101
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Zhang Z, Hu T, Lu G, Zhu L. Lessons from bamboo-eating pandas and their gut microbiome: Gut microbiome flow and applications. Evol Appl 2020; 13:615-619. [PMID: 32211055 PMCID: PMC7086052 DOI: 10.1111/eva.12915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/26/2022] Open
Abstract
The giant panda is one of the most endangered mammals in the world, and many studies have revealed their evolutionary adaptation to the local environment (e.g., dietary cellulose and cyanide) on the evidences from population genetics and their gut microbiome. Here, based on the results of our analysis of the giant panda gut microbiome, we concluded that instability and resilience are the two primary characteristics of the giant panda gut microbiome. This basic information may have an impact on giant panda conservation, as well the management of other animal species.
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Affiliation(s)
- Zheng Zhang
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Ting Hu
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Guoqing Lu
- Department of Biology University of Nebraska Omaha Omaha NE USA
| | - Lifeng Zhu
- College of Life Sciences Nanjing Normal University Nanjing China
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102
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Chong CW, Alkatheeri AHS, Ali N, Tay ZH, Lee YL, Paramasivam SJ, Jeevaratnam K, Low WY, Lim SHE. Association of antimicrobial resistance and gut microbiota composition in human and non-human primates at an urban ecotourism site. Gut Pathog 2020; 12:14. [PMID: 32175011 PMCID: PMC7063749 DOI: 10.1186/s13099-020-00352-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background The rise of nature-based ecotourism in the past decade has introduced unprecedented challenges in managing the increasing interaction between humans and animals. The potential transmission of antibiotic resistant microbes between humans and non-human primate populations is a concern due to their genetic similarity. Malaysia is well known for hotspots of wildlife diversity where non-human primates like monkeys and orangutans have become popular tourist attractions. In this study, we assessed the prevalence of antimicrobial resistant Staphylococcus aureus, Enterococcus species, and other Enterobacteriaceae in the faeces of human (HS) and two non-human primates (NHP) in Malaysia, the Long-tailed macaque (Macaca fascicularis, MF) and Silvered leaf monkey (Trachypithecus cristatus, TC). In addition, the faecal bacterial composition was profiled to evaluate the potential association between antibiotic resistant profiles and composition of gut microbiota. Results We tested the isolated bacteria using a selection of antibiotics. The results showed that both the number of antibiotic resistant strains and resistance level were higher in humans than NHPs. Overall, the composition of gut microbiome and pattern of antibiotic resistance showed that there was higher similarity between MF and TC, the two NHPs, than with HS. In addition, samples with higher levels of antibiotic resistance showed lower bacterial richness. Homo sapiens had the lowest bacterial diversity and yet it had higher abundance of Bacteroides. In contrast, NHPs displayed higher bacterial richness and greater prevalence of Firmicutes such as Ruminococceae and Oscillospira. Conclusion Higher antibiotic susceptibility in NHPs is likely related to low direct exposure to antibiotics. The lack of resistance may also suggest limited antimicrobial resistance transmission between humans and NHP. Nonetheless, continued monitoring over a long period will help mitigate the risk of anthropozoonosis and zooanthroponosis.
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Affiliation(s)
- C W Chong
- 1School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan Malaysia
| | - A H S Alkatheeri
- 2Health Science Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE
| | - N Ali
- 3Royal College of Surgeons in Ireland, Perdana University, MAEPS Building, 43400 Serdang, Selangor Malaysia
| | - Z H Tay
- 3Royal College of Surgeons in Ireland, Perdana University, MAEPS Building, 43400 Serdang, Selangor Malaysia
| | - Y L Lee
- 3Royal College of Surgeons in Ireland, Perdana University, MAEPS Building, 43400 Serdang, Selangor Malaysia
| | - S J Paramasivam
- 4Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL UK.,7Animal Neighbours Project, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL UK
| | - K Jeevaratnam
- 4Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL UK
| | - W Y Low
- 5Centre for Bioinformatics, School of Data Sciences, Perdana University, MAEPS Building, 43400 Serdang, Selangor Malaysia.,6The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371 Australia
| | - S H E Lim
- 2Health Science Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE.,3Royal College of Surgeons in Ireland, Perdana University, MAEPS Building, 43400 Serdang, Selangor Malaysia
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103
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Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL. Emerging Priorities for Microbiome Research. Front Microbiol 2020; 11:136. [PMID: 32140140 PMCID: PMC7042322 DOI: 10.3389/fmicb.2020.00136] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.
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Affiliation(s)
- Chad M. Cullen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | | | - Sinem Beyhan
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Clara E. Cho
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT, United States
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
- College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Matteo Convertino
- Nexus Group, Faculty of Information Science and Technology, Gi-CoRE Station for Big Data & Cybersecurity, Hokkaido University, Sapporo, Japan
| | - Sophie J. McCoy
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | | | - Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ananya Sen Gupta
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, United States
| | - Kevin Cheung
- Department of Dermatology, The University of Iowa, Iowa City, IA, United States
| | | | - Zhengqiao Zhao
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail L. Rosen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
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104
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Barnes EM, Carter EL, Lewis JD. Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa. Front Microbiol 2020; 11:101. [PMID: 32117131 PMCID: PMC7018939 DOI: 10.3389/fmicb.2020.00101] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/17/2020] [Indexed: 12/30/2022] Open
Abstract
Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.
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Affiliation(s)
- Elle M Barnes
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - Erin L Carter
- Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - J D Lewis
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
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105
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Mahmmod YS, Correa-Fiz F, Aragon V. Variations in association of nasal microbiota with virulent and non-virulent strains of Glaesserella (Haemophilus) parasuis in weaning piglets. Vet Res 2020; 51:7. [PMID: 32014043 PMCID: PMC6996185 DOI: 10.1186/s13567-020-0738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Glaesserella (formerly Haemophilus) parasuis causes Glässer’s disease, which results in high economic loss in the swine industry. To understand the polymicrobial interactions of G. parasuis and the nasal microbiota, the statistical association patterns of nasal colonizing bacteria with virulent and non-virulent strains of G. parasuis were studied accounting for the farm management practices as potential risk factors for the occurrence of Glässer’s disease. The nasal microbiota from 51 weaned-piglets from four farms with Glässer’s disease and three farms with no respiratory diseases was previously characterized and included in this study. The presence of virulent and/or non-virulent G. parasuis strains in the nasal cavities was determined in order to establish the potential association with other members of the nasal microbiota. Multivariate logistic and linear regression models were performed among the various members of nasal microbiota and G. parasuis. The multi-site production system and disease presence in the farm were both significantly associated with the presence of G. parasuis virulent strains in the nose of the piglets. Differential bacterial associations were observed with virulent or non-virulent G. parasuis. Chitinophagaceae, Corynebacteriaceae and Corynebacterium were positively associated with the virulent G. parasuis strains, while Enterobacteriaceae, Peptostreptococcaceae, Clostridium XI, and Escherichia/Shigella were negatively associated with virulent G. parasuis. On the other hand, Flavobacteriaceae, Planobacterium, and Phascolarctobacterium were positively associated with the non-virulent G. parasuis strains, while Rikenellaceae, Enterococcaceae, Odoribacter, and Corynebacterium were negatively associated with non-virulent G. parasuis. In conclusion, the nasal microbiota communities showed variations in the association with the G. parasuis strains type.
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Affiliation(s)
- Yasser S Mahmmod
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Bellaterra, Barcelona, Spain. .,Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt.
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Virginia Aragon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
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106
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Abstract
Endosymbiosis is found in all types of ecosystems and it can be sensitive to environmental changes due to the intimate interaction between the endosymbiont and the host. Indeed, global climate change disturbs the local ambient environment and threatens endosymbiotic species, and in some cases leads to local ecosystem collapse. Recent studies have revealed that the endosymbiont can affect holobiont (endosymbiont and host together) stress tolerance as much as the host does, and manipulation of the microbial partners in holobionts may mitigate the impacts of the environmental stress. Here, we first show how the endosymbiont presence affects holobiont stress tolerance by discussing three well-studied endosymbiotic systems, which include plant-fungi, aquatic organism-algae, and insect-bacteria systems. We then review how holobionts are able to alter their stress tolerance via associated endosymbionts by changing their endosymbiont composition, by adaptation of their endosymbionts, or by acclimation of their endosymbionts. Finally, we discuss how different transmission modes (vertical or horizontal transmission) might affect the adaptability of holobionts. We propose that the endosymbiont is a good target for modifying holobiont stress tolerance, which makes it critical to more fully investigate the role of endosymbionts in the adaptive responses of holobionts to stress.
