151
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Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH, Ley RE. Vertebrate host phylogeny influences gut archaeal diversity. Nat Microbiol 2021; 6:1443-1454. [PMID: 34702978 PMCID: PMC8556154 DOI: 10.1038/s41564-021-00980-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 09/16/2021] [Indexed: 01/04/2023]
Abstract
Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Silke Dauser
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sophie Maisch
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chris Walzer
- Wildlife Conservation Society, Bronx, NY, USA.,Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria.,Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, Krems an der Donau, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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152
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Hegg A, Radersma R, Uller T. A field experiment reveals seasonal variation in the
Daphnia
gut microbiome. OIKOS 2021. [DOI: 10.1111/oik.08530] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Reinder Radersma
- Dept of Biology, Lund Univ. Lund Sweden
- Centrum Wiskunde&Informatica Amsterdam the Netherlands
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153
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Xu J, Becker AAMJ, Luo Y, Zhang W, Ge B, Leng C, Wang G, Ding L, Wang J, Fu X, Janssens GPJ. The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves. Front Microbiol 2021; 12:701439. [PMID: 34659139 PMCID: PMC8511826 DOI: 10.3389/fmicb.2021.701439] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
The genomic signature of dog domestication reveals adaptation to a starch-rich diet compared with their ancestor wolves. Diet is a key element to shape gut microbial populations in a direct way as well as through coevolution with the host. We investigated the dynamics in the gut microbiota of dogs when shifting from a starch-rich, processed kibble diet to a nature-like raw meat diet, using wolves as a wild reference. Six healthy wolves from a local zoo and six healthy American Staffordshire Terriers were included. Dogs were fed the same commercial kibble diet for at least 3 months before sampling at day 0 (DC), and then switched to a raw meat diet (the same diet as the wolves) for 28 days. Samples from the dogs were collected at day 1 (DR1), week 1 (DR7), 2 (DR14), 3 (DR21), and 4 (DR28). The data showed that the microbial population of dogs switched from kibble diet to raw diet shifts the gut microbiota closer to that of wolves, yet still showing distinct differences. At phylum level, raw meat consumption increased the relative abundance of Fusobacteria and Bacteroidetes at DR1, DR7, DR14, and DR21 (q < 0.05) compared with DC, whereas no differences in these two phyla were observed between DC and DR28. At genus level, Faecalibacterium, Catenibacterium, Allisonella, and Megamonas were significantly lower in dogs consuming the raw diet from the first week onward and in wolves compared with dogs on the kibble diet. Linear discriminant analysis effect size (LEfSe) showed a higher abundance of Stenotrophomonas, Faecalibacterium, Megamonas, and Lactobacillus in dogs fed kibble diet compared with dogs fed raw diet for 28 days and wolves. In addition, wolves had greater unidentified Lachnospiraceae compared with dogs irrespective of the diets. These results suggested that carbohydrate-fermenting bacteria give way to protein fermenters when the diet is shifted from kibble to raw diet. In conclusion, some microbial phyla, families, and genera in dogs showed only temporary change upon dietary shift, whereas some microbial groups moved toward the microbial profile of wolves. These findings open the discussion on the extent of coevolution of the core microbiota of dogs throughout domestication.
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Affiliation(s)
- Jia Xu
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Anne A M J Becker
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Yu Luo
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Wenfu Zhang
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Bingqian Ge
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Chunqing Leng
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Guyue Wang
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Limin Ding
- Department of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianmei Wang
- Department of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | | | - Geert P J Janssens
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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154
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Thingholm LB, Bang C, Rühlemann MC, Starke A, Sicks F, Kaspari V, Jandowsky A, Frölich K, Ismer G, Bernhard A, Bombis C, Struve B, Rausch P, Franke A. Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans. BMC Microbiol 2021; 21:276. [PMID: 34635060 PMCID: PMC8504008 DOI: 10.1186/s12866-021-02337-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 368 stool samples from 38 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans. By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in westernized humans and platyrrhines, which is probably not only due to diet, but also to the social behavior and structure in these communities. Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammalian fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in westernized communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes, which promote the etiology of chronic diseases.
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Affiliation(s)
- Louise B Thingholm
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Annika Starke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Florian Sicks
- Tierpark Berlin-Friedrichsfelde GmbH, Berlin, Germany
| | - Verena Kaspari
- Tierparkvereinigung Neumuenster e.V, Neumuenster, Germany
| | | | | | | | | | - Claudia Bombis
- Tierpark Hagenbeck Gemeinnützige Gesellschaft mbH, Hamburg, Germany
| | - Barbara Struve
- Leintalzoo Schwaigern, Freudenmühle 1, 74193, Schwaigern, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany. .,University Hospital Schleswig Holstein (UKSH), Campus Kiel, Kiel, Germany.
