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Wang ZY, Xie WQ, Xiang ZY, Zhang CY, Xie YG, Quah RYC, Ding GH. Exploring the effects of environmentally relevant concentrations of tris(2-chloroethyl) phosphate on tadpole health: A comprehensive analysis of intestinal microbiota and hepatic transcriptome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174428. [PMID: 38964390 DOI: 10.1016/j.scitotenv.2024.174428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
Tris(2-chloroethyl) phosphate (TCEP), a chlorinated organophosphate ester, is commonly found in aquatic environments. Due to its various toxic effects, it may pose a risk to the health of aquatic organisms. However, the potential impacts of TCEP exposure on the intestinal microbiota and hepatic function in amphibians have not been reported. This study investigated the impact of long-term exposure to environmentally relevant concentrations of TCEP (0, 3, and 90 μg/L) on the intestinal microbiota and hepatic transcriptome of Polypedates megacephalus tadpoles. The results showed that the body size of the tadpoles decreased significantly with an increase in TCEP concentration. Additionally, TCEP exposure affected the diversity and composition of the intestinal microbiota in tadpoles, leading to significant changes in the relative abundance of certain bacterial groups (the genera Aeromonas decreased and Citrobacter increased) and potentially promoting a more even distribution of microbial species, as indicated by a significant increase in the Simpson index. Moreover, the impact of TCEP on hepatic gene expression profiles in tadpoles was significant, with the majority of differentially expressed genes (DEGs) (709 out of 906 total DEGs in 3 μg/L of TCEP versus control, and 344 out of 387 DEGs in 90 μg/L of TCEP versus control) being significantly down-regulated, which were primarily related to immune response and immune system process. Notably, exposure to TCEP significantly reduced the relative abundance of the genera Aeromonas and Cetobacterium in the tadpole intestine. This reduction was positively correlated with the down-regulated expression of immune-related genes in the liver of corresponding tadpoles. In summary, these findings provide empirical evidence of the potential health risks to tadpoles exposed to TCEP at environmentally relevant concentrations.
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Affiliation(s)
- Zi-Ying Wang
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China; College of Animal Science and Technology, Zhejiang A & F University, Lin'an, Zhejiang, China
| | - Wen-Qi Xie
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China
| | - Zi-Yong Xiang
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China
| | - Chi-Ying Zhang
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China
| | - Yi-Ge Xie
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China
| | - Roy You Chen Quah
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Guo-Hua Ding
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China.
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Castro LGZ, Sousa MR, Pereira LÉC, Martins DV, Oliveira FAS, Bezerra SGS, Melo VMM, Hissa DC. Pioneer access of the foam nest bacterial community of Leptodactylidae frogs and its biotechnological potential. BRAZ J BIOL 2024; 84:e280884. [PMID: 38922194 DOI: 10.1590/1519-6984.280884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/10/2024] [Indexed: 06/27/2024] Open
Abstract
Many anuran amphibians deposit their eggs in foam nests, biostructures that help protect the eggs and tadpoles from predators. Currently, there are no other identification and description studies of the cultivable microbiota role in the nests of the Leptodactylid frogs such as Physalaemus cuvieri, Leptodactylus vastus and Adenomera hylaedactyla. This study aimed to isolate and identify the culturable bacteria from these three anuran species' nests, as well as to prospect enzymes produced by this microbiota. Foam nests samples and environmental samples were diluted and viable cell count was determined. Bacterial morphotypes from foam nest samples were isolated through spread plate technique. Isolates' DNAs were extracted followed by rRNA 16S gene amplification and Sanger sequencing. To evaluate their enzymatic potential, the isolates were cultured in ATGE medium supplemented with starch (0.1% w/v), gelatin (3% w/v) and skimmed milk (1% w/v), to verify amylase and protease activity. A total of 183 bacterial morphotypes were isolated, comprising 33 bacterial genera. Proteobacteria phylum was the most abundant in all the three nests (79%). The genera Pseudomonas and Aeromonas were the most abundant taxon in P. cuvieri and L. vastus. In A. Hylaedactyla, were Enterobacter and Bacillus. Regarding enzymatic activities, 130 isolates displayed protease activity and 45 isolates were positive for amylase activity. Our results provide unprecedented information concerning culturable bacterial microbiota of the foam nests of the Leptodactylid frogs, as well as their potential for biomolecules of biotechnological interest.
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Affiliation(s)
- L G Z Castro
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - M R Sousa
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - L É C Pereira
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - D V Martins
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - F A S Oliveira
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - S G S Bezerra
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - V M M Melo
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
| | - D C Hissa
- Universidade Federal do Ceará - UFC, Departamento de Biologia, Fortaleza, CE, Brasil
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3
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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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Chai L, Song Y, Chen A, Jiang L, Deng H. Gut microbiota perturbations during larval stages in Bufo gargarizans tadpoles after Cu exposure with or without the presence of Pb. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122774. [PMID: 37871736 DOI: 10.1016/j.envpol.2023.122774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Cu and Pb are ubiquitous environmental contaminants, but there is limited information on their potential impacts on gut microbiota profile in anuran amphibians at different developmental stages during metamorphosis. In this study, Bufo gargarizans tadpoles were chronically exposed to Cu alone or Cu combined with Pb from Gs26 throughout metamorphosis. Morphology of tadpoles, histological characteristic and bacterial community of intestines were evaluated at three developmental stages: Gs33, Gs36, and Gs42. Results showed that Cu and Cu + Pb exposure caused various degrees of morphological and histological changes in guts at tested three stages. In addition, bacterial richness and diversity in tadpoles especially at Gs33 and Gs42 were disturbed by Cu and Cu + Pb. Beta diversity demonstrated that the bacterial community structures were influenced by both heavy metals exposure and developmental stages. Alterations in taxonomic composition were characterized by increased abundance of Proteobacteria and Firmicutes, reduction of Fusobacteriota, as well as decreased Cetobacterium and increased C39 at all three stages. Overall, response of gut bacterial diversity and composition to Cu stress depends on the developmental stage, while the altered patterns of bacterial community at Cu stress could be modified further by the presence of Pb. Moreover, predicted metabolic disorders were associated with shifts in bacterial community, but needs integrated information from metagenomic and metatranscriptomic analyses. These results contribute to the growing body of research about potential ecotoxicological effects of heavy metals on amphibian gut microbiota during metamorphosis.