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107
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Jacobs L, McMahon BH, Berendzen J, Longmire J, Gleasner C, Hengartner NW, Vuyisich M, Cohn JR, Jenkins M, Bartlow AW, Fair JM. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals. PLoS One 2019; 14:e0225858. [PMID: 31825977 PMCID: PMC6905524 DOI: 10.1371/journal.pone.0225858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/13/2019] [Indexed: 12/02/2022] Open
Abstract
Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.
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Affiliation(s)
- Lindsey Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Benjamin H. McMahon
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Joel Berendzen
- GenerisBio, Santa Fe, New Mexico, United States of America
| | - Jonathan Longmire
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cheryl Gleasner
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | | | - Judith R. Cohn
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marti Jenkins
- The Peregrine Fund, Boise, Idaho, United States of America
| | - Andrew W. Bartlow
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeanne M. Fair
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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108
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Bird S, Prewer E, Kutz S, Leclerc L, Vilaça ST, Kyle CJ. Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal. Ecol Evol 2019; 9:13202-13217. [PMID: 31871639 PMCID: PMC6912892 DOI: 10.1002/ece3.5768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022] Open
Abstract
The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture, and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters. These clusters are defined by Arctic Mainland and Island populations, including the following: (a) two mainland sampling locations of the Northwest Territories and Nunavut and (b) four locations of Victoria Island. Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.
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Affiliation(s)
- Samantha Bird
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
| | - Erin Prewer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
| | - Susan Kutz
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
- Canadian Wildlife Health CooperativeAlberta NodeFaculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
| | | | - Sibelle T. Vilaça
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Biology DepartmentTrent UniversityPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
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109
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Guo W, Mishra S, Wang C, Zhang H, Ning R, Kong F, Zeng B, Zhao J, Li Y. Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas ( Ailuropoda melanoleuca). Genes (Basel) 2019; 10:E827. [PMID: 31635158 PMCID: PMC6826394 DOI: 10.3390/genes10100827] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from "endangered" to "vulnerable" (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild.
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Affiliation(s)
- Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- School of Laboratory Medicine/Sichuan Provincial EngineeringLaboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu 610500, China.
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Ya'an 611830, Sichuan, China.
| | - Hemin Zhang
- China Conservation and Research Center for the Giant Panda, Ya'an 611830, Sichuan, China.
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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110
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Sun CH, Liu HY, Liu B, Yuan BD, Lu CH. Analysis of the Gut Microbiome of Wild and Captive Père David's Deer. Front Microbiol 2019; 10:2331. [PMID: 31636626 PMCID: PMC6787558 DOI: 10.3389/fmicb.2019.02331] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022] Open
Abstract
Père David’s deer (Elaphurus davidianus or milu) is a highly endangered species originating from China, and many deer are currently being raised in captivity for gradual re-introduction to the wild. Wild and captive deer currently live in the same region but have vastly different diets. In this study, we used 16S rRNA high-throughput sequencing to identify the healthy core microbiome in the gut of wild and captive Père David’s deer and investigate how dietary factors influence the gut microbiome by comparing their differences. A core shared gut microbiome was identified in healthy Père David’s deer, which was similar to that of other ruminants, mainly comprising the phyla Firmicutes and Bacteroidetes. There were no differences in the richness or diversity of the gut microbiome between the wild and captive deer. However, PCA and ANOSIM demonstrated clear differences in the microbial community structure between the captive and wild deer, which mainly manifested as changes in the relative abundance of 39 bacterial genera. As the majority of these genera were not dominant in the deer gut, no significant difference was detected in functional modules related to the microbiome between the two groups. Therefore, the difference in dietary factors does not appear to affect the healthy core gut microbiome between captive and wild Père David’s deer, suggesting strong co-evolution and the possibility of re-establishment in the wild. These data could guide future applications of population management in Père David’s deer conservation.
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Affiliation(s)
- Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Bin Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,Jiangsu Dafeng Père David's Deer National Nature Reserve, Yancheng, China
| | - Bao-Dong Yuan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Chang-Hu Lu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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111
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Mushegian AA, Tougeron K. Animal-Microbe Interactions in the Context of Diapause. THE BIOLOGICAL BULLETIN 2019; 237:180-191. [PMID: 31714855 DOI: 10.1086/706078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Dormancy and diapause are key adaptations in many organisms, enabling survival of temporarily or seasonally unsuitable environmental conditions. In this review, we examine how our understanding of programmed developmental and metabolic arrest during diapause intersects with the increasing body of knowledge about animal co-development and co-evolution with microorganisms. Host-microbe interactions are increasingly understood to affect a number of metabolic, physiological, developmental, and behavioral traits and to mediate adaptations to various environments. Therefore, it is timely to consider how microbial factors might affect the expression and evolution of diapause in a changing world. We examine how a range of host-microbe interactions, from pathogenic to mutualistic, may have an impact on diapause phenotypes. Conversely, we examine how the discontinuities that diapause introduces into animal host generations can affect the ecology of microbial communities and the evolution of host-microbe interactions. We discuss these issues as they relate to physiology, evolution of development, local adaptation, disease ecology, and environmental change. Finally, we outline research questions that bridge the historically distinct fields of seasonal ecology and host-microbe interactions.
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112
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Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring. Sci Rep 2019; 9:13679. [PMID: 31548611 PMCID: PMC6757053 DOI: 10.1038/s41598-019-50139-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.
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113
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Janse JJ, Langenberg MCC, Kos-Van Oosterhoud J, Ozir-Fazalalikhan A, Brienen EAT, Winkel BMF, Erkens MAA, van der Beek MT, van Lieshout L, Smits HH, Webster BL, Zandvliet ML, Verbeek R, Westra IM, Meij P, Visser LG, van Diepen A, Hokke CH, Yazdanbakhsh M, Roestenberg M. Establishing the Production of Male Schistosoma mansoni Cercariae for a Controlled Human Infection Model. J Infect Dis 2019; 218:1142-1146. [PMID: 29905805 DOI: 10.1093/infdis/jiy275] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/07/2018] [Indexed: 11/14/2022] Open
Abstract
To accelerate the development of novel vaccines for schistosomiasis, we set out to develop a human model for Schistosoma mansoni infection in healthy volunteers. During natural infections, female schistosomes produce eggs that give rise to morbidity. Therefore, we produced single-sex, male Schistosoma mansoni cercariae for human infection without egg production and associated pathology. Cercariae were produced in their intermediate snail hosts in accordance with the principles of good manufacturing practice (GMP). The application of GMP principles to an unconventional production process is a showcase for the controlled production of complex live challenge material in the European Union or under Food and Drug Administration guidance.
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Affiliation(s)
- Jacqueline J Janse
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | | | | | | | - Eric A T Brienen
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | - Béatrice M F Winkel
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | - Marianne A A Erkens
- Department of Medical Microbiology, Leiden University Medical Center, the Netherlands
| | - Martha T van der Beek
- Department of Medical Microbiology, Leiden University Medical Center, the Netherlands
| | | | - Hermelijn H Smits
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | - Bonnie L Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Zoology, Natural History Museum, London, United Kingdom
| | - Maarten L Zandvliet
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, the Netherlands
| | - Richard Verbeek
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, the Netherlands
| | - Inge M Westra
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, the Netherlands
| | - Pauline Meij
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, the Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center, the Netherlands
| | - Angela van Diepen
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | - Cornelis H Hokke
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, the Netherlands
| | - Meta Roestenberg
- Department of Parasitology, Leiden University Medical Center, the Netherlands.,Department of Infectious Diseases, Leiden University Medical Center, the Netherlands
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Karmacharya D, Manandhar P, Manandhar S, Sherchan AM, Sharma AN, Joshi J, Bista M, Bajracharya S, Awasthi NP, Sharma N, Llewellyn B, Waits LP, Thapa K, Kelly MJ, Vuyisich M, Starkenburg SR, Hero JM, Hughes J, Wultsch C, Bertola L, Fountain-Jones NM, Sinha AK. Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal. PLoS One 2019; 14:e0221868. [PMID: 31465520 PMCID: PMC6715213 DOI: 10.1371/journal.pone.0221868] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/17/2019] [Indexed: 02/01/2023] Open
Abstract
Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.