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155
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Brila I, Lavrinienko A, Tukalenko E, Ecke F, Rodushkin I, Kallio ER, Mappes T, Watts PC. Low-level environmental metal pollution is associated with altered gut microbiota of a wild rodent, the bank vole (Myodes glareolus). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148224. [PMID: 34380250 DOI: 10.1016/j.scitotenv.2021.148224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/08/2021] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
Mining and related industries are a major source of metal pollution. In contrast to the well-studied effects of exposure to metals on animal physiology and health, the impacts of environmental metal pollution on the gut microbiota of wild animals are virtually unknown. As the gut microbiota is a key component of host health, it is important to understand whether metal pollution can alter wild animal gut microbiota composition. Using a combination of 16S rRNA amplicon sequencing and quantification of metal levels in kidneys, we assessed whether multi-metal exposure (the sum of normalized levels of fifteen metals) was associated with changes in gut microbiota of wild bank voles (Myodes glareolus) from two locations in Finland. Exposure to increased metal load was associated with higher gut microbiota species diversity (α-diversity) and altered community composition (β-diversity), but not dispersion. Multi-metal exposure and increased levels of several metals (Cd, Hg, Pb and Se) were associated with differences in the abundance of microbial taxa, especially those within the families Clostridiales vadinBB60 group, Desulfovibrionaceae, Lachnospiraceae, Muribaculaceae and Ruminococcaceae. Our data indicate that even low-level metal pollution can affect the diversity of microbiota and be associated with deterministic differences in composition of host gut microbiota in wild animal populations. These findings highlight the need to study a broader range of metals and their cocktails that are more representative of the types of environmental exposure experienced by wild animals.
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Affiliation(s)
- Ilze Brila
- Ecology and Genetics Unit, University of Oulu, Oulu 90014, Finland; 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
| | - Eugene Tukalenko
- Ecology and Genetics Unit, University of Oulu, Oulu 90014, Finland; Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland; National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv 04050, Ukraine
| | - Frauke Ecke
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Ilia Rodushkin
- Division of Geosciences, Luleå University of Technology, 971 87 Luleå, Sweden; ALS Laboratory Group, ALS Scandinavia AB, Aurorum 10, 977 75 Luleå, Sweden
| | - Eva R Kallio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland; School of Resource Wisdom, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Tapio Mappes
- 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
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156
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Ingala MR, Albert L, Addesso A, Watkins MJ, Knutie SA. Differential effects of elevated nest temperature and parasitism on the gut microbiota of wild avian hosts. Anim Microbiome 2021; 3:67. [PMID: 34600588 PMCID: PMC8487522 DOI: 10.1186/s42523-021-00130-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/22/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Changes in wild animal gut microbiotas may influence host health and fitness. While many studies have shown correlations between gut microbiota structure and external factors, few studies demonstrate causal links between environmental variables and microbiota shifts. Here, we use a fully factorial experiment to test the effects of elevated ambient temperature and natural nest parasitism by nest flies (Protocalliphora sialia) on the gut microbiotas of two species of wild birds, the eastern bluebird (Sialia sialis) and the tree swallow (Tachycineta bicolor). RESULTS We find that bacterial communities from the nestlings of each host species show idiosyncratic responses to both heat and parasitism, with gut microbiotas of eastern bluebirds more disrupted by heat and parasitism than those of tree swallows. Thus, we find that eastern bluebirds are unable to maintain stable associations with their gut bacteria in the face of both elevated temperature and parasitism. In contrast, tree swallow gut microbiotas are not significantly impacted by either heat or nest parasitism. CONCLUSIONS Our results suggest that excess heat (e.g., as a result of climate change) may destabilize natural host-parasite-microbiota systems, with the potential to affect host fitness and survival in the Anthropocene.
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Affiliation(s)
- Melissa R Ingala
- Department of Vertebrate Zoology, National Museum of Natural History, Washington, D.C., USA.
| | - Lauren Albert
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Alyssa Addesso
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Mackenzie J Watkins
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sarah A Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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157
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Zhu D, Lu L, Zhang Z, Qi D, Zhang M, O'Connor P, Wei F, Zhu YG. Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome. ENVIRONMENT INTERNATIONAL 2021; 155:106703. [PMID: 34139588 DOI: 10.1016/j.envint.2021.106703] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/15/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to sub-adult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. Weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.
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Affiliation(s)
- Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lu Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China; College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Zejun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu 611081, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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158
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Wang L, Huang G, Hou R, Qi D, Wu Q, Nie Y, Zuo Z, Ma R, Zhou W, Ma Y, Hu Y, Yang Z, Yan L, Wei F. Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal. MICROBIOME 2021; 9:192. [PMID: 34548111 PMCID: PMC8456708 DOI: 10.1186/s40168-021-01142-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/10/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap. RESULTS Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species. CONCLUSIONS Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.
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Affiliation(s)
- Le Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangping Huang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenqiang Zuo
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, Guangzhou, China
| | - Rui Ma
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Wenliang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yingjie Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Li Yan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, Guangzhou, China.
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159
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Zhu L, Zhang Y, Cui X, Zhu Y, Dai Q, Chen H, Liu G, Yao R, Yang Z. Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense. Microbiol Spectr 2021; 9:e0075621. [PMID: 34406815 PMCID: PMC8552726 DOI: 10.1128/spectrum.00756-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.
