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Khadem S, Berry D, Al-Khlifeh E. Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan. Parasit Vectors 2024; 17:358. [PMID: 39180136 PMCID: PMC11342738 DOI: 10.1186/s13071-024-06451-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV). METHODS We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity. RESULTS Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p = 0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions. CONCLUSIONS This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.
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Affiliation(s)
- Sanaz Khadem
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Enas Al-Khlifeh
- Laboratory of Immunology, Department of Medical Laboratory Science, Al-Balqa Applied University, Al-Salt, Jordan.
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Liyanagama I, Oh S, Choi JH, Yi MH, Kim M, Yun S, Kang D, Kim SL, Ojeda Ayala MG, Odua F, Yong TS, Kim JY. Metabarcoding study of potential pathogens and zoonotic risks associated with dog feces in Seoul, South Korea. PLoS Negl Trop Dis 2024; 18:e0012441. [PMID: 39196875 PMCID: PMC11355564 DOI: 10.1371/journal.pntd.0012441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/30/2024] Open
Abstract
BACKGROUND A significant portion of South Korea's population, approximately a quarter, owns pets, with dogs being the most popular choice among them. However, studies analyzing the fecal organism communities of dogs in South Korea are lacking, and limited efforts have been exerted to identify pathogens with potential zoonotic implications. Therefore, this study aimed to investigate potential pathogens using metabarcoding analysis and evaluate the risk of zoonotic diseases in dog feces in Seoul, South Korea. METHODOLOGY Fecal samples were collected from both pet and stray dogs in the Mapo district of Seoul. Next-generation sequencing (NGS) was utilized, employing 16S rRNA amplicon sequencing to identify prokaryotic pathogens, and 18S rRNA amplicon sequencing for eukaryotic pathogens. The data obtained from the QIIME2 pipeline were subjected to various statistical analyses to identify different putative pathogens and their compositions. PRINCIPAL FINDINGS Significant variations in microbiota composition were found between stray and pet dogs, and putative prokaryotic and eukaryotic pathogens were identified. The most prevalent putative bacterial pathogens were Fusobacterium, Helicobacter, and Campylobacter. The most prevalent putative eukaryotic pathogens were Giardia, Pentatrichomonas, and Cystoisospora. Interestingly, Campylobacter, Giardia, and Pentatrichomonas were found to be significantly more prevalent in stray dogs than in pet dogs. The variation in the prevalence of potential pathogens in dog feces could be attributed to environmental factors, including dietary variances and interactions with wildlife, particularly in stray dogs. These factors likely contributed to the observed differences in pathogen occurrence between stray and pet dogs. CONCLUSIONS/SIGNIFICANCE This study offers valuable insights into the zoonotic risks associated with dog populations residing in diverse environments. By identifying and characterizing putative pathogens in dog feces, this research provides essential information on the impact of habitat on dog-associated pathogens, highlighting the importance of public health planning and zoonotic risk management.
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Affiliation(s)
- Isuru Liyanagama
- Department of Global Health and Disease Control, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
- Department of Animal Production and Health, Kandy, Sri Lanka
| | - Singeun Oh
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Tropical Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seodaemun-gu, Seoul, South Korea
| | - Jun Ho Choi
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myung-hee Yi
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myungjun Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sohyeon Yun
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongjun Kang
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soo Lim Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Maria Gloria Ojeda Ayala
- Department of Global Health and Disease Control, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Fred Odua
- Department of Global Health and Disease Control, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
- Production Department, Nakasongola, Uganda
| | - Tai-Soon Yong
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ju Yeong Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Tropical Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seodaemun-gu, Seoul, South Korea
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Bendová B, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Piálek J, Schmiedová L, Kreisinger J. The strength of gut microbiota transfer along social networks and genealogical lineages in the house mouse. FEMS Microbiol Ecol 2024; 100:fiae075. [PMID: 38730559 PMCID: PMC11134300 DOI: 10.1093/femsec/fiae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/23/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The gut microbiota of vertebrates is acquired from the environment and other individuals, including parents and unrelated conspecifics. In the laboratory mouse, a key animal model, inter-individual interactions are severely limited and its gut microbiota is abnormal. Surprisingly, our understanding of how inter-individual transmission impacts house mouse gut microbiota is solely derived from laboratory experiments. We investigated the effects of inter-individual transmission on gut microbiota in two subspecies of house mice (Mus musculus musculus and M. m. domesticus) raised in a semi-natural environment without social or mating restrictions. We assessed the correlation between microbiota composition (16S rRNA profiles), social contact intensity (microtransponder-based social networks), and mouse relatedness (microsatellite-based pedigrees). Inter-individual transmission had a greater impact on the lower gut (colon and cecum) than on the small intestine (ileum). In the lower gut, relatedness and social contact independently influenced microbiota similarity. Despite female-biased parental care, both parents exerted a similar influence on their offspring's microbiota, diminishing with the offspring's age in adulthood. Inter-individual transmission was more pronounced in M. m. domesticus, a subspecies, with a social and reproductive network divided into more closed modules. This suggests that the transmission magnitude depends on the social and genetic structure of the studied population.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | | | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Ľudovít Ďureje
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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Sikder S, Pierce D, Sarkar ER, McHugh C, Quinlan KGR, Giacomin P, Loukas A. Regulation of host metabolic health by parasitic helminths. Trends Parasitol 2024; 40:386-400. [PMID: 38609741 DOI: 10.1016/j.pt.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Obesity is a worldwide pandemic and major risk factor for the development of metabolic syndrome (MetS) and type 2 diabetes (T2D). T2D requires lifelong medical support to limit complications and is defined by impaired glucose tolerance, insulin resistance (IR), and chronic low-level systemic inflammation initiating from adipose tissue. The current preventative strategies include a healthy diet, controlled physical activity, and medication targeting hyperglycemia, with underexplored underlying inflammation. Studies suggest a protective role for helminth infection in the prevention of T2D. The mechanisms may involve induction of modified type 2 and regulatory immune responses that suppress inflammation and promote insulin sensitivity. In this review, the roles of helminths in counteracting MetS, and prospects for harnessing these protective mechanisms for the development of novel anti-diabetes drugs are discussed.
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Affiliation(s)
- Suchandan Sikder
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia.
| | - Doris Pierce
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia
| | - Eti R Sarkar
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia; College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, Queensland 4878, Australia
| | - Connor McHugh
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia; College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, Queensland 4878, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Paul Giacomin
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia; Macrobiome Therapeutics Pty Ltd, Cairns, Queensland 4878, Australia
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia; Macrobiome Therapeutics Pty Ltd, Cairns, Queensland 4878, Australia
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5
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Galla G, Praeg N, Rzehak T, Sprecher E, Colla F, Seeber J, Illmer P, Hauffe HC. Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem. Sci Rep 2024; 14:8715. [PMID: 38622248 PMCID: PMC11018758 DOI: 10.1038/s41598-024-59086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.
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Affiliation(s)
- Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy.
| | - Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Theresa Rzehak
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Else Sprecher
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Filippo Colla
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Julia Seeber
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
- National Biodiversity Future Center (NBFC), S.c.a.r.l., Palermo, Italy
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6
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Scholier T, Lavrinienko A, Kallio ER, Watts PC, Mappes T. Effects of past and present habitat on the gut microbiota of a wild rodent. Proc Biol Sci 2024; 291:20232531. [PMID: 38320610 PMCID: PMC10846943 DOI: 10.1098/rspb.2023.2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
The response of the gut microbiota to changes in the host environment can be influenced by both the host's past and present habitats. To quantify their contributions for two different life stages, we studied the gut microbiota of wild bank voles (Clethrionomys glareolus) by performing a reciprocal transfer experiment with adults and their newborn offspring between urban and rural forests in a boreal ecosystem. Here, we show that the post-transfer gut microbiota in adults did not shift to resemble the post-transfer gut microbiota of animals 'native' to the present habitat. Instead, their gut microbiota appear to be structured by both their past and present habitat, with some features of the adult gut microbiota still determined by the past living environment (e.g. alpha diversity, compositional turnover). By contrast, we did not find evidence of the maternal past habitat (maternal effects) affecting the post-transfer gut microbiota of the juvenile offspring, and only a weak effect of the present habitat. Our results show that both the contemporary living environment and the past environment of the host organism can structure the gut microbiota communities, especially in adult individuals. These data are relevant for decision-making in the field of conservation and wildlife translocations.