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Affiliation(s)
- Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
- School of Environment, Griffith University, Brisbane, Queensland, Australia
| | | | | | | | | | - Jyoti Joshi
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | - Manisha Bista
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | | | - Netra Sharma
- Environment Team, U.S. Agency for International Development, Kathmandu, Nepal
| | - Bronwyn Llewellyn
- Environment Team, U.S. Agency for International Development, Kathmandu, Nepal
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Kanchan Thapa
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Momchilo Vuyisich
- Applied Genomics, Los Alamos National Lab, Los Alamos, New Mexico, United States of America
| | - Shawn R. Starkenburg
- Applied Genomics, Los Alamos National Lab, Los Alamos, New Mexico, United States of America
| | - Jean-Marc Hero
- School of Science & Education, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
| | - Jane Hughes
- School of Environment, Griffith University, Brisbane, Queensland, Australia
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, United States of America
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, United States of America
| | - Laura Bertola
- Department of Biology, City College of New York, New York, United States of America
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Nicholas M. Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Amit K. Sinha
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
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Splivallo R, Vahdatzadeh M, Maciá-Vicente JG, Molinier V, Peter M, Egli S, Uroz S, Paolocci F, Deveau A. Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle Tuber aestivum. Front Microbiol 2019; 10:1437. [PMID: 31316485 PMCID: PMC6611097 DOI: 10.3389/fmicb.2019.01437] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/07/2019] [Indexed: 11/21/2022] Open
Abstract
Truffle fungi are well known for their enticing aromas partially emitted by microbes colonizing truffle fruiting bodies. The identity and diversity of these microbes remain poorly investigated, because few studies have determined truffle-associated bacterial communities while considering only a small number of fruiting bodies. Hence, the factors driving the assembly of truffle microbiomes are yet to be elucidated. Here we investigated the bacterial community structure of more than 50 fruiting bodies of the black truffle Tuber aestivum in one French and one Swiss orchard using 16S rRNA gene amplicon high-throughput sequencing. Bacterial communities from truffles collected in both orchards shared their main dominant taxa: while 60% of fruiting bodies were dominated by α-Proteobacteria, in some cases the β-Proteobacteria or the Sphingobacteriia classes were the most abundant, suggesting that specific factors (i.e., truffle maturation and soil properties) shape differently truffle-associated microbiomes. We further attempted to assess the influence in truffle microbiome variation of factors related to collection season, truffle mating type, degree of maturation, and location within the truffle orchards. These factors had differential effects between the two truffle orchards, with season being the strongest predictor of community variation in the French orchard, and spatial location in the Swiss one. Surprisingly, genotype and fruiting body maturation did not have a significant effect on microbial community composition. In summary, our results show, regardless of the geographical location considered, the existence of heterogeneous bacterial communities within T. aestivum fruiting bodies that are dominated by three bacterial classes. They also indicate that factors shaping microbial communities within truffle fruiting bodies differ across local conditions.
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Affiliation(s)
- Richard Splivallo
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Maryam Vahdatzadeh
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt, Germany
| | - Virginie Molinier
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.,UMR 5175 CEFE - CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, INSERM, Montpellier, France
| | - Martina Peter
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Simon Egli
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Stéphane Uroz
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 INRA - Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, Champenoux, France
| | - Francesco Paolocci
- National Research Council (CNR), Institute of Biosciences and Bioresources, Division of Perugia, Perugia, Italy
| | - Aurélie Deveau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 INRA - Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, Champenoux, France
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116
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Ingala MR, Becker DJ, Bak Holm J, Kristiansen K, Simmons NB. Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats. Ecol Evol 2019; 9:6508-6523. [PMID: 31236240 PMCID: PMC6580296 DOI: 10.1002/ece3.5228] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/28/2022] Open
Abstract
Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land-use change on wildlife microbiotas, we analyzed long-term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross-species pathogen transmission.
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Affiliation(s)
- Melissa R. Ingala
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNew York
- Division of Vertebrate Zoology, Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew York
| | - Daniel J. Becker
- Odum School of EcologyUniversity of GeorgiaAthensGeorgia
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGeorgia
- Department of BiologyIndiana UniversityBloomingtonIndiana
| | - Jacob Bak Holm
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Clinical‐MicrobiomicsCopenhagenDenmark
| | - Karsten Kristiansen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- BGIShenzhenChina
| | - Nancy B. Simmons
- Division of Vertebrate Zoology, Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew York
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117
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Hassell JM, Ward MJ, Muloi D, Bettridge JM, Robinson TP, Kariuki S, Ogendo A, Kiiru J, Imboma T, Kang'ethe EK, Öghren EM, Williams NJ, Begon M, Woolhouse MEJ, Fèvre EM. Clinically relevant antimicrobial resistance at the wildlife-livestock-human interface in Nairobi: an epidemiological study. Lancet Planet Health 2019; 3:e259-e269. [PMID: 31229001 PMCID: PMC6630895 DOI: 10.1016/s2542-5196(19)30083-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Antimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance. METHODS 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli, our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock. FINDINGS E coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485 samples), which varied between taxa and by foraging traits. Multiple isolates were resistant to one agent from at least seven antimicrobial classes tested for, and a single isolate was resistant to all antibiotics tested for in the study. The phenotypic diversity of antimicrobial-resistant E coli in wildlife was lower than in livestock, humans, and the environment. Within household compounds, statistical models identified two interfaces for exchange of antimicrobial resistance: between both rodents, humans and their rubbish, and seed-eating birds, humans and their rubbish; and between seed-eating birds, cattle, and bovine manure. INTERPRETATION Urban wildlife carry a high burden of clinically relevant antimicrobial-resistant E coli in Nairobi, exhibiting resistance to drugs considered crucial for human medicine by WHO. Identifiable traits of the wildlife contribute to this exposure; however, compared with humans, livestock, and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that wildlife are a net sink rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock, and both human and livestock waste within households, are exposed to more antimicrobial resistant phenotypes, and could therefore act as conduits for the dissemination of clinically relevant antimicrobial resistance to the wider environment. These results provide novel insight into the broader epidemiology of antimicrobial resistance in complex urban environments, characteristic of lower-middle-income countries. FUNDING UK Medical Research Council and CGIAR Research Program on Agriculture for Nutrition and Health.
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Affiliation(s)
- James M Hassell
- Institute of Infection and Global Health, University of Liverpool, Neston, UK; International Livestock Research Institute, Nairobi, Kenya
| | - Melissa J Ward
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Dishon Muloi
- International Livestock Research Institute, Nairobi, Kenya; Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Judy M Bettridge
- Institute of Infection and Global Health, University of Liverpool, Neston, UK; International Livestock Research Institute, Nairobi, Kenya
| | | | - Sam Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Allan Ogendo
- International Livestock Research Institute, Nairobi, Kenya
| | - John Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | | | - Elin M Öghren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nicola J Williams
- Institute of Infection and Global Health, University of Liverpool, Neston, UK
| | - Michael Begon
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mark E J Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Eric M Fèvre
- Institute of Infection and Global Health, University of Liverpool, Neston, UK; International Livestock Research Institute, Nairobi, Kenya.