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Affiliation(s)
- Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China.
| | - Yanjiao Song
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of Ministry of Water Resources, Chang'an University, Xi'an, 710054, China.
| | - Aixia Chen
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Ling Jiang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Hongzhang Deng
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
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5
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Brunetti AE, Lyra ML, Monteiro JPC, Zurano JP, Baldo D, Haddad CFB, Moeller AH. Convergence of gut microbiota in myrmecophagous amphibians. Proc Biol Sci 2023; 290:20232223. [PMID: 37964521 PMCID: PMC10646458 DOI: 10.1098/rspb.2023.2223] [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: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023] Open
Abstract
The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.
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Affiliation(s)
- Andrés E. Brunetti
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Juliane P. C. Monteiro
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Juan P. Zurano
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Puerto Iguazú, Misiones 3370, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
| | - Celio F. B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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Leonhardt F, Keller A, Arranz Aveces C, Ernst R. From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian. MICROBIAL ECOLOGY 2023; 86:2373-2385. [PMID: 37233803 PMCID: PMC10640505 DOI: 10.1007/s00248-023-02227-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.
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Affiliation(s)
- Franziska Leonhardt
- Faculty of Biology, Technical University of Dresden, 01062, Dresden, Germany.
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany.
| | - Alexander Keller
- Faculty of Biology, Ludwig-Maximilians-University of Munich, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Clara Arranz Aveces
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70173, Stuttgart, Germany
| | - Raffael Ernst
- Faculty of Biology, Technical University of Dresden, 01062, Dresden, Germany.
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany.
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7
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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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Khairulmunir M, Gani M, Karuppannan KV, Mohd-Ridwan AR, Md-Zain BM. High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger ( Pantheratigrisjacksoni) during fasting. Biodivers Data J 2023; 11:e104757. [PMID: 37711366 PMCID: PMC10498273 DOI: 10.3897/bdj.11.e104757] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota SamarahanMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
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9
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Jiang XR, Dai YY, Wang YR, Guo K, Du Y, Gao JF, Lin LH, Li P, Li H, Ji X, Qu YF. Dietary and Sexual Correlates of Gut Microbiota in the Japanese Gecko, Gekko japonicus (Schlegel, 1836). Animals (Basel) 2023; 13:ani13081365. [PMID: 37106928 PMCID: PMC10134999 DOI: 10.3390/ani13081365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Numerous studies have demonstrated that multiple intrinsic and extrinsic factors shape the structure and composition of gut microbiota in a host. The disorder of the gut microbiota may trigger various host diseases. Here, we collected fecal samples from wild-caught Japanese geckos (Gekko japonicus) and captive conspecifics fed with mealworms (mealworm-fed geckos) and fruit flies (fly-fed geckos), aiming to examine the dietary and sexual correlates of the gut microbiota. We used 16S rRNA gene sequencing technology to determine the composition of the gut microbiota. The dominant phyla with a mean relative abundance higher than 10% were Verrucomicrobiota, Bacteroidota, and Firmicutes. Gut microbial community richness and diversity were higher in mealworm-fed geckos than in wild geckos. Neither community evenness nor beta diversity of gut microbiota differed among wild, mealworm-fed, and fly-fed geckos. The beta rather than alpha diversity of gut microbiota was sex dependent. Based on the relative abundance of gut bacteria and their gene functions, we concluded that gut microbiota contributed more significantly to the host's metabolic and immune functions. A higher diversity of gut microbiota in mealworm-fed geckos could result from higher chitin content in insects of the order Coleoptera. This study not only provides basic information about the gut microbiota of G. japonicus but also shows that gut microbiota correlates with dietary habits and sex in the species.
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Affiliation(s)
- Xin-Ru Jiang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying-Yu Dai
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu-Rong Wang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Kun Guo
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Jian-Fang Gao
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Long-Hui Lin
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Peng Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hong Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yan-Fu Qu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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10
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Hou J, Long J, Xiang J, Pan W, Li D, Liu X. Ontogenetic characteristics of the intestinal microbiota of
Quasipaa spinosa
revealed by
16S rRNA
gene sequencing. Lett Appl Microbiol 2022; 75:1182-1192. [DOI: 10.1111/lam.13786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jingliang Hou
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
| | - Jiahang Long
- Hunan Fisheries Science Institute Changsha Hunan China
| | - Jianguo Xiang
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
| | | | - Deliang Li
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
| | - Xinhua Liu
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
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11
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Ruthsatz K, Domscheit M, Engelkes K, Vences M. Microplastics ingestion induces plasticity in digestive morphology in larvae of Xenopus laevis. Comp Biochem Physiol A Mol Integr Physiol 2022; 269:111210. [PMID: 35398256 DOI: 10.1016/j.cbpa.2022.111210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 01/16/2023]
Abstract
Global changes in temperature, predator introductions, and pollution might challenge animals by altering food conditions. A fast-growing source of environmental pollution are microplastics. If ingested with the natural food source, microplastics act as artificial fibers that reduce food quality by decreasing nutrient and energy density with possible ramifications for growth and development. Animals might cope with altered food conditions with digestive plasticity. We examined experimentally whether larvae of the African clawed frog (Xenopus laevis) exhibit digestive morphology plasticity (i.e., gut length, mass, and diameter) in response to microplastics ingestion. As natural systems contain non-digestible particles similar in size and shape to microplastics, we included cellulose as a natural fiber control group. Gut length and mass increased in response to microplastics and cellulose ingestion indicating that both types of fibers induced digestive plasticity. Body mass and body condition were similar across experimental groups, indicating that larvae fully compensated for low nutrient and energy density by developing longer intestines. The ability of a species to respond plastically to environmental variation, as X. laevis responded, indicates that this species might have the potential to cope with new conditions during global change, although it is uncertain whether this potential may be reduced in a multi-stressor environment.
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Affiliation(s)
- Katharina Ruthsatz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany.
| | - Marie Domscheit
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
| | - Karolin Engelkes
- Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany. https://twitter.com/KarolinEngelkes
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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12
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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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13
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Experimental manipulation of microbiota reduces host thermal tolerance and fitness under heat stress in a vertebrate ectotherm. Nat Ecol Evol 2022; 6:405-417. [PMID: 35256809 DOI: 10.1038/s41559-022-01686-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/28/2022] [Indexed: 12/11/2022]
Abstract
Identifying factors that influence how ectothermic animals respond physiologically to changing temperatures is of high importance given current threats of global climate change. Host-associated microbial communities impact animal physiology and have been shown to influence host thermal tolerance in invertebrate systems. However, the role of commensal microbiota in the thermal tolerance of ectothermic vertebrates is unknown. Here we show that experimentally manipulating the tadpole microbiome through environmental water sterilization reduces the host's acute thermal tolerance to both heat and cold, alters the thermal sensitivity of locomotor performance, and reduces animal survival under prolonged heat stress. We show that these tadpoles have reduced activities of mitochondrial enzymes and altered metabolic rates compared with tadpoles colonized with unmanipulated microbiota, which could underlie differences in thermal phenotypes. These results demonstrate a strong link between the microbiota of an ectothermic vertebrate and the host's thermal tolerance, performance and fitness. It may therefore be important to consider host-associated microbial communities when predicting species' responses to climate change.