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Affiliation(s)
- Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich 8092, Switzerland
| | - Eva R. Kallio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Phillip C. Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
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Li M, Wang S, Zhong L, Heděnec P, Tan Z, Wang R, Chen X, Zhang Y, Tang B, Zhou H, Qu J. Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities. Front Microbiol 2024; 14:1301480. [PMID: 38274745 PMCID: PMC10808676 DOI: 10.3389/fmicb.2023.1301480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Intestinal parasites, such as Eimeria, are common among plateau pika (Ochotona curzoniae). The gut microbiome is an essential driver of the host response to gastrointestinal parasites. However, the effects of intestinal protozoal parasites on the temporal variations in the gut microbiome and behavioral and physiological activities remain unknown. Our study conducted treatments involving experimental feeding of pika with Eimeria oocysts or anticoccidia under laboratory conditions to focus on the parasite-associated alterations in gut bacterial communities, host behavioral activity, physiology, and host-bacteria relationships. The results showed insignificant differences in bacterial community structures among treatments on the basis of Bray-Curtis distance metrics, whereas the patterns of temporal alterations in the bacterial communities were changed by the treatments. Bacterial alpha diversities did not vary with the treatments, and experimental feeding with Eimeria slowed down the decrement rate of alpha diversity. Furthermore, few bacterial members were significantly changed by the treatments-only the genus Ruminococcus and the species Ruminococcus flavefaciens, which were associated with energy metabolism. Experimental feeding with Eimeria modified the temporal variations in the bacterial members, including a lower loss rate of the relative abundance of the dominant families Muribaculaceae and Ruminococcaceae in the group with Eimeria experimental feeding. Moreover, a shifting energy trade-off was suggested by the parasite-induced increments in thyroid hormones (triiodothyronine and tetraiodothyronine) and decrements in exploration behavior in the group with Eimeria feeding. However, we did not detect specific connections between gut bacterial communities and pika behaviors and physiology in terms of energy trade-offs. Further in-depth research is needed to examine the role of Eimeria-modified differences in the gut bacteria of plateau pika.
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Affiliation(s)
- Maoping Li
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Province Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Suqin Wang
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Zhong
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Province Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Petr Heděnec
- Institute for Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Zhaoxian Tan
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| | - Rong Wang
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- School of Life Science, Qinghai Normal University, Xining, China
| | - Xinyang Chen
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingmin Tang
- Grassland Station of Qinghai Province, Xining, China
| | - Huakun Zhou
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Jiapeng Qu
- Sanjiangyuan Grassland Ecosystem National Observation and Research Station, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Province Key Laboratory of Animal Ecological Genomics, Xining, China
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Nemathaga M, Smith RM, Malatji DP. Interactions between the helminth and intestinal microbiome in smallholder chicken farming systems. Front Vet Sci 2023; 10:1309151. [PMID: 38179334 PMCID: PMC10766368 DOI: 10.3389/fvets.2023.1309151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Helminth parasite infections are widespread in smallholder farming systems affecting farmers and livestock animals. There are pathogenic parasites that populate the gut of their host and coexist closely with the gut microbiota. The physical and immunological environment of the gut can be modified by parasites and microbiota creating a wide range of interactions. These interactions modify the development of infection, affects overall host health, and can modify the way a host interacts with its bacterial microbiota. In addition, where there is a high worm burden parasites will affect the health of the host and intestinal tract colonization. This review highlights key studies on the interaction between helminth parasites and the intestinal microbiome to understand the relationship between parasitic worm infections and gut microbiome health in chickens. Finally, the review discusses modulations, molecular changes, and the importance of helminth-microbiome interactions for the host.
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Affiliation(s)
| | | | - Dikeledi P. Malatji
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Science, University of South Africa, Roodepoort, South Africa
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Bu X, Li Z, Zhao W, Zeng Q, Chen Y, Li W, Zou H, Li M, Wang G. Alterations of gut microbiota and short-chain fatty acids induced by Balantidium polyvacuolum in the hindgut of Xenocyprinae fishes providing new insights into the relationship among protozoa, gut microbiota and host. Front Microbiol 2023; 14:1295456. [PMID: 38075928 PMCID: PMC10702975 DOI: 10.3389/fmicb.2023.1295456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/30/2023] [Indexed: 10/16/2024] Open
Abstract
Introduction Parasitic ciliates are protozoans with a global distribution. Along with the gut microbiota, they have formed a micro-ecosystem that affects the host's nutrition, metabolism, and immunity. The interactions and relationships among the three components of this microecosystem (protozoa, gut microbiota, and host) remain only partially understood. Xenocypris fish and the unique ciliate Balantidium polyvacuolum in its hindgut are good materials to study the interplay. Methods In this study, 16S rRNA gene amplicon sequencing and short-chain fatty acids (SCFAs) identification were used. Network was also constructed to understand their relationships. Results We found that the gut microbiota of B. polyvacuolum-infected X. davidi and X. argentea had higher diversity, richness, and evenness than uninfected ones. B. polyvacuolum could lead to an increase of Fusobacterium and Chloroflexi in both X. davidi and X. argentea, while significantly increase the abundance of genera Romboutsia and Clostridium in X. argentea. Besides, B. polyvacuolum could significantly increase the content of total SCFAs and acetic acid in X. davidi and increase the concentrations of propionic, isobutyric and butanoic acids in X. argentea. Furthermore, correlation analyses showed that B. polyvacuolum may alter SCFAs by affecting key SCFAs-producing bacteria such as Clostridium and Cetobacterium. Discussion This study greatly expands our understanding of relationships among B. polyvacuolum, gut microbiota and host Xenocypris fish, which sheds new insights into the mechanism of interaction among protozoa, gut microbiota and host.
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Affiliation(s)
- Xialian Bu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhongyang Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Weishan Zhao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qingwen Zeng
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yushun Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wenxiang Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hong Zou
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Ming Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guitang Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
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10
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Florkowski MR, Hamer SA, Yorzinski JL. Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad096. [PMID: 37586886 DOI: 10.1093/femsec/fiad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.
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Affiliation(s)
- Melanie R Florkowski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
| | - Sarah A Hamer
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Schubot Center for Avian Health, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 701 Farm to Market Service Road, College Station, TX 77840, United States
| | - Jessica L Yorzinski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Department of Ecology and Conservation Biology, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
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11
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Moy M, Diakiw L, Amato KR. Human-influenced diets affect the gut microbiome of wild baboons. Sci Rep 2023; 13:11886. [PMID: 37482555 PMCID: PMC10363530 DOI: 10.1038/s41598-023-38895-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
Industrialized diets that incorporate processed foods and are often high in simple sugars and fats and low in fiber have myriad health impacts, many of which may operate via impacts on the gut microbiota. Examining how these diets affect the gut microbiota can be challenging given that lab animal models experience altered environmental contexts, and human studies include a suite of co-varying cultural and environmental factors that are likely to shape the gut microbiota alongside diet. To complement these approaches, we compare the microbiomes of wild populations of olive baboons (Papio anubis) with differential access to human trash high in processed foods, simple sugars, and fats in Rwanda's Akagera National Park. Baboons are a good model system since their microbiomes are compositionally similar to those of humans. Additionally, this population inhabits a common environment with different social groups consuming qualitatively different amounts of human trash, limiting variation in non-dietary factors. Using 16S rRNA gene amplicon sequencing we find that baboons with unlimited access to human trash have reduced microbial alpha diversity and reduced relative abundances of fiber-degrading taxa such as Ruminococcaceae, Prevotellaceae, and Lachnospiraceae. In contrast, baboons with limited access to human trash have a microbiome more similar to that of baboons with no access to human trash. Our results suggest that while a human-influenced diet high in processed foods, simple sugars, and fats is sufficient to alter the microbiome in wild baboons, there is a minimum threshold of dietary alteration that must occur before the microbiome is substantially altered. We recommend that data from wild primate populations such as these be used to complement ongoing research on diet-microbiome-health interactions in humans and lab animal models.
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Affiliation(s)
- Madelyn Moy
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura Diakiw
- Department of Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA.
