mountainous Area. COPEIA 2019. [DOI: 10.1643/ot-18-040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China
| | - Pei Hong
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (BX)
| | - Qiang Yu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China
| | - Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China
| | - Oscar Omondi Donde
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (BX)
| | - Bangding Xiao
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (BX)
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China
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Shu Y, Hong P, Tang D, Qing H, Omondi Donde O, Wang H, Xiao B, Wu H. Comparison of intestinal microbes in female and male Chinese concave-eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities. Microbiologyopen 2018; 8:e00749. [PMID: 30311422 PMCID: PMC6562124 DOI: 10.1002/mbo3.749] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/11/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
The Chinese concave‐eared frog (Odorrana tormota) is a rare and threatened species with remarkable sexual dimorphism. Intestinal microbes are understood to play important roles in animal physiology, growth, ecology, and evolution. However, little is known about the intestinal microbes in female and male frogs, as well as the contributing effect by gut infesting nematodes to the co‐habiting bacteria and their function in degradation food rich in chitin. Here, this study analyzed the microbiota of the intestinal tract of both female and male, healthy as well as nematode‐infested concave‐eared frogs using high throughput 16S rRNA sequencing and metagenomic techniques. The results showed that the bacterial composition of the microbiota at the phylum level was dominated by Firmicutes, Verrucomicrobia, Bacteroidetes, and Proteobacteria. The study also revealed that the community composition below the class level could be represent sex differences, particularly with regard to Enterobacteriales, Enterobacteriaceae, Peptostreptococcaceae, and Rikenellaceae, among others. Carbohydrate‐active enzyme‐encoding genes and modules were identified in related gut bacteria by metagenomic analysis, with Bacteroidia, Clostridia, and gammaproteobacteria predicted to be the main classes of chitin‐decomposing bacteria in the frog intestine. In addition, the abundance of some bacteria significantly increased or decreased in nematode‐infected hosts compared with healthy individuals, including Verrucomicrobia, Verrucomicrobiae, Negativicutes, Actinobacteria, and Bacilli, among others. This indicates that nematode infection may affect the richness and composition of some gut bacteria.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Pei Hong
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dong Tang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Hui Qing
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Oscar Omondi Donde
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Department of Environmental Science, Egerton University, Egerton, Kenya
| | - Huan Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Bangding Xiao
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
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