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14
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Yang B, Cui Z, Ning M, Chen Y, Wu Z, Huang H. Variation in the intestinal microbiota at different developmental stages of Hynobius maoershanensis. Ecol Evol 2022; 12:e8712. [PMID: 35342562 PMCID: PMC8931708 DOI: 10.1002/ece3.8712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/11/2022] Open
Abstract
Intestinal microbiota play an important role in the life of amphibians and its composition may vary by developmental stage. In this study, 16S rRNA high-throughput sequencing was used to profile the intestinal microbiota of Hynobius maoershanensis, which exclusively inhabit the Maoer Mountain swamp at an altitude of approximately 2,000 m. We characterized the bacterial composition, structure, and function of the microbiota of H. maoershanensis at different developmental stages. The alpha diversity was not markedly different for the Simpson, Shannon, Ace, and Sobs indices of microbes. The beta diversity revealed that there were age-related differences in the structure of the intestinal microbes of H. maoershanensis, specifically, at the phylum level. Bacteroidetes and Proteobacteria were the dominant bacteria present in the adult stage, and the relative abundance of Bacteroidetes was significantly higher compared with that of tadpoles. Firmicutes and Proteobacteria were the dominant phylum during the tadpole stage and their relative abundance was significantly higher compared with the adult period. Functional analysis revealed that the pathways associated with organismal systems and metabolism were significantly enriched in the adults, whereas human diseases, genetic information processing, and cellular processes were more enriched in the hindlimb bud stage. Human diseases and environmental information processing were more enriched in the forelimb bud stage at KEGG pathway level 1. Possibilities for the observed discrepancies include the adaptation to eating habits and the remodeling of the intestines during development. We speculated that H. maoershanensis adults may be more suitable to a high-fiber diet, whereas the tadpoles are associated with a carnivorous diet. Our study provides evidence of variations in the intestinal microbiota during development in amphibians, highlighting the influence of historical developments on the intestinal microbiota and an increased understanding of the importance of physiological characteristics in shaping the intestinal microbiota of amphibians. These data will help us formulate more effective protection measures for H. maoershanensis.
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Affiliation(s)
- Bo Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Zhenzhen Cui
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Meihong Ning
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Yu Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Huayuan Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
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15
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Du Y, Chen JQ, Liu Q, Fu JC, Lin CX, Lin LH, Li H, Qu YF, Ji X. Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768). Front Microbiol 2022; 12:771527. [PMID: 35069477 PMCID: PMC8770915 DOI: 10.3389/fmicb.2021.771527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have demonstrated that food shapes the structure and composition of the host’s oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.
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Affiliation(s)
- Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Jun-Qiong Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qian Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jian-Chao Fu
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Chi-Xian Lin
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
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16
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Tong Q, Cui LY, Bie J, Han XY, Hu ZF, Wang HB, Zhang JT. Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath. BMC Vet Res 2021; 17:333. [PMID: 34674716 PMCID: PMC8529755 DOI: 10.1186/s12917-021-03044-z] [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: 01/25/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Background Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined. Results The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high. Conclusions Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-03044-z.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.,Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, 154002, China.,College of Life Science, Jiamusi University, Jiamusi, 154007, China
| | - Li-Yong Cui
- Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, 154002, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Xiao-Yun Han
- College of Life Science, Jiamusi University, Jiamusi, 154007, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
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17
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Wang Y, Smith HK, Goossens E, Hertzog L, Bletz MC, Bonte D, Verheyen K, Lens L, Vences M, Pasmans F, Martel A. Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders. Sci Rep 2021; 11:20493. [PMID: 34650115 PMCID: PMC8516891 DOI: 10.1038/s41598-021-98995-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities. Here, we characterized diet and gut microbiome of fire salamander populations from three Belgian forests. We carried out DNA metabarcoding on fecal samples, targeting eukaryotic 18S rRNA of potential dietary prey items, and bacterial 16S rRNA of the concomitant gut microbiome. Our results demonstrated an abundance of soft-bodied prey in the diet of fire salamanders, and a significant difference in the diet composition between males and females. This sex-dependent effect on diet was also reflected in the gut microbiome diversity, which is higher in males than female animals. Proximity to human activities was associated with increased intestinal pathogen loads. Collectively, the data supports a relationship between diet, environment and intestinal microbiome in fire salamanders, with potential health implications.
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Affiliation(s)
- Yu Wang
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Hannah K. Smith
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Evy Goossens
- grid.5342.00000 0001 2069 7798Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Lionel Hertzog
- grid.5342.00000 0001 2069 7798Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium ,Thünen Institute for Biodiversity, Bundesallee 68, 38116 Brunswick, Germany
| | - Molly C. Bletz
- grid.6738.a0000 0001 1090 0254Evolutionary Biology Lab, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Brunswick, Germany
| | - Dries Bonte
- grid.5342.00000 0001 2069 7798Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Kris Verheyen
- grid.5342.00000 0001 2069 7798Forest & Nature Lab, Department of Environment, Ghent University, Geraardsberge Steenweg 267, 9090 Gontrode, Belgium
| | - Luc Lens
- grid.5342.00000 0001 2069 7798Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Miguel Vences
- grid.6738.a0000 0001 1090 0254Evolutionary Biology Lab, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Brunswick, Germany
| | - Frank Pasmans
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - An Martel
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology & Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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18
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Intra-Body Variations of Stable Isotope Ratios (δ13C, δ15N) and Influence of Storage Methods in Aquatic and Post-Aquatic Stages of the Common Toad, Bufo bufo. WATER 2021. [DOI: 10.3390/w13182544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Isotopic signatures of carbon and nitrogen are widely used for analysis of the structure of food webs in aquatic ecosystems. The study of animals raises a number of methodological questions, including choice of representative tissues and organs for sampling as well as storage of the studied organisms. Furthermore, the impacts of preservation methods can be tissue-specific, age-specific, and even taxon-specific; thus, studies of these impacts on particular taxa are necessary. We focused on the C and N isotope composition of the common toad (Bufo bufo), one of the most widespread European anuran amphibians. We hypothesized that its different tissues and organs may vary in isotopic composition, and ethanol and freezing may have different effects on isotopic values. Our results showed that both “tissue” and “storage method” factors significantly affected the δ13C values of tadpoles and postmetamorphic juveniles, whereas only the “tissue” factor had a significant effect on the δ15N values. The two stages, tadpoles and postmetamorphs, should be analyzed separately despite the brief postmetamorphic period of the juveniles. The skin, legs, muscles, and tail in tadpoles and legs, muscles and heart in juveniles can be used for δ13C and δ15N analysis regardless of the method of storage. The results will serve for the optimization of future study designs in isotopic ecology.