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Breen P, Winters AD, Nag D, Ahmad MM, Theis KR, Withey JH. Internal Versus External Pressures: Effect of Housing Systems on the Zebrafish Microbiome. Zebrafish 2019; 16:388-400. [PMID: 31145047 DOI: 10.1089/zeb.2018.1711] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Zebrafish (Danio rerio) are an attractive model organism for scientific studies, including host-microbe interactions. The organism is particularly useful for studying aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. Previous studies have established the presence of a core zebrafish intestinal microbiome, and tracked the development of the zebrafish intestinal microbiome from the larval stage to adulthood. An unexplored matter in this host-microbe relationship is the effect of the housing system on the zebrafish intestinal and tank water microbiomes. In this study, we used 16S rRNA gene sequencing to investigate the response of zebrafish intestinal and tank water microbiomes to a change in housing conditions. Zebrafish in the separated fish tanks showed no initial differences in the structures of their intestinal microbial profiles; the same prominent bacteria were present and abundant across tanks. Immediately after the housing switch, the zebrafish intestinal microbial profiles changed in composition and structure. Within 5 days of the housing switch, the intestinal microbiome had stabilized, and changed significantly from the prehousing switch profile. This study demonstrates that although external factors can significantly perturb and alter the zebrafish intestinal microbiome, the microbiome displays a large level of selective resilience whose primary members (namely Vibrio) persist.
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Affiliation(s)
- Paul Breen
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, Michigan
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, Michigan
| | - Dhrubajyoti Nag
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, Michigan
| | - Madison M Ahmad
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, Michigan
| | - Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, Michigan
| | - Jeffrey H Withey
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, Michigan
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Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun 2019; 10:2200. [PMID: 31097702 PMCID: PMC6522487 DOI: 10.1038/s41467-019-10191-3] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
- ICC Interuniversity Cooperation Centre Water & Health, 1160, Vienna, Austria
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Nathalie Schuster
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
- ICC Interuniversity Cooperation Centre Water & Health, 1160, Vienna, Austria
- Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, 3500, Krems an der Donau, Austria
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van Bruggen AHC, Goss EM, Havelaar A, van Diepeningen AD, Finckh MR, Morris JG. One Health - Cycling of diverse microbial communities as a connecting force for soil, plant, animal, human and ecosystem health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:927-937. [PMID: 30769316 DOI: 10.1016/j.scitotenv.2019.02.091] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 05/06/2023]
Abstract
The One Health concept proposes that there is a connection between human, animal and environmental health. Plants and their health are not explicitly included. In this review, we broaden the One Health concept to include soil, plant, animal and ecosystem health. We argue that the health conditions of all organisms in an ecosystem are interconnected through the cycling of subsets of microbial communities from the environment (in particular the soil) to plants, animals and humans, and back into the environment. After an introduction on health concepts, we present examples of community stability and resilience, diversity and interconnectedness as affected by pollutants, and integrity of nutrient cycles and energy flows. Next, we explain our concept of microbial cycling in relation to ecosystem health, and end with examples of plant and animal disease outbreaks in relation to microbial community composition and diversity. We conclude that we need a better understanding of the role of interconnected microbiomes in promoting plant and animal health and possible ways to stimulate a healthy, diverse microbiome throughout human-dominated ecosystems. We suggest that it is essential to maintain ecosystem and soil health through diversification of plant communities and oligotrophication of managed ecosystems.
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Affiliation(s)
- Ariena H C van Bruggen
- Department of Plant Pathology, University of Florida, Gainesville FL32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA.
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville FL32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA
| | - Arie Havelaar
- Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA; Department of Animal Science, University of Florida, Gainesville FL32611, USA
| | - Anne D van Diepeningen
- Business Unit Biointeractions and Plant Health, Wageningen UR, 6708 PB Wageningen, the Netherlands
| | - Maria R Finckh
- Faculty of Organic Agricultural Sciences, Ecological Plant Protection, University of Kassel, 37213 Witzenhausen, Germany
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA; Department of Medicine, School of Medicine, University of Florida, Gainesville FL32611, USA
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Charlton SJ, Nielsen MB, Pedersen CR, Thomsen L, Kristjansen MP, Sørensen TB, Pertoldi C, Strand J. Strong Heterogeneity in Advances in Cryopreservation Techniques in the Mammalian Orders. Zoolog Sci 2019; 35:1-22. [PMID: 29417894 DOI: 10.2108/zs170037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Between 1970 and 2012, vertebrate abundance has declined by 58% with an average annual decline of 2%, calling for serious action to prevent a mass extinction and an irreversible loss of biodiversity. Cryobanks and cryopreservation have the potential to assist and improve ex situ and in situ conservation strategies by storing valuable genetic material. A great deal of studies concerning cryopreservation have been performed within the class Mammalia, although no systematic overview has previously been presented. The objective of this study is therefore to evaluate the status, pattern and future of cryopreservation within Mammalia. A strong disproportional distribution of studies in examined orders is displayed. For the majority of examined orders less than 10% of species has been examined. However, the cryopreservation of germplasm has in several cases been successful and resulted in successful applications of assisted reproductive techniques (ARTs). Various obstacles are associated with the development of cryopreservation protocols, and among them the most prominent is interspecific differences in cryotolerance. Extrapolation of protocols in closely related species is considered the most applicable procedure, and a future supplement to overcome this problem is the examination and comparison of cryobiological traits. Successful protocols have been developed for the vast majority of domesticated mammals, which gives incentive for the further extrapolation of protocols in threatened species.
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Affiliation(s)
- Sebastian J Charlton
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mikkel B Nielsen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Carina R Pedersen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Lisette Thomsen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mads P Kristjansen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Thomas B Sørensen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Cino Pertoldi
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.,2 Aalborg Zoo, Aalborg, Mølleparkvej 63, 9000 Aalborg, Denmark
| | - Julie Strand
- 3 Randers Regnskov, Randers, Tørvebryggen 11, 8900 Randers, Denmark
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Bacterial communities of Aphis gossypii and Myzus persicae (Hemiptera: Aphididae) from pepper crops (Capsicum sp.). Sci Rep 2019; 9:5766. [PMID: 30962510 PMCID: PMC6453963 DOI: 10.1038/s41598-019-42232-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/21/2019] [Indexed: 11/09/2022] Open
Abstract
Insects harbor a wide variety of microorganisms that form complex and changing communities and play an important role in the biology and evolution of their hosts. Aphids have been used as model organisms to study microorganism-insect interactions. Almost all aphids are infected with the obligate endosymbiont Buchnera aphidicola and can host different bacteria that allow them to acquire traits of agronomic importance, such as resistance to high temperatures and/or defense against natural enemies. However, the bacterial communities of most aphid species remain poorly characterized. In this study, we used high-throughput DNA sequencing to characterize the bacterial communities of Aphis gossypii and Myzus persicae from two cultivable pepper species, Capsicum frutescens (Tabasco variety) and C. annuum (Cayenne variety), in four localities of southwestern Colombia. In addition, we evaluated the dynamics of A. gossypii-associated microorganisms on a seasonal basis. Our results show that the bacterial communities of A. gossypii and M. persicae are dominated by the primary endosymbiont B. aphidicola, while the presence of the facultative symbiont Arsenophonus sp. was only detected in one A. gossypii population from cayenne pepper. In addition to these two known symbionts, eight bacterial OTUs were identified that presented a frequency of 1% or more in at least one of the analyzed populations. The results show that the bacterial communities of aphids associated with pepper crops appears to be structured according to the host aphid species and the geographical location, while no differences were observed in the diversity of bacteria between host plants. Finally, the diversity and abundance of the A. gossypii bacterial community was variable among the four sampling points evaluated over the year and showed a relation with the aphid’s population dynamics. This study represents the first approach to the knowledge of the bacterial community present in chili pepper aphids from Colombia. Nevertheless, more in-depth studies, including replicates, are required to confirm the patterns observed in the microbial communities of aphids from pepper crops.
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Han S, Guan Y, Dou H, Yang H, Yao M, Ge J, Feng L. Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard ( Panthera pardus) using high-throughput sequencing. PeerJ 2019; 7:e6684. [PMID: 30944781 PMCID: PMC6441561 DOI: 10.7717/peerj.6684] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/26/2019] [Indexed: 12/16/2022] Open
Abstract
The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.