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12
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Schmiedová L, Kreisinger J, Kubovčiak J, Těšický M, Martin JF, Tomášek O, Kauzálová T, Sedláček O, Albrecht T. Gut microbiota variation between climatic zones and due to migration strategy in passerine birds. Front Microbiol 2023; 14:1080017. [PMID: 36819027 PMCID: PMC9928719 DOI: 10.3389/fmicb.2023.1080017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Decreasing biotic diversity with increasing latitude is an almost universal macroecological pattern documented for a broad range of taxa, however, there have been few studies focused on changes in gut microbiota (GM) across climatic zones. Methods Using 16S rRNA amplicon profiling, we analyzed GM variation between temperate (Czechia) and tropical (Cameroon) populations of 99 passerine bird species and assessed GM similarity of temperate species migrating to tropical regions with that of residents/short-distance migrants and tropical residents. Our study also considered the possible influence of diet on GM. Results We observed no consistent GM diversity differences between tropical and temperate species. In the tropics, GM composition varied substantially between dry and rainy seasons and only a few taxa exhibited consistent differential abundance between tropical and temperate zones, irrespective of migration behavior and seasonal GM changes. During the breeding season, trans-Saharan migrant GM diverged little from species not overwintering in the tropics and did not show higher similarity to tropical passerines than temperate residents/short-distance migrants. Interestingly, GM of two temperate-breeding trans-Saharan migrants sampled in the tropical zone matched that of tropical residents and converged with other temperate species during the breeding season. Diet had a slight effect on GM composition of tropical species, but no effect on GM of temperate hosts. Discussion Consequently, our results demonstrate extensive passerine GM plasticity, the dominant role of environmental factors in its composition and limited effect of diet.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,*Correspondence: Jakub Kreisinger,
| | - Jan Kubovčiak
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | | | - Oldřich Tomášek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Tereza Kauzálová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Ondřej Sedláček
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
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13
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Boisseau M, Dhorne-Pollet S, Bars-Cortina D, Courtot É, Serreau D, Annonay G, Lluch J, Gesbert A, Reigner F, Sallé G, Mach N. Species interactions, stability, and resilience of the gut microbiota - Helminth assemblage in horses. iScience 2023; 26:106044. [PMID: 36818309 PMCID: PMC9929684 DOI: 10.1016/j.isci.2023.106044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/16/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The nature and strength of interactions entertained among helminths and their host gut microbiota remain largely unexplored. Using 40 naturally infected Welsh ponies, we tracked the gut microbiota-cyathostomin temporal dynamics and stability before and following anthelmintic treatment and the associated host blood transcriptomic response. High shedders harbored 14 species of cyathostomins, dominated by Cylicocyclus nassatus. They exhibited a highly diverse and temporal dynamic gut microbiota, with butyrate-producing Clostridia likely driving the ecosystem steadiness and host tolerance toward cyathostomins infection. However, anthelmintic administration sharply bent the microbial community. It disrupted the ecosystem stability and the time-dependent network of interactions, affecting longer term microbial resilience. These observations highlight how anthelmintic treatments alter the triangular relationship of parasite, host, and gut microbiota and open new perspectives for adding nutritional intervention to current parasite management strategies.
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Affiliation(s)
- Michel Boisseau
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France,IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France
| | - Sophie Dhorne-Pollet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - David Bars-Cortina
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Élise Courtot
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| | - Delphine Serreau
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| | - Gwenolah Annonay
- INRAE, US UMR 1426, Genomic platform, 31326 Castanet-Tolosan, France
| | - Jérôme Lluch
- INRAE, US UMR 1426, Genomic platform, 31326 Castanet-Tolosan, France
| | - Amandine Gesbert
- INRAE, UE Physiologie Animale de l’Orfrasière, 37380 Nouzilly, France
| | - Fabrice Reigner
- INRAE, UE Physiologie Animale de l’Orfrasière, 37380 Nouzilly, France
| | - Guillaume Sallé
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France,Corresponding author
| | - Núria Mach
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France,IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France,Corresponding author
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14
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The impact of the striped field mouse's range expansion on communities of native small mammals. Sci Rep 2023; 13:753. [PMID: 36641462 PMCID: PMC9840622 DOI: 10.1038/s41598-022-26919-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.
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15
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Kim SL, Choi JH, Yi MH, Lee S, Kim M, Oh S, Lee IY, Jeon BY, Yong TS, Kim JY. Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius. Parasit Vectors 2022; 15:486. [PMID: 36564849 PMCID: PMC9789561 DOI: 10.1186/s13071-022-05608-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis. METHODS We conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified. RESULTS Among the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group. CONCLUSIONS This study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.
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Affiliation(s)
- Soo Lim Kim
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Jun Ho Choi
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Myung-hee Yi
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Seogwon Lee
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Myungjun Kim
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Singeun Oh
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - In-Yong Lee
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Bo-Young Jeon
- grid.15444.300000 0004 0470 5454Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, 26493 Republic of Korea
| | - Tai-Soon Yong
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Ju Yeong Kim
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
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16
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Changes in resident microbiota associated with mice susceptibility or resistance to the intestinal trematode Echinostoma caproni. Parasitology 2022; 149:1781-1793. [PMID: 36176223 PMCID: PMC10090781 DOI: 10.1017/s0031182022001366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Echinostoma caproni (Trematoda: Echinostomatidae) is an intestinal trematode with no tissue phases in the definitive host that has been extensively used as an experimental model to study the factors that determine resistance against intestinal helminths. In E. caproni infections in mice, interleukin-25 (IL-25) plays a critical role and it is required for the resistance to infection. However, little is known on the factors that determine its production. Primary E. caproni infection in mice is characterized by the development of chronic infections and elevated worm recovery, in relation to a local Th1 response with elevated production of interferon-γ. However, partial resistance against secondary E. caproni infections in ICR (Institute of Cancer Research) mice is developed after the chemotherapeutic cure of a primary infection and the innately produced IL-25 after pharmacological treatment. In this paper, we analyse the potential role of intestinal microbiota in the production of IL-25, and the subsequent resistance to infection. For this purpose, we analysed the production of IL-25 under conditions of experimental dysbiosis and also the changes in the resident microbiota in primary infections, pharmacological curation and secondary infections. The results obtained showed that resident microbiota play a major role in the production of IL-25 and the appearance of members of the phylum Verrucomicrobia as a consequence of the curation of the primary infection could be related to the partial resistance to secondary infection.
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17
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Doolin ML, Weinstein SB, Dearing MD. PINWORMS ARE ASSOCIATED WITH TAXONOMIC BUT NOT FUNCTIONAL DIFFERENCES IN THE GUT MICROBIOME OF WHITE-THROATED WOODRATS (NEOTOMA ALBIGULA). J Parasitol 2022; 108:408-418. [PMID: 36066907 DOI: 10.1645/22-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Vertebrates rely on their gut microbiome for digestion, and changes to gut microbial communities can impact host health. Past work, primarily in model organisms, has revealed that endoparasites disrupt the gut microbiome. Here, using wild-caught white-throated woodrats (Neotoma albigula), we tested whether naturally acquired parasite infections are associated with different microbiome structure and function. We surveyed wild N. albigula in eastern Utah for gastrointestinal parasites in the spring and fall of 2019, using traditional fecal float methods and testing a PCR-based approach to detect infection. We tested whether the host gut microbiome structure and function differed based on infection with the most prevalent parasite, the pinworm Lamotheoxyuris ackerti. In spring, infected and uninfected animals had significantly different microbiomes, but these differences were not detected in the fall. However, for both sampling periods, infection was associated with differences in particular microbial taxa determined by differential abundance analysis. As N. albigula rely on their microbiomes to digest both fiber and the plant defensive compound oxalate, we compared microbiome function by measuring dry matter digestibility and oxalate intake in infected and uninfected animals. Although we expected infected animals to have reduced fiber degradation and oxalate intake, we found no difference in microbiome function using these assays. This work suggests that parasite effects on the microbiome may be difficult to detect in complex natural systems, and more studies in wild organisms are warranted.
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Affiliation(s)
- Margaret L Doolin
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112
| | - Sara B Weinstein
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112
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18
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Schmid DW, Fackelmann G, Wasimuddin, Rakotondranary J, Ratovonamana YR, Montero BK, Ganzhorn JU, Sommer S. A framework for testing the impact of co-infections on host gut microbiomes. Anim Microbiome 2022; 4:48. [PMID: 35945629 PMCID: PMC9361228 DOI: 10.1186/s42523-022-00198-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 02/07/2023] Open
Abstract
Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.
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19
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Izvekova GI. Parasitic Infections and Intestinal Microbiota: A Review. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022040070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Sun L, Zhu M, Zhang L, Peng M, Li C, Wang L, Wang W, Ma Z, Li S, Zeng W, Yin M, Wang W, Chunyu W. Differences in microbiome of healthy Sprague Dawley rats with Paragonimus proliferus infection and potential pathogenic role of microbes in paragonimiasis. Acta Trop 2022; 233:106578. [PMID: 35779592 DOI: 10.1016/j.actatropica.2022.106578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
Paragonimiasis, which is caused by Paragonimus, is considered to be a neglected tropical disease by the World Health Organization. The pathogenicity of Paragonimus mainly manifests as mechanical damage and immunotoxicity caused by adult worms and larvae. However, microbiota associated with Paragonimus and potential disturbance of host microbiota after infection are unknown. Paragonimus proliferus is a rare species, and its successful infection rate in experimental rats is 100%. In the current study, we compared the microbial community in lung tissues, small intestine contents, and fecal samples from Sprague Dawley (SD) rats with and without P. proliferus infection. To determine the impact of P. proliferus on the microbial community in rats, we identified the microbiota in adult worms of P. proliferus via high-throughput sequencing. Results showed dramatic differences in the composition of microbiota in lung tissues between infected and uninfected rats. Paragonimus metacercariae introduced both environmental and gut microbes into the lung tissues of rats. Many potentially pathogenic microbes were also found in the lung of infected rats. Paragonimus infection increased the chances of potentially pathogenic microbiota invading and colonizing the lungs. However, for the purpose of long-term parasitism, there might be a complex interrelationship between Paragonimus and microorganisms. Our study might shed lights on the understanding of the pathogenicity of Paragonimus.