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19
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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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20
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Belasen AM, Riolo MA, Bletz MC, Lyra ML, Toledo LF, James TY. Geography, Host Genetics, and Cross-Domain Microbial Networks Structure the Skin Microbiota of Fragmented Brazilian Atlantic Forest Frog Populations. Ecol Evol 2021; 11:9293-9307. [PMID: 34306622 PMCID: PMC8293785 DOI: 10.1002/ece3.7594] [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: 05/03/2020] [Revised: 08/31/2020] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti-Bd bacteria were not broadly negatively co-associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial.
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Affiliation(s)
- Anat M. Belasen
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Maria A. Riolo
- Center for Complex SystemsUniversity of MichiganAnn ArborMIUSA
| | - Molly C. Bletz
- Department of BiologyUniversity of Massachusetts BostonBostonMAUSA
| | - Mariana L. Lyra
- Instituto de BiociênciasUniversidade Estadual PaulistaRio ClaroBrazil
| | - L. Felipe Toledo
- Laboratório de História Natural de Anfíbios BrasileirosDepartamento de Biologia AnimalInstituto de BiologiaUniversidade Estadual de CampinasCampinasBrazil
| | - Timothy Y. James
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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21
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Fontaine SS, Mineo PM, Kohl KD. Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages. FEMS Microbiol Ecol 2021; 97:6129798. [PMID: 33547890 DOI: 10.1093/femsec/fiab021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each of the newt's three physiologically distinct developmental stages to determine if each hosted a unique community, or if the two stages which share an aquatic habitat (larvae and adults) harbored more similar communities than those of the third stage, the terrestrial juvenile eft. Additionally, we assessed how the contribution of selective processes to gut microbial assembly changed through development. We found that structurally, each life stage harbored a distinct community, which may be attributable to host factors. Further, across development, we found that community assembly processes shifted from a predominance of neutral to selective forces. However, habitat may also be important in determining community membership and diversity due the uniqueness of eft communities based on these metrics. Our results are similar to those in other vertebrate taxa, suggesting that gut microbiota assembly processes may be conserved across diverse lineages.
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Affiliation(s)
- Samantha S Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Patrick M Mineo
- Department of Biology, Elmhurst University, Elmhurst, IL 60126, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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22
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Vera Candioti F, Dos Santos Dias PH, Rowley JJL, Hertwig S, Haas A, Altig R. Anatomical features of the phytotelma dwelling, egg-eating, fanged tadpoles of Rhacophorus vampyrus (Anura: Rhacophoridae). J Morphol 2021; 282:769-778. [PMID: 33713040 DOI: 10.1002/jmor.21348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/09/2022]
Abstract
Tadpoles of the Vampire tree frog Rhacophorus vampyrus differ substantially from other rhacophorid tadpoles, by having profound modifications in external morphology. The morphological peculiarities of this species likely correlate with their arboreal microhabitat and strict oophagous diet. In this work, we examine buccal and musculoskeletal anatomy and compare them to other rhacophorid and egg-eating larvae. The shape and arrangement of cartilages of the lower jaw are unique among tadpoles, and the lack of a palatoquadrate suspensorium is only known in the distantly related macrophagous tadpoles of the dicroglossid Occidozyga baluensis. The cranial musculature is massive, and the morphology of several mandibular, hyoid, and abdominal muscles could be related to the ingestion and transit of large eggs. In the buccal cavity, conspicuous aspects are the absence of ridges and papillae, and the development of a unique glandular zone in the buccal floor. Finally, observations of the skeletal support of keratinized mouthparts allow us to present a topography-based hypothesis of homology of the conspicuous fangs of these tadpoles.
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Affiliation(s)
- Florencia Vera Candioti
- Unidad Ejecutora Lillo (Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo), Tucumán, Argentina
| | - Pedro Henrique Dos Santos Dias
- Naturhistorisches Museum der Burgergemeinde Bern, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jodi J L Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.,Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, New South Wales, Australia
| | - Stefan Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Alexander Haas
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany
| | - Ronald Altig
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
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23
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Ibáñez A, Bletz MC, Quezada G, Geffers R, Jarek M, Vences M, Steinfartz S. No impact of a short-term climatic "El Niño" fluctuation on gut microbial diversity in populations of the Galápagos marine iguana (Amblyrhynchus cristatus). Naturwissenschaften 2021; 108:7. [PMID: 33528676 PMCID: PMC7854437 DOI: 10.1007/s00114-020-01714-w] [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: 05/26/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 01/05/2023]
Abstract
Gut microorganisms are crucial for many biological functions playing a pivotal role in the host's well-being. We studied gut bacterial community structure of marine iguana populations across the Galápagos archipelago. Marine iguanas depend heavily on their specialized gut microbiome for the digestion of dietary algae, a resource whose growth was strongly reduced by severe "El Niño"-related climatic fluctuations in 2015/2016. As a consequence, marine iguana populations showed signs of starvation as expressed by a poor body condition. Body condition indices (BCI) varied between island populations indicating that food resources (i.e., algae) are affected differently across the archipelago during 'El Niño' events. Though this event impacted food availability for marine iguanas, we found that reductions in body condition due to "El Niño"-related starvation did not result in differences in bacterial gut community structure. Species richness of gut microorganisms was instead correlated with levels of neutral genetic diversity in the distinct host populations. Our data suggest that marine iguana populations with a higher level of gene diversity and allelic richness may harbor a more diverse gut microbiome than those populations with lower genetic diversity. Since low values of these diversity parameters usually correlate with small census and effective population sizes, we use our results to propose a novel hypothesis according to which small and genetically less diverse host populations might be characterized by less diverse microbiomes. Whether such genetically depauperate populations may experience additional threats from reduced dietary flexibility due to a limited intestinal microbiome is currently unclear and calls for further investigation.