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Affiliation(s)
- Siyu Han
- Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, State Forestry and Grassland Administration Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard National Park, State Forestry and Grassland Administration Amur tiger and Amur leopard Monitoring and Research Center, College of Life Science, Beijing Normal University, Beijing, China
| | - Yu Guan
- Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, State Forestry and Grassland Administration Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard National Park, State Forestry and Grassland Administration Amur tiger and Amur leopard Monitoring and Research Center, College of Life Science, Beijing Normal University, Beijing, China
| | - Hailong Dou
- College of Life Sciences, Qufu Normal University, Shandong, China
| | - Haitao Yang
- Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, State Forestry and Grassland Administration Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard National Park, State Forestry and Grassland Administration Amur tiger and Amur leopard Monitoring and Research Center, College of Life Science, Beijing Normal University, Beijing, China
| | - Meng Yao
- Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, State Forestry and Grassland Administration Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard National Park, State Forestry and Grassland Administration Amur tiger and Amur leopard Monitoring and Research Center, College of Life Science, Beijing Normal University, Beijing, China
| | - Jianping Ge
- Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, State Forestry and Grassland Administration Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard National Park, State Forestry and Grassland Administration Amur tiger and Amur leopard Monitoring and Research Center, College of Life Science, Beijing Normal University, Beijing, China
| | - Limin Feng
- Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, State Forestry and Grassland Administration Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard National Park, State Forestry and Grassland Administration Amur tiger and Amur leopard Monitoring and Research Center, College of Life Science, Beijing Normal University, Beijing, China
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Wang L, Ding J, Yang Z, Chen H, Yao R, Dai Q, Ding Y, Zhu L. Père David's deer gut microbiome changes across captive and translocated populations: Implications for conservation. Evol Appl 2019; 12:622-635. [PMID: 30828378 PMCID: PMC6383733 DOI: 10.1111/eva.12743] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022] Open
Abstract
The gut microbial composition and function are shaped by different factors (e.g., host diet and phylogeny). Gut microbes play an important role in host nutrition and development. The gut microbiome may be used to evaluate the host potential environmental adaptation. In this study, we focused on the coevolution of the gut microbiome of captive and translocated Père David's deer populations (Elaphurus davidianus; Chinese: Père David's deer). To address this, we used several different macro- and micro-ecological approaches (landscape ecology, nutritional methods, microscopy, isotopic analysis, and metagenomics). In this long-term study (2011-2014), we observed some dissimilarities in gut microbiome community and function between the captive and wild/translocated Dafeng Père David's deer populations. These differences might link microbiome composition with deer diet within a given season. The proportion of genes coding for putative enzymes (endoglucanase, beta-glucosidase, and cellulose 1,4-beta-cellobiosidase) involved in cellulose digestion in the gut microbiome of the captive populations was higher than that of the translocated population, possibly because of the high proportion of cellulose, hemicellulose, and lignin in the plants most consumed by the captive populations. However, the two enzymes (natA and natB) involved in sodium transport system were enriched in the gut microbiome in translocated population, possibly because of their high salt diet (e.g., Spartina alterniflora). Thus, our results suggested that Père David's deer gut microorganisms potentially coevolved with host diet, and reflected the local adaptation of translocated population in the new environment (e.g., new dietary plants: Spartina alterniflora). A current problem for Père David's deer conservation is the saturation of captive populations. Given that the putative evolutionary adaptation of Père David's deer gut microbiome and its possible applications in conservation, the large area of wetlands along the Yellow Sea dominated by S. alterniflora might be the major translocation region in the future.
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Affiliation(s)
- Lei Wang
- Nanjing Normal UniversityCollege of Life SciencesNanjingChina
| | | | - Zhisong Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
| | - Hua Chen
- Shanghai Biozeron Bioinformatics CenterShanghaiChina
| | - Ran Yao
- Nanjing Normal UniversityCollege of Life SciencesNanjingChina
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of SciencesChengduChina
| | - Yuhua Ding
- Jiangsu Dafeng Milu National Nature ReserveDafengChina
| | - Lifeng Zhu
- Nanjing Normal UniversityCollege of Life SciencesNanjingChina
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Stalder GL, Pinior B, Zwirzitz B, Loncaric I, Jakupović D, Vetter SG, Smith S, Posautz A, Hoelzl F, Wagner M, Hoffmann D, Kübber-Heiss A, Mann E. Gut microbiota of the European Brown Hare (Lepus europaeus). Sci Rep 2019; 9:2738. [PMID: 30804494 PMCID: PMC6390100 DOI: 10.1038/s41598-019-39638-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/21/2019] [Indexed: 12/14/2022] Open
Abstract
Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.
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Affiliation(s)
- G L Stalder
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria.
| | - B Pinior
- Department for Farm Animals and Veterinary Public Health, Institute for Veterinary Public Health, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
| | - B Zwirzitz
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - I Loncaric
- Department of Pathobiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
| | - D Jakupović
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - S G Vetter
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - S Smith
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - A Posautz
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - F Hoelzl
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - M Wagner
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - D Hoffmann
- Game Conservancy Deutschland e. V., Schloßstrasse 1, 86732, Oettingen, Germany
| | - A Kübber-Heiss
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, 1160, Vienna, Austria
| | - E Mann
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria
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Antwis RE, Edwards KL, Unwin B, Walker SL, Shultz S. Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhino. MICROBIOME 2019; 7:27. [PMID: 30770764 PMCID: PMC6377766 DOI: 10.1186/s40168-019-0639-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/29/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Host microbiomes play a role in hormone production and subsequent fertility in humans, but this is less well understood in non-model organisms. This is of particular relevance to species in zoo-based conservation breeding programmes, as relationships between host microbiome composition and reproductive output may allow for the development of microbial augmentation strategies to improve success. Here, we characterise faecal bacterial communities of breeding and non-breeding eastern black rhino (Diceros bicornis michaeli) using 16S rRNA gene amplicon sequencing and quantify progestagen and glucocorticoid metabolite concentrations through enzyme immunoassays to identify such relationships. RESULTS We identified significant differences in black rhino gut microbiome composition according to ID, institution, breeding success and ovarian cycle phase. In particular, the gut microbiome during pregnancy and post-parturition was significantly altered. Around a third of bacterial genera showed more than ± 10% correlation with either progestagen and/or glucocorticoid concentration, and in general, microbial genera correlated with both hormones in the same direction. Through a combination of analyses, we identified four genera (Aerococcaceae, Atopostipes, Carnobacteriaceae and Solobacterium) that were significantly associated with breeding success, pregnancy and/or post-parturition, and higher faecal progestagen metabolite concentrations. These genera had a lower-than-average relative abundance in the gut microbiome. CONCLUSION Our results indicate that many members of the gut microbiome of black rhino are associated with hormone production and breeding success, and some members of the rare microbiota appear to be particularly important. Although the directionality of the relationship is unclear, the variation in gut microbiome communities represents a potential biomarker of reproductive health. We identified four genera that were associated with multiple indicators of reproductive output; these could be candidate probiotics to improve the breeding success of black rhino in zoo-based conservation breeding programmes. Further work is required to understand the efficacy and feasibility of this, either directly through microbial augmentation (e.g. probiotics) or indirectly via dietary manipulation or prebiotics.
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Affiliation(s)
- Rachael E Antwis
- School of Environment and Life Sciences, University of Salford, Salford, UK.
| | - Katie L Edwards
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Bryony Unwin
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Susan L Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Susanne Shultz
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
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128
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Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol 2019; 27:105-117. [DOI: 10.1016/j.tim.2018.11.003] [Citation(s) in RCA: 421] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/06/2018] [Accepted: 11/05/2018] [Indexed: 01/18/2023]
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129
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Trevelline BK, Fontaine SS, Hartup BK, Kohl KD. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc Biol Sci 2019; 286:20182448. [PMID: 30963956 PMCID: PMC6364583 DOI: 10.1098/rspb.2018.2448] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers the effects, both direct and indirect, of anthropogenic disturbances on wildlife physiology and health. A recent surge in research has revealed that host-associated microbiota-the archaeal, bacterial, fungal and viral communities residing on and inside organisms-profoundly influence animal health, and that these microbial communities can be drastically altered by anthropogenic activities. Therefore, conservation practitioners should consider the disruption of host-associated microbial diversity as a serious threat to wildlife populations. Despite the tremendous potential for microbiome research to improve conservation outcomes, few efforts have been made to truly integrate these fields. In this review, we call for the microbial renaissance of conservation biology, where biodiversity of host-associated microbiota is recognized as an essential component of wildlife management practices. Using evidence from the existing literature, we will examine the known effects of anthropogenic activities on the diversity of host-associated microbial communities and integrate approaches for maintaining microbial diversity to successfully achieve conservation objectives.