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Affiliation(s)
- Le Sun
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Min Zhu
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China; Department of Clinical Laboratory, Jiangyou People's Hospital, Mianyang, Sichuan 621700, China
| | - Lei Zhang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Man Peng
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Cuiying Li
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Liming Wang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Weiqun Wang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Zhiqiang Ma
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China; The Third People's Hospital of Kunming, Kunming, Yunnan 650043, China
| | - Shenghao Li
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China; The Third People's Hospital of Kunming, Kunming, Yunnan 650043, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Min Yin
- School of Medicine, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan 650091, China.
| | - Wenlin Wang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China.
| | - Weixun Chunyu
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China.
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Bendová B, Mikula O, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Martin JF, Piálek J, Schmiedová L, Kreisinger J. Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions. FEMS Microbiol Ecol 2022; 98:6620832. [PMID: 35767862 DOI: 10.1093/femsec/fiac078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are therefore an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under semi-natural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of co-divergence with their hosts. Helicobacters represent promising candidates for studying GM-host co-adaptations and the fitness effects of their interactions.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ondřej Mikula
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Dagmar Čížková
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Jaroslav Piálek
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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22
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Watts PC, Mappes T, Tukalenko E, Mousseau TA, Boratyński Z, Møller AP, Lavrinienko A. Interpretation of gut microbiota data in the 'eye of the beholder': A commentary and re-evaluation of data from 'Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone'. J Anim Ecol 2022; 91:1535-1545. [PMID: 35694772 PMCID: PMC9541917 DOI: 10.1111/1365-2656.13667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of ingested fungi (e.g. edible macrofungi, polypores, lichens and ectomycorrhizae) and gut mycobiota (e.g. microfungi and yeasts), which mask the patterns of inter‐ and intraspecific variation in the authentic gut mycobiota. Implying that ‘faecal samples are not an accurate indicator of gut composition’ creates an unnecessary controversy about faecal sampling because the comparison of samples from the caecum and faeces confounds many other possible drivers (including different animals from different locations, sampled in different years) of variation in gut microbiota. It is relevant also that Antwis et al.'s (2021) data lack statistical power to detect an effect of exposure to radionuclides on the gut microbiota because (1) all of their samples of Apodemus mice had experienced a medium or high total absorbed dose rate and (2) they did not collect samples of bank voles (M. glareolus) from replicate contaminated and uncontaminated locations. Discussion of Antwis et al.'s (2021) analysis, especially the claims presented in the Abstract, is important to prevent controversy about the outcome of research on the biological impacts of wildlife inhabiting the CEZ.
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Affiliation(s)
- Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Eugene Tukalenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv, Ukraine
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Zbyszek Boratyński
- CIBIO/InBio, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Anders P Møller
- Laboratoire d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud 11, Orsay Cedex, France
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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23
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Shanebeck KM, Besson AA, Lagrue C, Green SJ. The energetic costs of sub-lethal helminth parasites in mammals: a meta-analysis. Biol Rev Camb Philos Soc 2022; 97:1886-1907. [PMID: 35678252 DOI: 10.1111/brv.12867] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 01/07/2023]
Abstract
Parasites, by definition, have a negative effect on their host. However, in wild mammal health and conservation research, sub-lethal infections are commonly assumed to have negligible health effects unless parasites are present in overwhelming numbers. Here, we propose a definition for host health in mammals that includes sub-lethal effects of parasites on the host's capacity to adapt to the environment and maintain homeostasis. We synthesized the growing number of studies on helminth parasites in mammals to assess evidence for the relative magnitude of sub-lethal effects of infection across mammal taxa based on this expanded definition. Specifically, we develop and apply a framework for organizing disparate metrics of parasite effects on host health and body condition according to their impact on an animal's energetic condition, defined as the energetic burden of pathogens on host physiological and behavioural functions that relate directly to fitness. Applying this framework within a global meta-analysis of helminth parasites in wild, laboratory and domestic mammal hosts produced 142 peer-reviewed studies documenting 599 infection-condition effects. Analysing these data within a multiple working hypotheses framework allowed us to evaluate the relative weighted contribution of methodological (study design, sampling protocol, parasite quantification methods) and biological (phylogenetic relationships and host/parasite life history) moderators to variation in the magnitude of health effects. We found consistently strong negative effects of infection on host energetic condition across taxonomic groups, with unusually low heterogeneity in effect sizes when compared with other ecological meta-analyses. Observed effect size was significantly lower within cross-sectional studies (i.e. observational studies that investigated a sub-set of a population at a single point in time), the most prevalent methodology. Furthermore, opportunistic sampling led to a weaker negative effect compared to proactive sampling. In the model of host taxonomic group, the effect of infection on energetic condition in carnivores was not significant. However, when sampling method was included, it explained substantial inter-study variance; proactive sampling showing a strongly significant negative effect while opportunistic sampling detected only a weak, non-significant effect. This may partly underlie previous assumptions that sub-lethal parasites do not have significant effects on host health. We recommend future studies adopt energetic condition as the framework for assessing parasite effects on wildlife health and provide guidelines for the selection of research protocols, health proxies, and relating infection to fitness.
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Affiliation(s)
- Kyle M Shanebeck
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, Canada
| | - Anne A Besson
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand
| | - Clement Lagrue
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, Canada.,Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand.,Department of Conservation, 265 Princes Street, Dunedin, 9016, New Zealand
| | - Stephanie J Green
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, Canada
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24
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Mason B, Petrzelkova KJ, Kreisinger J, Bohm T, Cervena B, Fairet E, Fuh T, Gomez A, Knauf S, Maloueki U, Modry D, Shirley MH, Tagg N, Wangue N, Pafco B. Gastrointestinal symbiont diversity in wild gorilla: a comparison of bacterial and strongylid communities across multiple localities. Mol Ecol 2022; 31:4127-4145. [PMID: 35661299 DOI: 10.1111/mec.16558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/17/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Western lowland gorillas (Gorilla gorilla gorilla) are Critically Endangered and show continued population decline. Consequently, pressure mounts to better understand their conservation threats and ecology. Gastrointestinal symbionts, such as bacterial and eukaryotic communities, are believed to play vital roles in the physiological landscape of the host. Gorillas host a broad spectrum of eucaryotes, so called parasites, with strongylid nematodes being particularly prevalent. While these communities are partially consistent, they are also shaped by various ecological factors, such as diet or habitat type. To investigate gastrointestinal symbionts of wild western lowland gorillas, we analysed 215 faecal samples from individuals in five distinct localities across the Congo Basin, using high-throughput sequencing techniques. We describe the gut bacterial microbiome and genetic diversity of strongylid communities, including strain-level identification of amplicon sequence variants (ASVs). We identified strongylid ASVs from eight genera and bacterial ASVs from twenty phyla. We compared these communities across localities, with reference to varying environmental factors among populations, finding differences in alpha diversity and community compositions of both gastrointestinal components. Moreover, we also investigated covariation between strongylid nematodes and the bacterial microbiome, finding correlations between strongylid taxa and Prevotellaceae and Rikenellaceae ASVs that were consistent across multiple localities. Our research highlights complexity of the bacterial microbiome and strongylid communities in several gorilla populations and emphasizes potential interactions between these two symbiont communities. This study provides a framework for ongoing research into strongylid nematode diversity, and their interactions with the bacterial microbiome, amongst great apes.