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Affiliation(s)
- Alejandro Ibáñez
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany. .,Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387, Kraków, Poland.
| | - Molly C Bletz
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Galo Quezada
- Dirección Parque Nacional Galápagos, Puerto Ayora, Santa Cruz, Galápagos, Ecuador
| | - Robert Geffers
- Department of Genome Analytics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sebastian Steinfartz
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany. .,Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Talstrasse 33, 04103, Leipzig, Germany.
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24
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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: 23] [Impact Index Per Article: 5.8] [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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25
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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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26
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Zhou J, Zhao YT, Dai YY, Jiang YJ, Lin LH, Li H, Li P, Qu YF, Ji X. Captivity affects diversity, abundance, and functional pathways of gut microbiota in the northern grass lizard Takydromus septentrionalis. Microbiologyopen 2020; 9:e1095. [PMID: 32666685 PMCID: PMC7520994 DOI: 10.1002/mbo3.1095] [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: 02/29/2020] [Revised: 05/15/2020] [Accepted: 05/30/2020] [Indexed: 12/14/2022] Open
Abstract
Animals in captivity undergo a range of environmental changes from wild animals. An increasing number of studies show that captivity significantly affects the abundance and community structure of gut microbiota. The northern grass lizard (Takydromus septentrionalis) is an extensively studied lacertid lizard and has a distributional range covering the central and southeastern parts of China. Nonetheless, little is known about the gut microbiota of this species, which may play a certain role in nutrient and energy metabolism as well as immune homeostasis. Here, we examined the differences in the gut microbiota between two groups (wild and captive) of lizards through 16S rRNA sequencing using the Illumina HiSeq platform. The results demonstrated that the dominant microbial components in both groups consisted of Proteobacteria, Firmicutes, and Tenericutes. The two groups did not differ in the abundance of these three phyla. Citrobacter was the most dominant genus in wild lizards, while Morganella was the most dominant genus in captive lizards. Moreover, gene function predictions showed that genes at the KEGG pathway levels2 were more abundant in wild lizards than in captive lizards but, at the KEGG pathway levels1, the differences in gene abundances between wild and captive lizards were not significant. In summary, captivity exerted a significant impact on the gut microbial community structure and diversity in T. septentrionalis, and future work could usefully investigate the causes of these changes using a comparative approach.
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Affiliation(s)
- Jin Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yu-Tian Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying-Yu Dai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yi-Jin Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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27
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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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28
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Woodhams DC, Bletz MC, Becker CG, Bender HA, Buitrago-Rosas D, Diebboll H, Huynh R, Kearns PJ, Kueneman J, Kurosawa E, LaBumbard BC, Lyons C, McNally K, Schliep K, Shankar N, Tokash-Peters AG, Vences M, Whetstone R. Host-associated microbiomes are predicted by immune system complexity and climate. Genome Biol 2020; 21:23. [PMID: 32014020 PMCID: PMC6996194 DOI: 10.1186/s13059-019-1908-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. RESULTS Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate. CONCLUSIONS Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.
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Affiliation(s)
- Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Molly C. Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - C. Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Hayden A. Bender
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Daniel Buitrago-Rosas
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Hannah Diebboll
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Roger Huynh
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Patrick J. Kearns
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Jordan Kueneman
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Emmi Kurosawa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | | | - Casandra Lyons
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Kerry McNally
- School for the Environment, University of Massachusetts, Boston, MA 02125 USA
- Animal Health Department, New England Aquarium, Boston, MA 02110 USA
| | - Klaus Schliep
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nachiket Shankar
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Amanda G. Tokash-Peters
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, RN1, Butare, Rwanda
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
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29
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Ya J, Ju Z, Wang H, Zhao H. Exposure to cadmium induced gut histopathological damages and microbiota alterations of Chinese toad (Bufo gargarizans) larvae. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:449-456. [PMID: 31121551 DOI: 10.1016/j.ecoenv.2019.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/09/2019] [Accepted: 05/12/2019] [Indexed: 06/09/2023]
Abstract
Cadmium (Cd) is highly hazardous to both terrestrial and aquatic life and it also has multiple negative impacts on amphibian tadpoles and frogs. However, its effects on gut health of amphibian tadpoles are still poorly understood. We used Chinese toad (Bufo gargarizans) tadpoles to examine the effects of chronic cadmium exposure on gut histology and intestinal microbiota by using regular histology analysis and high-throughput sequencing techniques. Tadpoles were exposed to cadmium concentrations at 0, 5, 100 and 200 μg L-1 from Gosner stage 26 to 38. Our results showed 100 and 200 μg L-1 cadmium exposure caused severe gut histopathological alterations while 5 μg L-1 cadmium exposure induced subtle intestine damage. Moreover, species diversity, taxonomic composition and community structure of gut microbiota were influenced by cadmium exposure. Species diversity and richness decreased gradually with the increase of cadmium concentration. Microbial communities of tadpoles in 100 and 200 μg L-1 cadmium exposure groups were remarkably different from those in control group. Furthermore, the relative abundances of prevalent phyla such as Proteobacteria, Bacteroidetes and Firmicutes and dominant genera such as Klebsiella and Aeromonas were also affected by cadmium exposure. We concluded that cadmium could be harmful to tadpole health by inducing intestinal damages and gut microbiota changes.