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Affiliation(s)
- Brian K. Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha S. Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barry K. Hartup
- Department of Conservation Medicine, International Crane Foundation, Baraboo, WI, USA
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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130
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Comizzoli P, Power M. Reproductive Microbiomes in Wild Animal Species: A New Dimension in Conservation Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1200:225-240. [PMID: 31471799 DOI: 10.1007/978-3-030-23633-5_8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Communities of microbes have coevolved in animal organisms and are found in almost every part of the body. Compositions of those communities (microbiota) as well as their genomes and genes (microbiomes) are critical for functional regulations of the body organ systems-the digestive or 'gut' microbiome being the most described so far. Based on extensive research in humans, microbiomes in the reproductive tract may play a role in reproductive functions and pregnancy. However, in wild animal species, those microbiomes have been poorly studied, and as a result, little is known about their involvement in fertility or parental/offspring health. This emerging research area is highly relevant to conservation biology from captive breeding management to successful reintroduction or maintenance of wild populations. The objective of this chapter is to review current knowledge about reproductive microbiomes in healthy wild animal species. While recognizing the current technical limits of microbial identification in all animal species, we also explore the link between microbial communities (within female or male reproductive systems) and fertility, from conception to birth outcome. In addition, it is critical to understanding how reproductive microbiomes are affected by environmental factors (including captivity, contact with other individuals, or changes in the ecosystem) to optimize conservation efforts. Thus, reproductive microbiomes represent a novel dimension in conservation biology that will likely gain importance in the future.
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Affiliation(s)
- Pierre Comizzoli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.
| | - M Power
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
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Monterroso P, Godinho R, Oliveira T, Ferreras P, Kelly MJ, Morin DJ, Waits LP, Alves PC, Mills LS. Feeding ecological knowledge: the underutilised power of faecal
DNA
approaches for carnivore diet analysis. Mamm Rev 2018. [DOI: 10.1111/mam.12144] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Teresa Oliveira
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM) Ronda de Toledo 12 Ciudad Real 13071 Spain
| | - Marcella J. Kelly
- Department of Fish and Wildlife ConservationVirginia Tech 146 Cheatham Hall Blacksburg VA 24061‐0321 USA
| | - Dana J. Morin
- Cooperative Wildlife Research LaboratorySouthern Illinois University 251 Lincoln Drive Carbondale IL 62901 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Paulo C. Alves
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
- Office of Research and Creative ScholarshipUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
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Kristensen TN, Ketola T, Kronholm I. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 2018; 1476:5-22. [PMID: 30259990 DOI: 10.1111/nyas.13974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 08/24/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Environments are changing rapidly, and to cope with these changes, organisms have to adapt. Adaptation can take many shapes and occur at different speeds, depending on the type of response, the trait, the population, and the environmental conditions. The biodiversity crisis that we are currently facing illustrates that numerous species and populations are not capable of adapting with sufficient speed to ongoing environmental changes. Here, we discuss current knowledge on the ability of animals and plants to adapt to environmental stress on different timescales, mainly focusing on thermal stress and ectotherms. We discuss within-generation responses that can be fast and induced within minutes or hours, evolutionary adaptations that are often slow and take several generations, and mechanisms that lay somewhere in between and that include epigenetic transgenerational effects. To understand and predict the impacts of environmental change and stress on biodiversity, we suggest that future studies should (1) have an increased focus on understanding the type and speed of responses to fast environmental changes; (2) focus on the importance of environmental fluctuations and the predictability of environmental conditions on adaptive capabilities, preferably in field studies encompassing several fitness components; and (3) look at ecosystem responses to environmental stress and their resilience when disturbed.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | - Tarmo Ketola
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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133
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Wenzel MA, Douglas A, Piertney SB. Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons). PLoS One 2018; 13:e0202212. [PMID: 30157257 PMCID: PMC6114722 DOI: 10.1371/journal.pone.0202212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/29/2018] [Indexed: 02/05/2023] Open
Abstract
The increasingly recognised effects of microbiomes on the eco-evolutionary dynamics of their hosts are promoting a view of the "hologenome" as an integral host-symbiont evolutionary entity. For example, sex-ratio distorting reproductive parasites such as Wolbachia are well-studied pivotal drivers of invertebrate reproductive processes, and more recent work is highlighting novel effects of microbiome assemblages on host mating behaviour and developmental incompatibilities that underpin or reinforce reproductive isolation processes. However, examining the hologenome and its eco-evolutionary effects in natural populations is challenging because microbiome composition is considerably influenced by environmental factors. Here we illustrate these challenges in a sympatric species complex of intertidal isopods (Jaera albifrons spp.) with pervasive sex-ratio distortion and ecological and behavioural reproductive isolation mechanisms. We deep-sequence the bacterial 16S rRNA gene among males and females collected in spring and summer from two coasts in north-east Scotland, and examine microbiome composition with a particular focus on reproductive parasites. Microbiomes of all species were diverse (overall 3,317 unique sequences among 3.8 million reads) and comprised mainly Proteobacteria and Bacteroidetes taxa typical of the marine intertidal zone, in particular Vibrio spp. However, we found little evidence of the reproductive parasites Wolbachia, Rickettsia, Spiroplasma and Cardinium, suggesting alternative causes of sex-ratio distortion. Notwithstanding, a significant proportion of the variance in microbiome composition among samples was explained by sex (14.1 %), nested within geographic (26.9 %) and seasonal (39.6 %) variance components. The functional relevance of this sex signal was difficult to ascertain given the absence of reproductive parasites, the ephemeral nature of the species assemblages and substantial environmental variability. These results establish the Jaera albifrons species complex as an intriguing system for examining the effects of microbiomes on reproductive processes and speciation, and highlight the difficulties associated with snapshot assays of microbiome composition in dynamic and complex environments.
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Affiliation(s)
- Marius A. Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Stuart B. Piertney
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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134
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Ma Z(S, Li L, Li W. Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity. Front Microbiol 2018; 9:1619. [PMID: 30131772 PMCID: PMC6090070 DOI: 10.3389/fmicb.2018.01619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023] Open
Abstract
A human body hosts a relatively independent microbiome including five major regional biomes (i.e., airway, oral, gut, skin, and urogenital). Each of them may possess different regional characteristics with important implications to our health and diseases (i.e., so-termed microbiome associated diseases). Nevertheless, these regional microbiomes are connected with each other through diffusions and migrations. Here, we investigate the within-body (intra-individual) distribution feature of microbiome diversity via diversity area relationship (DAR) modeling, which, to the best of our knowledge, has not been systematically studied previously. We utilized the Hill numbers for measuring alpha and beta-diversities and built 1,200 within-body DAR models with to date the most comprehensive human microbiome datasets of 18 sites from the human microbiome project (HMP) cohort. We established the intra-DAR profile (z-q pattern: the diversity scaling parameter z of the power law (PL) at diversity order q = 0-3), intra-PDO (pair-wise diversity overlap) profile (g-q), and intra-MAD (maximal accrual diversity) profile (D max-q) for the within-body biogeography of the human microbiome. These profiles constitute the "maps" of the within-body biogeography, and offer important insights on the within-body distribution of the human microbiome. Furthermore, we investigated the heterogeneity among individuals in their biogeography parameters and found that there is not an "average Joe" that can represent majority of individuals in a cohort or population. For example, we found that most individuals in the HMP cohort have relatively lower maximal accrual diversity (MAD) or in the "long tail" of the so-termed power law distribution. In the meantime, there are a small number of individuals in the cohort who possess disproportionally higher MAD values. These findings may have important implications for personalized medicine of the human microbiome associated diseases in practice, besides their theoretical significance in microbiome research such as establishing the baseline for the conservation of human microbiome.