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Affiliation(s)
- Bethan Mason
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences.,Liberec Zoo, Liberec, Czech Republic
| | | | - Torsten Bohm
- African Parks, Odzala-Kokoua National Park, Republic of, Congo
| | | | - Emilie Fairet
- SFM Safari Gabon, Loango National Park, Gabon.,Wildlife Conservation Society, New York, NY, USA
| | | | - Andres Gomez
- Department of Animal Science, University of Minnesota Twin Cities, St. Paul, Minnesota
| | - Sascha Knauf
- Institute of International Animal Health / One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Ulrich Maloueki
- African Parks, Odzala-Kokoua National Park, Republic of, Congo
| | - David Modry
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences.,Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences Prague
| | - Matthew H Shirley
- SFM Safari Gabon, Loango National Park, Gabon.,Institute of Environment, Florida International University, North Miami, FL, USA
| | - Nikki Tagg
- Project Grands Singes, , Centre for Research and Conservation, Royal Zoological Society of Antwerp
| | | | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences
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25
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From germ-free to wild: modulating microbiome complexity to understand mucosal immunology. Mucosal Immunol 2022; 15:1085-1094. [PMID: 36065057 DOI: 10.1038/s41385-022-00562-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 02/04/2023]
Abstract
The gut microbiota influences host responses at practically every level, and as research into host-microbe interactions expands, it is not surprising that we are uncovering similar roles for the microbiota at other barrier sites, such as the lung and skin. Using standard laboratory mice to assess host-microbe interactions, or even host intrinsic responses, can be challenging, as slight variations in the microbiota can affect experimental outcomes. When it comes to designing and selecting an appropriate level of microbial diversity and community structure for colonization of our laboratory rodents, we have more choices available to us than ever before. Here we will discuss the different approaches used to modulate microbial complexity that are available to study host-microbe interactions. We will describe how different models have been used to answer distinct biological questions, covering the entire microbial spectrum, from germ-free to wild.
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26
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Castañeda S, Paniz-Mondolfi A, Ramírez JD. Detangling the Crosstalk Between Ascaris, Trichuris and Gut Microbiota: What´s Next? Front Cell Infect Microbiol 2022; 12:852900. [PMID: 35694539 PMCID: PMC9174645 DOI: 10.3389/fcimb.2022.852900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 11/25/2022] Open
Abstract
Helminth infections remain a global public health issue, particularly in low- and middle-income countries, where roundworms from theTrichuris and Ascaris genera are most prevalent. These geohelminths not only impact human health but most importantly also affect animal well-being, in particular the swine industry. Host-helminth parasite interactions are complex and at the same time essential to understand the biology, dynamics and pathophysiology of these infections. Within these interactions, the immunomodulatory capacity of these helminths in the host has been extensively studied. Moreover, in recent years a growing interest on how helminths interact with the intestinal microbiota of the host has sparked, highlighting how this relationship plays an essential role in the establishment of initial infection, survival and persistence of the parasite, as well as in the development of chronic infections. Identifying the changes generated by these helminths on the composition and structure of the host intestinal microbiota constitutes a field of great scientific interest, since this can provide essential and actionable information for designing effective control and therapeutic strategies. Helminths like Trichuris and Ascaris are a focus of special importance due to their high prevalence, higher reinfection rates, resistance to anthelmintic therapy and unavailability of vaccines. Therefore, characterizing interactions between these helminths and the host intestinal microbiota represents an important approach to better understand the nature of this dynamic interface and explore novel therapeutic alternatives based on management of host microbiota. Given the extraordinary impact this may have from a biological, clinical, and epidemiological public health standpoint, this review aims to provide a comprehensive overview of current knowledge and future perspectives examining the parasite-microbiota interplay and its impact on host immunity.
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Affiliation(s)
- Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Juan David Ramírez, ;
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27
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Marsh KJ, Raulo AM, Brouard M, Troitsky T, English HM, Allen B, Raval R, Venkatesan S, Pedersen AB, Webster JP, Knowles SCL. Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations. Front Microbiol 2022; 13:809735. [PMID: 35547129 PMCID: PMC9083407 DOI: 10.3389/fmicb.2022.809735] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/08/2022] [Indexed: 12/03/2022] Open
Abstract
The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.
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Affiliation(s)
- Kirsty J Marsh
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Cornwall, United Kingdom
| | - Aura M Raulo
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc Brouard
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Tanya Troitsky
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Holly M English
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Bryony Allen
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Rohan Raval
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Saudamini Venkatesan
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy B Pedersen
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Sarah C L Knowles
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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28
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Lutermann H. Socializing in an Infectious World: The Role of Parasites in Social Evolution of a Unique Rodent Family. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.879031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transmission of parasites between hosts is facilitated by close contact of hosts. Consequently, parasites have been proposed as an important constraint to the evolution of sociality accounting for its rarity. Despite the presumed costs associated with parasitism, the majority of species of African mole-rats (Family: Bathyergidae) are social. In fact, only the extremes of sociality (i.e., solitary and singular breeding) are represented in this subterranean rodent family. But how did bathyergids overcome the costs of parasitism? Parasite burden is a function of the exposure and susceptibility of a host to parasites. In this review I explore how living in sealed burrow systems and the group defenses that can be employed by closely related group members can effectively reduce the exposure and susceptibility of social bathyergids to parasites. Evidence suggests that this can be achieved largely by investment in relatively cheap and flexible behavioral rather than physiological defense mechanisms. This also shifts the selection pressure for parasites on successful transmission between group members rather than transmission between groups. In turn, this constrains the evolution of virulence and favors socially transmitted parasites (e.g., mites and lice) further reducing the costs of parasitism for social Bathyergidae. I conclude by highlighting directions for future research to evaluate the mechanisms proposed and to consider parasites as facilitators of social evolution not only in this rodent family but also other singular breeders.
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29
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Relevance of Helminth-Microbiota Interplay in the Host Immune Response. Cell Immunol 2022; 374:104499. [DOI: 10.1016/j.cellimm.2022.104499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
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30
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Guiver E, Galan M, Lippens C, Bellenger J, Faivre B, Sorci G. Increasing helminth infection burden depauperates the diversity of the gut microbiota and alters its composition in mice. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2022; 2:100082. [PMID: 36589866 PMCID: PMC9795360 DOI: 10.1016/j.crpvbd.2022.100082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/29/2022] [Accepted: 02/14/2022] [Indexed: 01/04/2023]
Abstract
The gut microbiota constitutes a diverse community of organisms with pervasive effects on host homeostasis. The diversity and composition of the gut microbiota depend on both intrinsic (host genetics) and extrinsic (environmental) factors. Here, we investigated the reaction norms of fecal microbiota diversity and composition in three strains of mice infected with increasing doses of the gastrointestinal nematode Heligmosomoides polygyrus. We found that α-diversity (bacterial taxonomic unit richness) declined along the gradient of infective doses, and β-diversity (dissimilarity between the composition of the microbiota of uninfected and infected mice) increased as the infective dose increased. We did not find evidence for genotype by environment (host strain by infective dose) interactions, except when focusing on the relative abundance of the commonest bacterial families. A simulation approach also showed that significant genotype by environment interactions would have been hardly found even with much larger sample size. These results show that increasing parasite burden progressively depauperates microbiota diversity and contributes to rapidly change its composition, independently from the host genetic background.
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Affiliation(s)
- Emmanuel Guiver
- Biogéosciences, CNRS UMR 6282, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Maxime Galan
- Centre de Biologie pour la Gestion des Populations, CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 755 Avenue du Campus Agropolis, CS 30016, 34988 Montferrier-sur-Lez Cedex, France
| | - Cédric Lippens
- Biogéosciences, CNRS UMR 6282, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Jérôme Bellenger
- Lipides Nutrition Cancer, INSERM UMR 1231, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Bruno Faivre
- Biogéosciences, CNRS UMR 6282, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Gabriele Sorci
- Biogéosciences, CNRS UMR 6282, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
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31
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Franz M, Whyte L, Atwood TC, Laidre KL, Roy D, Watson SE, Góngora E, McKinney MA. Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions. Sci Rep 2022; 12:522. [PMID: 35017585 PMCID: PMC8752607 DOI: 10.1038/s41598-021-04340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022] Open
Abstract
Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.
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Affiliation(s)
- Megan Franz
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Todd C Atwood
- United States Geological Survey (USGS), Alaska Science Center, University Drive, Anchorage, AK, 99508, USA
| | - Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Greenland Institute of Natural Resources, P.O. Box 570, Nuuk, Greenland
| | - Denis Roy
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Sophie E Watson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK
| | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Melissa A McKinney
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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Adams NE, Becker MA, Edmands S. Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox. Front Microbiol 2021; 12:748323. [PMID: 34925262 PMCID: PMC8672056 DOI: 10.3389/fmicb.2021.748323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.