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Affiliation(s)
- Jing Ya
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Zongqi Ju
- 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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30
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Tong Q, Liu XN, Hu ZF, Ding JF, Bie J, Wang HB, Zhang JT. Effects of Captivity and Season on the Gut Microbiota of the Brown Frog ( Rana dybowskii). Front Microbiol 2019; 10:1912. [PMID: 31507549 PMCID: PMC6716059 DOI: 10.3389/fmicb.2019.01912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota of amphibians is affected by exogenous and endogenous factors. We performed a comprehensive analysis using high-throughput sequencing technology and functional predictions and observed general changes in the gut microbiota of frogs in different growth stages, seasons, and growth environments. There were no significant differences in microbial richness and diversity between juvenile and adult wild frogs, between the summer and autumn groups of captive frogs, or between wild and captive frogs. There were significant differences in the gut microbiota community structure of Rana dybowskii between the summer and autumn groups of captive frogs and between wild and captive R. dybowskii, whereas the differences between juvenile and adult wild frogs were not significant. The dominant gut bacterial phyla in frogs from both captive and wild environments included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Linear discriminant effect size (LEfSe) analysis showed that Bacteroidetes and Firmicutes were significantly enriched in captive and wild R. dybowskii, respectively linear discriminant analysis (LDA > 4). The core operational taxonomical units (OTUs) that were found in >90% of all frogs tested encompassed 15 core OTUs. The captive frogs exhibited 15 core OTUs in addition to the above overall core microbiota, whereas the wild frogs exhibited 19 core OTUs in addition to the above overall core microbiota. Predictions made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that eleven KEGG pathways, such as infectious diseases, immune system diseases, metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, metabolism of terpenoids and polyketides, neurodegenerative diseases, and transport and catabolism, were enriched in captive frogs. The relative abundance of several red-leg-syndrome-related pathogens increased significantly in captive frogs compared with that in wild frogs. To our knowledge, this is the first study on the effects of individual seasons and captivity on the gut microbiota of frogs.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-Ning Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia-Feng Ding
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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31
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Tang W, Zhu G, Shi Q, Yang S, Ma T, Mishra SK, Wen A, Xu H, Wang Q, Jiang Y, Wu J, Xie M, Yao Y, Li D. Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions. Microbiologyopen 2019; 8:e00789. [PMID: 30848054 PMCID: PMC6612554 DOI: 10.1002/mbo3.789] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
The gut microbiota helps the host to absorb nutrients and generate immune responses that can affect host behavior, development, reproduction, and overall health. However, in most of the previous studies, microbiota was sampled mainly using feces and intestinal contents from mammals but not from wild reptiles. Here, we described the bacterial profile from five different gastrointestinal tract (GIT) segments (esophagus, stomach, small intestine, large intestine, and cloaca) of three wild Rhabdophis subminiatus using 16S rRNA V4 hypervariable amplicon sequencing. Forty-seven bacterial phyla were found in the entire GIT, of which Proteobacteria, Firmicutes, and Bacteroidetes were predominant. The results showed a significant difference in microbial diversity between the upper GIT segments (esophagus and stomach) and lower GIT segments (large intestine and cloaca). An obvious dynamic distribution of Fusobacteria and Bacteroidetes was observed, which mainly existed in the lower GIT segments. Conversely, the distribution of Tenericutes was mainly observed in the upper GIT. We also predicted the microbial functions in the different GIT segments, which showed that microbiota in each segments played an important role in higher membrane transport and carbohydrate and amino acid metabolism. Microbes in the small intestine were also mainly involved in disease-related systems, while in the large intestine, they were associated with membrane transport and carbohydrate metabolism. This is the first study to investigate the distribution of the gut microbiota and to predict the microbial function in R. subminiatus. The composition of the gut microbiota certainly reflects the diet and the living environment of the host. Furthermore, these findings provide vital evidence for the diagnosis and treatment of gut diseases in snakes and offer a direction for a model of energy budget research.
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Affiliation(s)
- Wenjiao Tang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Guangxiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qian Shi
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Shijun Yang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Shailendra Kumar Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Anxiang Wen
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Huailiang Xu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Qin Wang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yanzhi Jiang
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Jiayun Wu
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Meng Xie
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Yongfang Yao
- College of Life ScienceSichuan Agricultural UniversityYa’anChina
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
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32
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Greenspan SE, Lyra ML, Migliorini GH, Kersch-Becker MF, Bletz MC, Lisboa CS, Pontes MR, Ribeiro LP, Neely WJ, Rezende F, Romero GQ, Woodhams DC, Haddad CFB, Toledo LF, Becker CG. Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense. Proc Biol Sci 2019; 286:20190924. [PMID: 31238845 DOI: 10.1098/rspb.2019.0924] [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] [Indexed: 12/14/2022] Open
Abstract
The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness.
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Affiliation(s)
- Sasha E Greenspan
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Mariana L Lyra
- 2 Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista , Rio Claro , SP 13506-900 , Brazil
| | - Gustavo H Migliorini
- 3 Programa de Pós-graduação em Biologia Animal, Universidade Estadual Paulista 'Júlio de Mesquita Filho' , São José do Rio Preto SP 15054-000 , Brazil
| | - Mônica F Kersch-Becker
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Molly C Bletz
- 4 Department of Biology, University of Massachusetts Boston , Boston, MA 02125 , USA
| | | | - Mariana R Pontes
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil.,8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Luisa P Ribeiro
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil.,8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Wesley J Neely
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Felipe Rezende
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Gustavo Q Romero
- 7 Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas SP 13083-862 , Brazil
| | - Douglas C Woodhams
- 4 Department of Biology, University of Massachusetts Boston , Boston, MA 02125 , USA
| | - Célio F B Haddad
- 2 Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista , Rio Claro , SP 13506-900 , Brazil
| | - Luís Felipe Toledo
- 8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - C Guilherme Becker
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
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33
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Estrada A, Hughey MC, Medina D, Rebollar EA, Walke JB, Harris RN, Belden LK. Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling. PeerJ 2019; 7:e7044. [PMID: 31275740 PMCID: PMC6590418 DOI: 10.7717/peerj.7044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/27/2019] [Indexed: 12/28/2022] Open
Abstract
The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts.
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Affiliation(s)
- Angie Estrada
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Balboa, Ancón, Panamá, Panamá
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34
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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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35
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36
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Zhang M, Gaughan S, Chang Q, Chen H, Lu G, Wang X, Xu L, Zhu L, Jiang J. Age-related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus). Microbiologyopen 2018; 8:e00778. [PMID: 30585426 PMCID: PMC6612560 DOI: 10.1002/mbo3.778] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 01/24/2023] Open
Abstract
The composition of the intestinal microbial community may vary across developmental stages. In this study, we explored how this microbial community shifted along the intestinal tract of the Chinese giant salamander (Andrias davidianus) at various ages. Next-generation sequencing was used to sequence the bacterial 16S rRNA gene from different kind of samples, including the stomach, duodenum, ileum, and rectum. The highest mean relative abundance of the bacterial community in the gastrointestinal tract shifted in relation to age: within the first year, Bacteroidetes (47.76%) dominated the gut microbiome, whereas Proteobacteria was the most dominant at age 2 (32.88%) and age 3 (30.78%), and finally, Firmicutes was the most dominant at age 4 (34.70%). The overall richness of the gut bacterial community also generally increased from age 2 to 4. Hierarchical cluster analysis revealed that the gut microbiome at age 2 had greater variability than that at either age 3 or 4, likely representing a shift in diet from yolk or redworms as a juvenile to shrimp or crab as an adult. As these salamanders develop, their gastrointestinal tracts increase in complexity, and this compartmentalization may also facilitate an increase in microbial gut diversity.