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Affiliation(s)
- Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Wendy Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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135
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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136
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Reich I, Ijaz UZ, Gormally M, Smith CJ. 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Sci Rep 2018; 8:10402. [PMID: 29991804 PMCID: PMC6039444 DOI: 10.1038/s41598-018-28720-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/25/2018] [Indexed: 01/20/2023] Open
Abstract
The EU-protected slug Geomalacus maculosus Allman occurs only in the West of Ireland and in northern Spain and Portugal. We explored the microbial community found within the faeces of Irish specimens with a view to determining whether a core microbiome existed among geographically isolated slugs which could give insight into the adaptations of G. maculosus to the available food resources within its habitat. Faecal samples of 30 wild specimens were collected throughout its Irish range and the V3 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq. To investigate the influence of diet on the microbial composition, faecal samples were taken and sequenced from six laboratory reared slugs which were raised on two different foods. We found a widely diverse microbiome dominated by Enterobacteriales with three core OTUs shared between all specimens. While the reared specimens appeared clearly separated by diet in NMDS plots, no significant difference between the slugs fed on the two different diets was found. Our results indicate that while the majority of the faecal microbiome of G. maculosus is probably dependent on the microhabitat of the individual slugs, parts of it are likely selected for by the host.
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Affiliation(s)
- Inga Reich
- Applied Ecology Unit, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, Scotland, UK.
| | - Mike Gormally
- Applied Ecology Unit, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Cindy J Smith
- School of Engineering, University of Glasgow, Glasgow, Scotland, UK.
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137
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Zeng Y, Zeng D, Zhou Y, Niu L, Deng J, Li Y, Pu Y, Lin Y, Xu S, Liu Q, Xiong L, Zhou M, Pan K, Jing B, Ni X. Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda. Front Microbiol 2018; 9:1411. [PMID: 30026734 PMCID: PMC6042058 DOI: 10.3389/fmicb.2018.01411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia-Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia-Shigella.
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Affiliation(s)
- Yan Zeng
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Jiabo Deng
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Yang Li
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Yang Pu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Yicen Lin
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Shuai Xu
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Qian Liu
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Lvchen Xiong
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Mengjia Zhou
- Sichuan Animal Science Research Institute, Chengdu, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
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138
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Simons AL, Churches N, Nuzhdin S. High turnover of faecal microbiome from algal feedstock experimental manipulations in the Pacific oyster (Crassostrea gigas). Microb Biotechnol 2018; 11:848-858. [PMID: 29749083 PMCID: PMC6116748 DOI: 10.1111/1751-7915.13277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022] Open
Abstract
The composition of digestive microbiomes is known to be a significant factor in the health of a variety of hosts, including animal livestock. Therefore, it is important to ascertain how readily the microbiome can be significantly altered. To this end, the role of changing diet on the digestive microbiome of the Pacific oyster (Crassostrea gigas) was assessed via weekly faecal sampling. Over the course of 12 weeks, isolated individual oysters were fed either a control diet of Tetraselmis algae (Tet) or a treatment diet which shifted in composition every 4 weeks. Weekly faecal samples from all oysters were taken to characterize their digestive bacterial microbiota. Concurrent weekly sampling of the algal feed cultures was performed to assess the effect of algal microbiomes, independent of the algal type, on the microbiomes observed in the oyster samples. Changing the algal feed was found to be significantly associated with changes in the faecal microbiome over a timescale of weeks between control and treatment groups. No significant differences between individual microbiomes were found within control and treatment groups. This suggests the digestive microbiome of the Pacific oyster can be quickly and reproducibly manipulated.
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Affiliation(s)
- Ariel Levi Simons
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
| | - Nathan Churches
- Molecular and Computation Biology, University of Southern California Dana and David Dornsife College of Letters Arts and Sciences, Los Angeles, CA, USA
| | - Sergey Nuzhdin
- Molecular and Computation Biology, University of Southern California Dana and David Dornsife College of Letters Arts and Sciences, Los Angeles, CA, USA
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139
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The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition. Sci Rep 2018; 8:3214. [PMID: 29453448 PMCID: PMC5816653 DOI: 10.1038/s41598-018-21117-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Nutrition and health of northern white-cheeked gibbons (Nomascus leucogenys) are considered to be primarily influenced by the diversity of their gastrointestinal tract (GIT) microbiota. However, the precise composition, structure, and role of the gibbon GIT microbiota remain unclear. Microbial communities from the GITs of gibbons from Nanning (NN, n = 36) and Beijing (BJ, n = 20) Zoos were examined through 16S rRNA sequencing. Gibbon’s GITs microbiomes contained bacteria from 30 phyla, dominated by human-associated microbial signatures: Firmicutes, Bacteroidetes, and Proteobacteria. Microbial species richness was markedly different between adult gibbons (>8 years) under distinct captive conditions. The relative abundance of 14 phyla varied significantly in samples of adults in BJ versus NN. Among the age groups examined in NN, microbiota of adult gibbons had greater species variation and richer community diversity than microbiota of nursing young (<6 months) and juveniles (2–5 years). Age-dependent increases in the relative abundances of Firmicutes and Fibrobacteres were detected, along with simultaneous increases in dietary fiber intake. A few differences were detected between sex cohorts in NN, suggesting a very weak correlation between sex and GIT microbiota. This study is the first to taxonomically identify gibbon’s GITs microbiota confirming that microbiota composition varies with age and captive condition.
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140
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Diversity and metabolic potential of the microbiota associated with a soil arthropod. Sci Rep 2018; 8:2491. [PMID: 29410494 PMCID: PMC5802828 DOI: 10.1038/s41598-018-20967-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/24/2018] [Indexed: 01/08/2023] Open
Abstract
Springtails are important members of the soil fauna and play a key role in plant litter decomposition, for example through stimulation of the microbial activity. However, their interaction with soil microorganisms remains poorly understood and it is unclear which microorganisms are associated to the springtail (endo) microbiota. Therefore, we assessed the structure of the microbiota of the springtail Orchesella cincta (L.) using 16S rRNA gene amplicon sequencing. Individuals were sampled across sites in the field and the microbiota and in particular the endomicrobiota were investigated. The microbiota was dominated by the families of Rickettsiaceae, Enterobacteriaceae and Comamonadaceae and at the genus level the most abundant genera included Rickettsia, Chryseobacterium, Pseudomonas, and Stenotrophomonas. Microbial communities were distinct for the interior of the springtails for measures of community diversity and exhibited structure according to collection sites. Functional analysis of the springtail bacterial community suggests that abundant members of the microbiota may be associated with metabolism including decomposition processes. Together these results add to the understanding of the microbiota of springtails and interaction with soil microorganisms including their putative functional roles.
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141
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Williams CL, Caraballo-Rodríguez AM, Allaband C, Zarrinpar A, Knight R, Gauglitz JM. Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2019.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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142
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Koo H, Hakim JA, Morrow CD, Andersen DT, Bej AK. Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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143
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Moghadam NN, Thorshauge PM, Kristensen TN, de Jonge N, Bahrndorff S, Kjeldal H, Nielsen JL. Strong responses of Drosophila melanogaster microbiota to developmental temperature. Fly (Austin) 2017; 12:1-12. [PMID: 29095113 DOI: 10.1080/19336934.2017.1394558] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Physiological responses to changes in environmental conditions such as temperature may partly arise from the resident microbial community that integrates a wide range of bio-physiological aspects of the host. In the present study, we assessed the effect of developmental temperature on the thermal tolerance and microbial community of Drosophila melanogaster. We also developed a bacterial transplantation protocol in order to examine the possibility of reshaping the host bacterial composition and assessed its influence on the thermotolerance phenotype. We found that the temperature during development affected thermal tolerance and the microbial composition of male D. melanogaster. Flies that developed at low temperature (13°C) were the most cold resistant and showed the highest abundance of Wolbachia, while flies that developed at high temperature (31°C) were the most heat tolerant and had the highest abundance of Acetobacter. In addition, feeding newly eclosed flies with bacterial suspensions from intestines of flies developed at low temperatures changed the heat tolerance of recipient flies. However, we were not able to link this directly to a change in the host bacterial composition.
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Affiliation(s)
- Neda N Moghadam
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark
| | - Pia Mai Thorshauge
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark
| | - Torsten N Kristensen
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark.,b Department of Bioscience , Aarhus University , C.F. Møllers Allé, Aarhus C, Denmark
| | - Nadieh de Jonge
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark
| | - Simon Bahrndorff
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark
| | - Henrik Kjeldal
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark
| | - Jeppe Lund Nielsen
- a Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H, Aalborg E, Denmark
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144
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Tiede J, Scherber C, Mutschler J, McMahon KD, Gratton C. Gut microbiomes of mobile predators vary with landscape context and species identity. Ecol Evol 2017; 7:8545-8557. [PMID: 29075470 PMCID: PMC5648672 DOI: 10.1002/ece3.3390] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/19/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
Landscape context affects predator–prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.