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Affiliation(s)
- Nicole E Adams
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Madeleine A Becker
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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Barelli C, Donati C, Albanese D, Pafčo B, Modrý D, Rovero F, Hauffe HC. Interactions between parasitic helminths and gut microbiota in wild tropical primates from intact and fragmented habitats. Sci Rep 2021; 11:21569. [PMID: 34732823 PMCID: PMC8566450 DOI: 10.1038/s41598-021-01145-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/18/2021] [Indexed: 02/08/2023] Open
Abstract
The mammalian gastrointestinal tract harbours a highly complex ecosystem composed of a variety of micro- (bacteria, fungi, viruses, protozoans) and macro-organisms (helminths). Although most microbiota research focuses on the variation of single gut components, the crosstalk between components is still poorly characterized, especially in hosts living under natural conditions. We investigated the gut micro-biodiversity (bacteria, fungi and helminths) of 158 individuals of two wild non-human primates, the Udzungwa red colobus (Procolobus gordonorum) and the yellow baboon (Papio cynocephalus). These species have contrasting diets and lifestyles, but live sympatrically in both human-impacted and pristine forests in the Udzungwa Mountains of Tanzania. Using non-invasive faecal pellets, helminths were identified using standard microscopy while bacteria and fungi were characterized by sequencing the V1–V3 variable region of the 16S rRNA gene for bacteria and the ITS1–ITS2 fragment for fungi. Our results show that both diversity and composition of bacteria and fungi are associated with variation in helminth presence. Although interactions differed by habitat type, in both primates we found that Strongyloides was negatively associated and Trichuris was positively associated with bacterial and fungal richness. To our knowledge, this is one of the few studies demonstrating an interaction between helminth and gut microbiota communities in wild non-human primates.
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Affiliation(s)
- Claudia Barelli
- Conservation Genetic Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele All'Adige, Italy. .,Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Claudio Donati
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele All'Adige, Italy
| | - Davide Albanese
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele All'Adige, Italy
| | - Barbora Pafčo
- Department of Pathology and Parasitology, University of Veterinary Sciences, Brno, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - David Modrý
- Department of Pathology and Parasitology, University of Veterinary Sciences, Brno, Czech Republic.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Heidi C Hauffe
- Conservation Genetic Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele All'Adige, Italy
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Martínez-Mota R, Righini N, Mallott EK, Gillespie TR, Amato KR. The relationship between pinworm (Trypanoxyuris) infection and gut bacteria in wild black howler monkeys (Alouatta pigra). Am J Primatol 2021; 83:e23330. [PMID: 34529285 DOI: 10.1002/ajp.23330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/17/2021] [Accepted: 09/04/2021] [Indexed: 12/21/2022]
Abstract
Gut bacteria may coexist with other groups of organisms, such as nematode parasites, that inhabit the gastrointestinal tract of primates; however, the possible effects of endoparasites on bacterial communities are frequently overlooked. Here we explored whether infection with Trypanoxyuris, an oxyurid gastrointestinal parasite, is associated with changes in the gut bacterial community of wild black howler monkeys (Alouatta pigra), by comparing gut bacterial communities of consistently infected individuals and individuals that never tested positive for Trypanoxyuris throughout different months across the year. We additionally controlled for other sources of variation reported to influence the primate microbiome including individual identity, social group, and seasonality. Trypanoxyuris infection was not related to differences in gut bacterial alpha diversity, but was weakly associated with differences in gut bacterial community structure. In contrast, among the covariates considered, both individual identity and social group were more strongly associated with variation in the howler gut bacterial community. Our results suggest that gastrointestinal parasites may be associated, to some extent, with shifts in the gut bacterial communities hosted by free-ranging primates, although a causal link still needs to be established. Further studies of wild primate hosts infected with parasite species with different pathogenicity are needed to better elucidate health-related consequences from the parasite-microbiome interplay.
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Affiliation(s)
- Rodolfo Martínez-Mota
- Centro de Investigaciones Tropicales (CITRO), Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Nicoletta Righini
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición (IICAN), Universidad de Guadalajara, Ciudad Guzmán, Jalisco, Mexico
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Thomas R Gillespie
- Department of Environmental Sciences, Program in Population Biology, Ecology, and Evolutionary Biology, Emory University, Atlanta, Georgia, USA.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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35
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Eleftheriou A. Implications for One Health of Anthelmintic Use in Wildlife Conservation Programs. ECOHEALTH 2021; 18:280-282. [PMID: 34601702 DOI: 10.1007/s10393-021-01556-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Andreas Eleftheriou
- Wildlife Biology Program, University of Montana, 32 Campus Drive, FOR 109, Missoula, MT, 59812, USA.
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36
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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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Lawson MAE, Roberts IS, Grencis RK. The interplay between Trichuris and the microbiota. Parasitology 2021; 148:1-8. [PMID: 34075861 PMCID: PMC8660641 DOI: 10.1017/s0031182021000834] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Parasitic worms are amongst the most common pathogens to infect humans and have a long-established history of inflicting disease in their hosts. There is a large body of evidence that states intestine-dwelling helminths ensure their survival by influencing the host immune response against them. In recent years, it has become apparent that the large and diverse microbial communities that exist in the gastrointestinal (GI) tract of the host and within the parasite itself have a pivotal role in worm survival and persistence. Using a variety of mouse models (including laboratory, germ-free and rewilded mice), there have been new insights into how bacteria and worms interact with each other; this includes the discovery that Trichuris is unable to hatch and/or infect their host in the absence of bacteria, and that these worms contain a Trichuris-specific gut microbiota. These interactions are determined in part by the capacity of the host, gut microbiota and worms to communicate via metabolites such as butyrate, which are microbially derived and have known immunoregulatory properties. By exploring the contribution of gut bacteria to worm infections and the intricate relationship that exists between them, an exciting and emerging field in whipworm parasitology is established.
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Affiliation(s)
- Melissa A. E. Lawson
- Lydia Becker Institute for Immunology and Inflammation, Manchester, M13 9PT, UK
- Wellcome Trust Centre for Cell Matrix Research, Manchester, M13 9PT, UK
- Division of Infection, Immunity and Respiratory Medicine, Manchester, M13 9PT, UK
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Ian S. Roberts
- Lydia Becker Institute for Immunology and Inflammation, Manchester, M13 9PT, UK
- Division of Infection, Immunity and Respiratory Medicine, Manchester, M13 9PT, UK
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Richard K. Grencis
- Lydia Becker Institute for Immunology and Inflammation, Manchester, M13 9PT, UK
- Wellcome Trust Centre for Cell Matrix Research, Manchester, M13 9PT, UK
- Division of Infection, Immunity and Respiratory Medicine, Manchester, M13 9PT, UK
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
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Buchheister S, Bleich A. Health Monitoring of Laboratory Rodent Colonies-Talking about (R)evolution. Animals (Basel) 2021; 11:1410. [PMID: 34069175 PMCID: PMC8155880 DOI: 10.3390/ani11051410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/02/2021] [Accepted: 05/10/2021] [Indexed: 01/15/2023] Open
Abstract
The health monitoring of laboratory rodents is essential for ensuring animal health and standardization in biomedical research. Progress in housing, gnotobiotic derivation, and hygienic monitoring programs led to enormous improvement of the microbiological quality of laboratory animals. While traditional health monitoring and pathogen detection methods still serve as powerful tools for the diagnostics of common animal diseases, molecular methods develop rapidly and not only improve test sensitivities but also allow high throughput analyses of various sample types. Concurrently, to the progress in pathogen detection and elimination, the research community becomes increasingly aware of the striking influence of microbiome compositions in laboratory animals, affecting disease phenotypes and the scientific value of research data. As repeated re-derivation cycles and strict barrier husbandry of laboratory rodents resulted in a limited diversity of the animals' gut microbiome, future monitoring approaches will have to reform-aiming at enhancing the validity of animal experiments. This review will recapitulate common health monitoring concepts and, moreover, outline strategies and measures on coping with microbiome variation in order to increase reproducibility, replicability and generalizability.
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Affiliation(s)
| | - André Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany;
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39
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Sabey KA, Song SJ, Jolles A, Knight R, Ezenwa VO. Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota. THE ISME JOURNAL 2021; 15:1359-1371. [PMID: 33328653 PMCID: PMC8115229 DOI: 10.1038/s41396-020-00855-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/07/2023]
Abstract
Changes in the gut microbiota during pathogen infection are often predicted to influence disease outcomes. However, studies exploring whether pathogens induce microbiota shifts have yielded inconsistent results. This suggests that variation in infection, rather than the presence of infection alone, might shape pathogen-microbiota relationships. For example, most hosts are coinfected with multiple pathogens simultaneously, and hosts vary in how long they are infected, which may amplify or diminish microbial shifts expected in response to a focal pathogen. We used a longitudinal anthelmintic treatment study of free-ranging African buffalo (Syncerus caffer) to examine whether (i) coinfection with bovine tuberculosis (Mycobacterium bovis, TB) and gastrointestinal nematodes, and (ii) the duration of TB infection, modified effects of single pathogens on the gut microbiota. By accounting for the interaction between TB and nematodes, we found that coinfection affected changes in microbial abundance associated with single infections. Furthermore, the duration of TB infection predicted more microbiota variation than the presence of TB. Importantly, coinfection and infection duration had nearly as much influence on microbial patterns as demographic and environmental factors commonly examined in microbiota research. These findings demonstrate that acknowledging infection heterogeneities may be crucial to understanding relationships between pathogens and the gut microbiota.