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Affiliation(s)
- Mengjie Zhang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina,College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Sarah Gaughan
- Department of BiologyUniversity of Nebraska at OmahaOmahaNebraska
| | - Qing Chang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Hua Chen
- Shanghai Biozeron Bioinformatics CenterShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaNebraska
| | - Xungang Wang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Liangliang Xu
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina,College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjingChina,Department of BiologyUniversity of Nebraska at OmahaOmahaNebraska
| | - Jianping Jiang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
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37
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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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38
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Lyra ML, Bletz MC, Haddad CFB, Vences M. The Intestinal Microbiota of Tadpoles Differs from Those of Syntopic Aquatic Invertebrates. MICROBIAL ECOLOGY 2018; 76:121-124. [PMID: 29159493 DOI: 10.1007/s00248-017-1109-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects. All groups had substantial numbers of exclusive bacterial operational taxonomic units (OTUs) in their guts, but also shared a high proportion of OTUs, probably corresponding to transient environmental bacteria. Significant differences were found for all pairwise comparisons of tadpoles and snails with the major groups of insects, but not among insect groups or between snails and tadpoles. The similarity between tadpoles and snails may be related to similar feeding mode as both snails and tadpoles scratch biofilms and algae from surfaces; however, this requires confirmation due to low sample sizes. Overall, the gut microbiota differences found among syntopic aquatic animals are likely shaped by both food preferences and host identity.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Zoologia, Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP, 13506-900, Brazil.
| | - Molly C Bletz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Célio F B Haddad
- Departamento de Zoologia, Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP, 13506-900, Brazil
- Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
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39
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Chai L, Dong Z, Chen A, Wang H. Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis. Arch Microbiol 2018; 200:1087-1099. [PMID: 29748695 DOI: 10.1007/s00203-018-1523-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/11/2018] [Accepted: 05/03/2018] [Indexed: 01/05/2023]
Abstract
The assembly of intestinal microbial communities can play major roles in animal development. We hypothesized that intestinal microbial communities could mirror the developmental programs of amphibian metamorphosis. Here, we surveyed the morphological parameters of the body and intestine of Bufo gargarizans at varying developmental stages and inventoried the intestinal microbial communities of B. gargarizans at four key developmental stages via 16S rDNA gene sequencing. Firstly, our survey showed that during metamorphosis, body weight and intestinal weight were reduced by 56.8 and 91.8%, respectively. Secondly, the gut bacterial diversity of B. gargarizans decreased with metamorphosis and the composition of the tadpoles' intestinal microbiota varied across metamorphosis. Compared to aquatic larvae, terrestrial juveniles showed major shifts in microbial composition, including reduction in Proteobacteria and Actinobacteria, increases in Bacteroidetes and Fusobacteria, and the appearance of Verrucomicrobia. Firmicutes in four developmental stages showed similar abundance at the phylum level, but in each stage was driven by distinct genera. Enterobacter, Aeromonas, Mucinivorans and Bacteroides also changed in abundance and were found to be significantly correlated with loss of body or intestinal tissue during metamorphosis. These results indicate a shift in intestinal microbial community composition throughout amphibian metamorphosis.
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Affiliation(s)
- Lihong Chai
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710054, People's Republic of China.,Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710062, People's Republic of China
| | - Zhongmin Dong
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS, B3H 3C3, Canada
| | - Aixia Chen
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710054, People's Republic of China.,Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710062, People's Republic of China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
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40
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Bates KA, Clare FC, O'Hanlon S, Bosch J, Brookes L, Hopkins K, McLaughlin EJ, Daniel O, Garner TWJ, Fisher MC, Harrison XA. Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure. Nat Commun 2018; 9:693. [PMID: 29449565 PMCID: PMC5814395 DOI: 10.1038/s41467-018-02967-w] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
Host-associated microbes are vital for combatting infections and maintaining health. In amphibians, certain skin-associated bacteria inhibit the fungal pathogen Batrachochytrium dendrobatidis (Bd), yet our understanding of host microbial ecology and its role in disease outbreaks is limited. We sampled skin-associated bacteria and Bd from Pyrenean midwife toad populations exhibiting enzootic or epizootic disease dynamics. We demonstrate that bacterial communities differ between life stages with few shared taxa, indicative of restructuring at metamorphosis. We detected a significant effect of infection history on metamorph skin microbiota, with reduced bacterial diversity in epizootic populations and differences in community structure and predicted function. Genome sequencing of Bd isolates supports a single introduction to the Pyrenees and reveals no association between pathogen genetics and epidemiological trends. Our findings provide an ecologically relevant insight into the microbial ecology of amphibian skin and highlight the relative importance of host microbiota and pathogen genetics in predicting disease outcome. Amphibian skin microbe communities have been putatively associated with the severity of chytrid fungal disease. Here, the authors show that different types of disease dynamics (enzootic versus epizootic) are associated with different microbiota in the host populations.