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Affiliation(s)
- Julia Tiede
- Institute of Landscape Ecology University of Muenster Muenster Germany.,Department of Crop Sciences University of Goettingen Goettingen Germany.,Department of Entomology University of Wisconsin-Madison Madison WI USA
| | - Christoph Scherber
- Institute of Landscape Ecology University of Muenster Muenster Germany.,Department of Crop Sciences University of Goettingen Goettingen Germany
| | - James Mutschler
- Departments of Civil and Environmental Engineering and Bacteriology University of Wisconsin-Madison Madison WI USA
| | - Katherine D McMahon
- Departments of Civil and Environmental Engineering and Bacteriology University of Wisconsin-Madison Madison WI USA
| | - Claudio Gratton
- Department of Entomology University of Wisconsin-Madison Madison WI USA
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145
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Kohl KD, Carey HV. A place for host-microbe symbiosis in the comparative physiologist's toolbox. ACTA ACUST UNITED AC 2017; 219:3496-3504. [PMID: 27852759 DOI: 10.1242/jeb.136325] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Abstract
Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host-microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables - including sampling regime, environmental parameters, host metadata and analytical methods - can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 53705, USA
| | - Hannah V Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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146
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Hernández-Gómez O, Hoverman JT, Williams RN. Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders ( Cryptobranchus alleganiensis alleganiensis). Front Microbiol 2017; 8:1379. [PMID: 28785252 PMCID: PMC5519570 DOI: 10.3389/fmicb.2017.01379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/07/2017] [Indexed: 12/29/2022] Open
Abstract
Multicellular hosts maintain complex associations with microbial communities. While microbial communities often serve important functional roles for their hosts, our understanding of the local and regional processes that structure these communities remains limited. Metacommunity analyses provide a promising tool for investigating mechanisms shaping microbiome heterogeneity, which is essential for predicting functional variation between hosts. Using a metacommunity framework, we examined heterogeneity in the skin microbiome of the eastern hellbender (Cryptobranchus alleganiensis alleganiensis). Hellbenders are broadly distributed throughout river systems in the eastern United States, but are present in specific environmental locations throughout their range. The large range of the species and history of population fragmentation suggest that local and regional processes contribute to the distribution of cutaneous symbiont diversity. Therefore, we characterized the skin and environmental bacterial communities at eight rivers throughout the range of the species. We observed variation among hellbender populations in skin microbial community diversity and proportion of shared operational taxonomic units (OTUs) between animal and river water communities. Among populations sampled, we noted significant clumped OTU turnover (i.e., Clementsian structure) resulting in unique cutaneous communities. In addition, we observed a significant positive correlation between skin community divergence and hellbender population genetic divergence. Host-population skin community dissimilarity did not correlate strongly with distance between sampling locations, indicating a weak spatial effect on the distribution of symbionts. These results suggest that species sorting mechanisms (i.e., local processes) structure local skin microbial communities in hellbenders. The variation in skin community composition observed among host populations foreshadows a similar pattern in important functional characteristics (e.g., resistance to dysbiosis). Future work should focus on investigating forces shaping microbiome structure in eastern hellbenders, examining functional variation among populations, and evaluating effectiveness of microbiome management recommendations.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, West LafayetteIN, United States
| | - Jason T Hoverman
- Department of Forestry and Natural Resources, Purdue University, West LafayetteIN, United States
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West LafayetteIN, United States
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147
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Abstract
All humans, animals, and plants are holobionts. Holobionts comprise the host and a myriad of interacting microorganisms-the microbiota. The hologenome encompasses the genome of the host plus the composite of all microbial genomes (the microbiome). In health, there is a fine-tuned and resilient equilibrium within the members of the microbiota and between them and the host. This relative stability is maintained by a high level of microbial diversity, a delicate bio-geographic distribution of microorganisms, and a sophisticated and intricate molecular crosstalk among the multiple components of the holobiont. Pathobionts are temporarily benign microbes with the potential, under modified ecosystem conditions, to become key players in disease. Pathobionts may be endogenous, living for prolonged periods of time inside or on the host, or exogenous, invading the host during opportunistic situations. In both cases, the end result is the transformation of the beneficial microbiome into a health-perturbing pathobiome. We hypothesize that probably all diseases of holobionts, acute or chronic, infectious or non-infectious, and regional or systemic, are characterized by a perturbation of the healthy microbiome into a diseased pathobiome.
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Affiliation(s)
- Silvio D Pitlik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Omry Koren
- Faculty of Medicine, Bar Ilan University, Safed, Israel.
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148
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Menke S, Gillingham MAF, Wilhelm K, Sommer S. Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research. Front Microbiol 2017; 8:102. [PMID: 28197142 PMCID: PMC5281576 DOI: 10.3389/fmicb.2017.00102] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/13/2017] [Indexed: 02/01/2023] Open
Abstract
The investigation of wildlife gastrointestinal microbiomes by next-generation sequencing approaches is a growing field in microbial ecology and conservation. Such studies often face difficulties in sample preservation if neither freezing facilities nor liquid nitrogen (LQN) are readily available. Thus, in order to prevent microbial community changes because of bacterial growth after sampling, preservation buffers need to be applied to samples. However, the amount of microbial community variation attributable to the different preservation treatments and potentially affecting biological interpretation is hardly known. Here, we sampled feces of 11 sheep (Ovis aries sp.) by using swabs and analyzed the effect of air-drying, an inexpensive self-made nucleic acid preservation buffer (NAP), DNA/RNA Shield™, and RNAlater®, each together with freezing (for 10 days) or storing at room temperature (for 10 days) prior to 16S rRNA gene high-throughput sequencing to determine bacterial communities. Results revealed that the proportions of operational taxonomic units (OTUs) belonging to a bacterial phylum were affected by the preservation treatments, and that alpha diversities [observed OTUs, Shannon index, and phylogenetic diversity (PD)] were lower in all preservation treatments than in samples taken by forensic swabs and immediately frozen which is considered as the favored preservation treatment in the absence of any logistic constraints. Overall, NAP had better preservation qualities than RNAlater® and DNA/RNA Shield™ making this self-made buffer a valuable solution in wildlife microbiome studies.
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Affiliation(s)
- Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
| | - Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
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149
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Bahrndorff S, de Jonge N, Skovgård H, Nielsen JL. Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms. PLoS One 2017; 12:e0169753. [PMID: 28081167 PMCID: PMC5232358 DOI: 10.1371/journal.pone.0169753] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 12/21/2016] [Indexed: 11/18/2022] Open
Abstract
The housefly feeds and reproduces in animal manure and decaying organic substances and thus lives in intimate association with various microorganisms including human pathogens. In order to understand the variation and association between bacteria and the housefly, we used 16S rRNA gene amplicon sequencing to describe bacterial communities of 90 individual houseflies collected within and between ten dairy farms in Denmark. Analysis of gene sequences showed that the most abundant classes of bacteria found across all sites included Bacilli, Clostridia, Actinobacteria, Flavobacteria, and all classes of Proteobacteria and at the genus level the most abundant genera included Corynebacterium, Lactobacillus, Staphylococcus, Vagococcus, Weissella, Lactococcus, and Aerococcus. Comparison of the microbiota of houseflies revealed a highly diverse microbiota compared to other insect species and with most variation in species richness and diversity found between individuals, but not locations. Our study is the first in-depth amplicon sequencing study of the housefly microbiota, and collectively shows that the microbiota of single houseflies is highly diverse and differs between individuals likely to reflect the lifestyle of the housefly. We suggest that these results should be taken into account when addressing the transmission of pathogens by the housefly and assessing the vector competence variation under natural conditions.
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Affiliation(s)
- Simon Bahrndorff
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Henrik Skovgård
- Department of Agroecology, University of Aarhus, Slagelse, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
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