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Affiliation(s)
- Kate A Sabey
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Anna Jolles
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Vanessa O Ezenwa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
- Odum School of Ecology, University of Georgia, Athens, GA, USA.
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40
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Allen NR, Taylor-Mew AR, Wilkinson TJ, Huws S, Phillips H, Morphew RM, Brophy PM. Modulation of Rumen Microbes Through Extracellular Vesicle Released by the Rumen Fluke Calicophoron daubneyi. Front Cell Infect Microbiol 2021; 11:661830. [PMID: 33959516 PMCID: PMC8096352 DOI: 10.3389/fcimb.2021.661830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
Parasite derived extracellular vesicles (EVs) have been proposed to play key roles in the establishment and maintenance of infection. Calicophoron daubneyi is a newly emerging parasite of livestock with many aspects of its underpinning biology yet to be resolved. This research is the first in-depth investigation of EVs released by adult C. daubneyi. EVs were successfully isolated using both differential centrifugation and size exclusion chromatography (SEC), and morphologically characterized though transmission electron microscopy (TEM). EV protein components were characterized using a GeLC approach allowing the elucidation of comprehensive proteomic profiles for both their soluble protein cargo and surface membrane bound proteins yielding a total of 378 soluble proteins identified. Notably, EVs contained Sigma-class GST and cathepsin L and B proteases, which have previously been described in immune modulation and successful establishment of parasitic flatworm infections. SEC purified C. daubneyi EVs were observed to modulate rumen bacterial populations by likely increasing microbial species diversity via antimicrobial activity. This data indicates EVs released from adult C. daubneyi have a role in establishment within the rumen through the regulation of microbial populations offering new routes to control rumen fluke infection and to develop molecular strategies to improve rumen efficiency.
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Affiliation(s)
- Nathan R Allen
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Aspen R Taylor-Mew
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Toby J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Sharon Huws
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Helen Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Russell M Morphew
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Peter M Brophy
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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41
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Kashinskaya EN, Simonov EP, Andree KB, Vlasenko PG, Polenogova OV, Kiriukhin BA, Solovyev MM. Microbial community structure in a host-parasite system: the case of Prussian carp and its parasitic crustaceans. J Appl Microbiol 2021; 131:1722-1741. [PMID: 33728808 DOI: 10.1111/jam.15071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/27/2021] [Accepted: 03/09/2021] [Indexed: 01/17/2023]
Abstract
AIMS The aim of the study was to investigate the skin microbiota of Prussian carp infested by ectoparasites from the genera Argulus and Lernaea. METHODS AND RESULTS Associated microbiota of skin of Prussian carp and ectoparasites were investigated by sequencing of the V3, V4 hypervariable regions of 16S rRNA using Illumina MiSeq sequencing platform. CONCLUSIONS According to the Spearman rank correlation test, the increasing load of ulcerations of the skin of Prussian carp was weakly negatively correlated with reduction in the abundance of the following taxa: Acrobacter, bacteria C39 (Rhodocyclaceae), Rheinheimera, Comamonadaceae, Helicobacteraceae and Vogesella. In this study, the microbiota of ectoparasites from the genera Lernaea and Argulus were characterized for the first time. The microbiota associated with L. cyprinacea was significantly different from microbial communities of intact skin mucosa of both infested and uninfested fish and skin ulcers (ADONIS, P ≤ 0·05). The microbiota associated with parasitic crustaceans L. cyprinacea were dominated by unclassified bacteria from Comamonadaceae, Aeromonadaceae families and Vogesella. The dominant microbiota of A. foliaceus were represented by Flavobacterium, Corynebacterium and unclassified Comamonadaceae. SIGNIFICANCE AND IMPACT OF THE STUDY Results from these studies indicate that ectoparasites have the potential to alter skin microbiota, which can play a possible role in the transmission of secondary bacterial infections in fish, caused by pathogenic bacteria.
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Affiliation(s)
- E N Kashinskaya
- Research Group of Physiology and Genetics of Hydrobionts, Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - E P Simonov
- Research Group of Physiology and Genetics of Hydrobionts, Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Institute of Environmental and Agricultural Biology, University of Tyumen, Tyumen, Russia
| | - K B Andree
- Instituto de Investigación y Tecnología Agroalimentarias, Cultius Aquàtics, Tarragona, Spain
| | - P G Vlasenko
- Research Group of Physiology and Genetics of Hydrobionts, Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - O V Polenogova
- Research Group of Physiology and Genetics of Hydrobionts, Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - B A Kiriukhin
- Institute of Environmental and Agricultural Biology, University of Tyumen, Tyumen, Russia
| | - M M Solovyev
- Research Group of Physiology and Genetics of Hydrobionts, Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Biological Institute, Tomsk State University, Tomsk, Russia
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42
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Bacterial profiling of Haemonchus contortus gut microbiome infecting Dohne Merino sheep in South Africa. Sci Rep 2021; 11:5905. [PMID: 33723324 PMCID: PMC7961046 DOI: 10.1038/s41598-021-85282-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/26/2021] [Indexed: 11/09/2022] Open
Abstract
A metagenomic approach was used to study the gut microbiome of Haemonchus contortus field strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classified and sexually differentiated using morphometric characters and was further confirmed through molecular identification. We investigated differences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identified between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of different gastrointestinal nematode microbiomes with the host.
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43
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Salgado-Caxito M, Benavides JA, Munita JM, Rivas L, García P, Listoni FJP, Moreno-Switt AI, Paes AC. Risk factors associated with faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli among dogs in Southeast Brazil. Prev Vet Med 2021; 190:105316. [PMID: 33725561 DOI: 10.1016/j.prevetmed.2021.105316] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/24/2021] [Accepted: 02/28/2021] [Indexed: 12/11/2022]
Abstract
Faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R E. coli) in dogs has been reported worldwide and can reduce the effectiveness of treatments against bacterial infections. However, the drivers that influence faecal carriage of ESC-R E. coli in dogs are poorly understood. The aims of this study were to estimate the prevalence of ESC-R E. coli among dogs prior to their admission to a veterinary teaching hospital and to identify risk factors associated with the faecal carriage of ESC-R E. coli. Rectal swabs (n = 130) were collected from dogs and screened for ESC-R E. coli using MacConkey agar supplemented with cefotaxime (2 μg/mL). E. coli species was confirmed by MALDI-TOF and screening of extended-spectrum beta-lactamase (ESBL) genes was conducted by multiplex PCR. Questionnaires were completed by each dog's owner to test several human and dog characteristics associated with ESC-R E. coli. The prevalence of faecal carriage of ESC-R E. coli was 9.2 % and 67 % of ESC-R E. coli isolates harboured ESBL genes including CTX-M alone or in combination with TEM. All ESC-R E. coli isolates were resistant to ceftriaxone, cefpodoxime, and cefotaxime and were susceptible to cefoxitin and carbapenems. The likelihood of carrying ESC-R E. coli was 15 times higher (OR = 14.41 [95 % CI: 1.80-38.02], p < 0.01) if the dog was treated with antibiotics 3-12 months prior to sampling and 8 times higher (OR = 7.96 [95 % CI: 2.96-92.07], p < 0.01) if the dog had direct contact with livestock, but 15 times lower (OR = 0.07 [95 % CI: 0.01-0.32], p < 0.01) if the dog was dewormed during the previous year. Our findings confirm the faecal carriage of ESC-R E. coli in subclinical dogs and call for further investigation regarding the impact of deworming on antibiotic-resistant bacteria in companion animals.