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Affiliation(s)
- Kieran A Bates
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK. .,Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Frances C Clare
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Simon O'Hanlon
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC, Jose Gutierrez Abascal 2, 28006, Madrid, Spain
| | - Lola Brookes
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Emilia J McLaughlin
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Olivia Daniel
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
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41
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Huang BH, Chang CW, Huang CW, Gao J, Liao PC. Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity. Front Microbiol 2018; 8:2670. [PMID: 29375532 PMCID: PMC5768659 DOI: 10.3389/fmicb.2017.02670] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022] Open
Abstract
The physiological impact of agricultural pollution, habitat disturbance, and food source variability on amphibian remains poorly understood. By comparing the composition and predicted functions of gut microbiota of two frog species from forest and farmland, we quantified the effects of the exogenous environment and endogenous filters on gut microbiota and the corresponding functions. However, compositional differences of the gut microbiota between the frog species were not detected, even when removing roughly 80–88% of the confounding effect produced by common and shared bacteria (i.e., generalists) and those taxa deemed too rare. The habitat effect accounted for 14.1% of the compositional difference of gut microbial specialists, but host and host × habitat effects were not significant. Similar trends of a significant habitat effect, at an even higher level (26.0%), for the physiological and metabolic functions of gut microbiota was predicted. A very obvious skewing of the relative abundance of functional groups toward farmland habitats reflects the highly diverse bacterial functions of farmland frogs, in particular related to pathogenic disease and pesticide degradation, which may be indication of poor adaptation or strong selective pressure against disease. These patterns reflect the impacts of agricultural activities on frogs and how such stresses may be applied in an unequal manner for different frog species.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chun-Wen Chang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Technical Service Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Chih-Wei Huang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.,Faculty of Resources and Environment, Baotou Teachers' College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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42
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Knutie SA, Shea LA, Kupselaitis M, Wilkinson CL, Kohl KD, Rohr JR. Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs. Integr Comp Biol 2017; 57:732-742. [PMID: 28662573 PMCID: PMC5886343 DOI: 10.1093/icb/icx028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Food resources can affect the health of organisms by altering their symbiotic microbiota and affecting energy reserves for host defenses against parasites. Different diets can vary in their macronutrient content and therefore they might favor certain bacterial communities of the host and affect the development and maintenance of the immune system, such as the inflammatory or antibody responses. Thus, testing the effect of diet, especially for animals with wide diet breadths, on host-associated microbiota and defenses against parasites might be important in determining infection and disease risk. Here, we test whether the early-life diet of Cuban tree frogs (Osteopilus septentrionalis) affects early- and later-life microbiota as well as later-life defenses against skin-penetrating, gut worms (Aplectana hamatospicula). We fed tadpoles two ecologically common diets: a diet of conspecifics or a diet of algae (Arthrospira sp.). We then: (1) characterized the gut microbiota of tadpoles and adults; and (2) challenged adult frogs with parasitic worms and measured host resistance (including the antibody-mediated immune response) and tolerance of infections. Tadpole diet affected bacterial communities in the guts of tadpoles but did not have enduring effects on the bacterial communities of adults. In contrast, tadpole diet had enduring effects on host resistance and tolerance of infections in adult frogs. Frogs that were fed a conspecific-based diet as tadpoles were more resistant to worm penetration compared with frogs that were fed an alga-based diet as tadpoles, but less resistant to worm establishment, which may be related to their suppressed antibody response during worm establishment. Furthermore, frogs that were fed a conspecific-based diet as tadpoles were more tolerant to the effect of parasite abundance on host mass during worm establishment. Overall, our study demonstrates that the diet of Cuban tree frog tadpoles affects the gut microbiota and defenses against parasitic gut worms of frogs, but these effects depend on the stage of the host and infection, respectively.
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Affiliation(s)
- Sarah A. Knutie
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Lauren A. Shea
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Marinna Kupselaitis
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | | | - Kevin D. Kohl
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jason R. Rohr
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
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43
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Bletz MC, Archer H, Harris RN, McKenzie VJ, Rabemananjara FCE, Rakotoarison A, Vences M. Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar. Front Microbiol 2017; 8:1530. [PMID: 28861051 PMCID: PMC5563069 DOI: 10.3389/fmicb.2017.01530] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/28/2017] [Indexed: 12/30/2022] Open
Abstract
Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae) was enriched on terrestrial frogs. The presence of shared bacterial OTUs across geographic regions for selected host genera suggests the presence of core microbial communities which in Madagascar, might be driven more strongly by a species’ preference for specific microhabitats than by the physical, physiological or biochemical properties of their skin. These results corroborate that both host and environmental factors are driving community assembly of amphibian cutaneous microbial communities, and provide an improved foundation for elucidating their role in disease resistance.
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Affiliation(s)
- Molly C Bletz
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany.,Department of Biology, James Madison University, HarrisonburgVA, United States
| | - Holly Archer
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, United States
| | - Reid N Harris
- Department of Biology, James Madison University, HarrisonburgVA, United States
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, United States
| | | | - Andolalao Rakotoarison
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany.,Mention Biologie et Biodiversité Animale, University of AntananarivoAntananarivo, Madagascar
| | - Miguel Vences
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany
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44
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Bletz MC, Perl RGB, Vences M. Skin microbiota differs drastically between co-occurring frogs and newts. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170107. [PMID: 28484639 PMCID: PMC5414276 DOI: 10.1098/rsos.170107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/07/2017] [Indexed: 05/10/2023]
Abstract
Diverse microbial assemblages inhabit amphibian skin and are known to differ among species; however, few studies have analysed these differences in systems that minimize confounding factors, such as season, location or host ecology. We used high-throughput amplicon sequencing to compare cutaneous microbiotas among two ranid frogs (Rana dalmatina, R. temporaria) and four salamandrid newts (Ichthyosaura alpestris, Lissotriton helveticus, L. vulgaris, Triturus cristatus) breeding simultaneously in two ponds near Braunschweig, Germany. We found that bacterial communities differed strongly and consistently between these two distinct amphibian clades. While frogs and newts had similar cutaneous bacterial richness, their bacterial composition strongly differed. Average Jaccard distances between frogs and newts were over 0.5, while between species within these groups distances were only 0.387 and 0.407 for frogs and newts, respectively. At the operational taxonomic unit (OTU) level, 31 taxa exhibited significantly different relative abundances between frogs and newts. This finding suggests that chemical or physical characteristics of these amphibians' mucosal environments provide highly selective conditions for bacterial colonizers. Multi-omics analyses of hosts and their microbiota as well as directed efforts to understand chemical differences in the mucosal environments (e.g. pH), and the specificities of host-produced compounds against potential colonizers will help to better understand this intriguing pattern.
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45
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Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nat Commun 2016; 7:13699. [PMID: 27976718 PMCID: PMC5171763 DOI: 10.1038/ncomms13699] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Complex microbial communities inhabit vertebrate digestive systems but thorough understanding of the ecological dynamics and functions of host-associated microbiota within natural habitats is limited. We investigate the role of environmental conditions in shaping gut and skin microbiota under natural conditions by performing a field survey and reciprocal transfer experiments with salamander larvae inhabiting two distinct habitats (ponds and streams). We show that gut and skin microbiota are habitat-specific, demonstrating environmental factors mediate community structure. Reciprocal transfer reveals that gut microbiota, but not skin microbiota, responds differentially to environmental change. Stream-to-pond larvae shift their gut microbiota to that of pond-to-pond larvae, whereas pond-to-stream larvae change to a community structure distinct from both habitat controls. Predicted functions, however, match that of larvae from the destination habitats in both cases. Thus, microbial function can be matched without taxonomic coherence and gut microbiota appears to exhibit metagenomic plasticity.
Host-associated microbial communities can shift in structure or function when hosts change locations. Bletz et al. reciprocally transfer salamander larvae between pond and stream habitats to show that gut microbiomes shift in function, but not necessarily taxonomic identities, when hosts encounter a new environment.
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46
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Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Caviedes-Vidal E, Bordenstein SR. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol 2016; 26:1175-1189. [PMID: 27862531 DOI: 10.1111/mec.13921] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022]
Abstract
Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Antonio Brun
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Melisa Magallanes
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Joshua Brinkerhoff
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Alejandro Laspiur
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Juan Carlos Acosta
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Enrique Caviedes-Vidal
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA
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