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Affiliation(s)
- Marília Salgado-Caxito
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, Sao Paulo State University (UNESP), Botucatu, Brazil; Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.
| | - Julio A Benavides
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile; Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jose M Munita
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile; Genomics and Resistant Microbes Group, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Lina Rivas
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile; Genomics and Resistant Microbes Group, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Patricia García
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile; Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernando J P Listoni
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Andrea I Moreno-Switt
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile; Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Antonio C Paes
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, Sao Paulo State University (UNESP), Botucatu, Brazil
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Mair I, McNeilly TN, Corripio-Miyar Y, Forman R, Else KJ. Embracing nature's complexity: Immunoparasitology in the wild. Semin Immunol 2021; 53:101525. [PMID: 34785137 PMCID: PMC8713030 DOI: 10.1016/j.smim.2021.101525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/12/2022]
Abstract
A wealth of research is dedicated to understanding how resistance against parasites is conferred and how parasite-driven pathology is regulated. This research is in part driven by the hope to better treatments for parasitic diseases of humans and livestock, and in part by immunologists who use parasitic infections as biomedical tools to evoke physiological immune responses. Much of the current mechanistic knowledge has been discovered in laboratory studies using model organisms, especially the laboratory mouse. However, wildlife are also hosts to a range of parasites. Through the study of host-parasite interactions in these non-laboratory systems we can gain a deeper understanding of parasite immunology in a more natural, complex environment. With a focus on helminth parasites, we here explore the insights gained into parasite-induced immune responses through (for immunologists) non-conventional experimental systems, and how current core findings from laboratory studies are reflected in these more natural conditions. The quality of the immune response is undoubtedly a central player in susceptibility versus resistance, as many laboratory studies have shown. Yet, in the wild, parasite infections tend to be chronic diseases. Whilst reading our review, we encourage the reader to consider the following questions which may (only) be answered by studying naturally occurring parasites in the wild: a) what type of immune responses are mounted against parasites in different hosts in the wild, and how do they vary within an individual over time, between individuals of the same species and between species? b) can we use wild or semi-wild study systems to understand the evolutionary drivers for tolerance versus resistance towards a parasite? c) what determines the ability of the host to cope with an infection and is there a link with the type of immune response mounted? d) can we modulate environmental factors to manipulate a wild animal's immune response to parasitic infections, with translation potential for humans, wildlife, and livestock? and e) in context of this special issue, what lessons for Type 2 immunity can we glean from studying animals in their natural environments? Further, we aim to integrate some of the knowledge gained in semi-wild and wild settings with knowledge gained from traditional laboratory-based research, and to raise awareness for the opportunities (and challenges) that come with integrating a multitude of naturally-occurring variables into immunoparasitological research.
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Affiliation(s)
- Iris Mair
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Oxford Road Manchester, M13 9PT, UK.
| | - Tom N McNeilly
- Disease Control Department, Moredun Research Institute, Midlothian, EH26 0PZ, Scotland, UK
| | - Yolanda Corripio-Miyar
- Disease Control Department, Moredun Research Institute, Midlothian, EH26 0PZ, Scotland, UK
| | - Ruth Forman
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Oxford Road Manchester, M13 9PT, UK
| | - Kathryn J Else
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Oxford Road Manchester, M13 9PT, UK.
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Pane S, Sacco A, Iorio A, Romani L, Putignani L. Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota. Int J Mol Sci 2021; 22:ijms22042131. [PMID: 33669932 PMCID: PMC7924877 DOI: 10.3390/ijms22042131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples’ ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.
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Affiliation(s)
- Stefania Pane
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (S.P.); (A.S.)
| | - Anna Sacco
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (S.P.); (A.S.)
| | - Andrea Iorio
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Lorenza Romani
- Immunology and Infectious Diseases Unit, University Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
- Correspondence: ; Tel.: +39-06-6859-4127
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Determinants of Eimeria and Campylobacter infection dynamics in UK domestic sheep: the role of co-infection. Parasitology 2021; 148:623-629. [PMID: 33541446 PMCID: PMC10090772 DOI: 10.1017/s0031182021000044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coccidiosis caused by Eimeria species is a well-recognized disease of livestock. Enteric Eimeria infections are common, but disease usually only manifests when infection intensity is abnormally high. Campylobacter species are important zoonotic enteric bacterial pathogens for which livestock are important reservoir hosts. The diversity and epidemiology of ovine Eimeria and Campylobacter infections on two farms in north-western England were explored through a 24-month survey of shedding in sheep feces. Most animals were infected with at least one of 10 different Eimeria species, among which E. bakuensis and E. ovinoidalis were most common. An animal's age and the season of sampling were associated with the probability and intensity of Eimeria infection. Season of sampling was also associated with the probability of Campylobacter infection. Interestingly, higher intensities of Eimeria infections were significantly more common in animals not co-infected with Campylobacter. We explored the determinants of E. bakuensis and E. ovinoidalis infections, observing that being infected with either significantly increased the likelihood of infection with the other. The prevalence of E. ovinoidalis infections was significantly lower in sheep infected with Campylobacter. Recognition that co-infectors shape the dynamics of parasite infection is relevant to the design of effective infection control programmes.
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Moustafa MAM, Chel HM, Thu MJ, Bawm S, Htun LL, Win MM, Oo ZM, Ohsawa N, Lahdenperä M, Mohamed WMA, Ito K, Nonaka N, Nakao R, Katakura K. Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments. Sci Rep 2021; 11:741. [PMID: 33436882 PMCID: PMC7803949 DOI: 10.1038/s41598-020-80537-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.
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Affiliation(s)
- Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Hla Myet Chel
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - May June Thu
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
- Department of Food and Drug Administration, Ministry of Health and Sports, Zabu Thiri, Nay Pyi Taw, 15011, Myanmar
| | - Saw Bawm
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Mar Mar Win
- Rector Office, University of Veterinary Science, Yezin, Nay Pyi Taw, 15013, Myanmar
| | - Zaw Min Oo
- Department of Extraction, Myanma Timber Enterprise, Insein, Yangon, Myanmar
| | | | - Mirkka Lahdenperä
- Department of Public Health, Turku University Hospital, University of Turku, Turku, Finland
| | | | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan.
| | - Ken Katakura
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
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Kuthyar S, Kowalewski MM, Roellig DM, Mallott EK, Zeng Y, Gillespie TR, Amato KR. Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria. Ecol Evol 2021; 11:45-57. [PMID: 33437414 PMCID: PMC7790644 DOI: 10.1002/ece3.6910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/27/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.
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Affiliation(s)
- Sahana Kuthyar
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
| | - Martin M. Kowalewski
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
- Estación Biológica CorrientesMuseo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN‐CONICET)CorrientesArgentina
| | - Dawn M. Roellig
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention (CDC)AtlantaGAUSA
| | | | - Yan Zeng
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
| | - Thomas R. Gillespie
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
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Eukaryotic and Prokaryotic Microbiota Interactions. Microorganisms 2020; 8:microorganisms8122018. [PMID: 33348551 PMCID: PMC7767281 DOI: 10.3390/microorganisms8122018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.
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50
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Daniels SP, Leng J, Swann JR, Proudman CJ. Bugs and drugs: a systems biology approach to characterising the effect of moxidectin on the horse's faecal microbiome. Anim Microbiome 2020; 2:38. [PMID: 33499996 PMCID: PMC7807906 DOI: 10.1186/s42523-020-00056-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/02/2020] [Indexed: 02/08/2023] Open
Abstract
Background Anthelmintic treatment is a risk factor for intestinal disease in the horse, known as colic. However the mechanisms involved in the onset of disease post anthelmintic treatment are unknown. The interaction between anthelmintic drugs and the gut microbiota may be associated with this observed increase in risk of colic. Little is known about the interaction between gut microbiota and anthelmintics and how treatment may alter microbiome function. The objectives of this study were: To characterise (1) faecal microbiota, (2) feed fermentation kinetics in vitro and (3) metabolic profiles following moxidectin administration to horses with very low (0 epg) adult strongyle burdens. Hypothesis: Moxidectin will not alter (1) faecal microbiota, (2) feed fermentation in vitro, or, (3) host metabolome. Results Moxidectin increased the relative abundance of Deferribacter spp. and Spirochaetes spp. observed after 160 h in moxidectin treated horses. Reduced in vitro fibre fermentation was observed 16 h following moxidectin administration in vivo (P = 0.001), along with lower pH in the in vitro fermentations from the moxidectin treated group. Metabolic profiles from urine samples did not differ between the treatment groups. However metabolic profiles from in vitro fermentations differed between moxidectin and control groups 16 h after treatment (R2 = 0.69, Q2Y = 0.48), and within the moxidectin group between 16 h and 160 h post moxidectin treatment (R2 = 0.79, Q2Y = 0.77). Metabolic profiles from in vitro fermentations and fermentation kinetics both indicated altered carbohydrate metabolism following in vivo treatment with moxidectin. Conclusions These data suggest that in horses with low parasite burdens moxidectin had a small but measurable effect on both the community structure and the function of the gut microbiome.
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Affiliation(s)
- S P Daniels
- School of Equine Management and Science, Royal Agricultural University, Cirencester, Gloucestershire, GL9 6JS, UK. .,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7TE, UK.
| | - J Leng
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7TE, UK
| | - J R Swann
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - C J Proudman
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7TE, UK
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