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Affiliation(s)
- Lifeng Zhu
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yongyong Zhang
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Xinyuan Cui
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Ran Yao
- College of Life Sciences, Nanjing Norma University, Nanjing, China
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160
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Filek K, Trotta A, Gračan R, Di Bello A, Corrente M, Bosak S. Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta). Anim Microbiome 2021; 3:59. [PMID: 34479653 PMCID: PMC8417999 DOI: 10.1186/s42523-021-00120-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Background Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions. Results We describe the oral and cloacal microbiota of Mediterranean loggerhead sea turtles by 16S rRNA gene sequencing to compare the microbial communities of wild versus turtles in, or after, rehabilitation at the Adriatic Sea rescue centers and clinics. Our results show that the oral microbiota is more sensitive to environmental shifts than the cloacal microbiota, and that it does retain a portion of microbial taxa regardless of the shift from the wild and into rehabilitation. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities. Conclusions We provide the first insights into the oral microbial communities of wild and rehabilitated loggerhead sea turtles, and establish a framework for quick and non-invasive sampling of oral and cloacal microbial communities, useful for the expansion of the sample collection in wild loggerhead sea turtles. Finally, our investigation of effects of captivity on the gut-associated microbial community provides a baseline for studying the impact of husbandry conditions on turtles’ health and survival upon their return to the wild. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00120-5.
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Affiliation(s)
- Klara Filek
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia
| | - Adriana Trotta
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Romana Gračan
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia
| | - Antonio Di Bello
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Marialaura Corrente
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia.
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161
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Yan Y, Ren S, Duan Y, Lu C, Niu Y, Wang Z, Inglis B, Ji W, Zheng Y, Si W. Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson's disease. NPJ Biofilms Microbiomes 2021; 7:69. [PMID: 34475403 PMCID: PMC8413421 DOI: 10.1038/s41522-021-00242-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/02/2021] [Indexed: 02/03/2023] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. However, it is unclear whether microbiota and metabolites have demonstrated changes at early PD due to the difficulties in diagnosis and identification of early PD in clinical practice. In a previous study, we generated A53T transgenic monkeys with early Parkinson's symptoms, including anxiety and cognitive impairment. Here we analyzed the gut microbiota by metagenomic sequencing and metabolites by targeted gas chromatography. The gut microbiota analysis showed that the A53T monkeys have higher degree of diversity in gut microbiota with significantly elevated Sybergistetes, Akkermansia, and Eggerthella lenta compared with control monkeys. Prevotella significantly decreased in A53T transgenic monkeys. Glyceric acid, L-Aspartic acid, and p-Hydroxyphenylacetic acid were significantly elevated, whereas Myristic acid and 3-Methylindole were significantly decreased in A53T monkeys. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (KO0131) and the oxidative phosphorylation reaction (KO2147) were significantly increased in metabolic pathways of A53T monkeys. Our study suggested that the transgenic A53T and α-syn aggregation may affect the intestine microbiota and metabolites of rhesus monkeys, and the identified five compositional different metabolites that are mainly associated with mitochondrial dysfunction may be related to the pathogenesis of PD.
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Affiliation(s)
- Yaping Yan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Shuchao Ren
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yanchao Duan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Chenyu Lu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Zhengbo Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Briauna Inglis
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
| | - Wei Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
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162
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Harrison XA, McDevitt AD, Dunn JC, Griffiths SM, Benvenuto C, Birtles R, Boubli JP, Bown K, Bridson C, Brooks DR, Browett SS, Carden RF, Chantrey J, Clever F, Coscia I, Edwards KL, Ferry N, Goodhead I, Highlands A, Hopper J, Jackson J, Jehle R, da Cruz Kaizer M, King T, Lea JMD, Lenka JL, McCubbin A, McKenzie J, de Moraes BLC, O'Meara DB, Pescod P, Preziosi RF, Rowntree JK, Shultz S, Silk MJ, Stockdale JE, Symondson WOC, de la Pena MV, Walker SL, Wood MD, Antwis RE. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proc Biol Sci 2021; 288:20210552. [PMID: 34403636 PMCID: PMC8370808 DOI: 10.1098/rspb.2021.0552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.
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Affiliation(s)
| | - Allan D. McDevitt
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenny C. Dunn
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, UK
| | - Sarah M. Griffiths
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Chiara Benvenuto
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jean P. Boubli
- School of Science, Engineering and Environment, University of Salford, UK
| | - Kevin Bown
- School of Science, Engineering and Environment, University of Salford, UK
| | - Calum Bridson
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S. Browett
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, Ireland
- Wildlife Ecological and Osteological Consultancy, Wicklow, Ireland
| | - Julian Chantrey
- Institute of Veterinary Science, University of Liverpool, UK
| | - Friederike Clever
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, UK
| | - Katie L. Edwards
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, UK
| | - Andrew Highlands
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jane Hopper
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
| | - Joseph Jackson
- School of Science, Engineering and Environment, University of Salford, UK
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Tony King
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
- School of Anthropology and Conservation, University of Kent, UK
| | - Jessica M. D. Lea
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Jessica L. Lenka
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Jack McKenzie
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Denise B. O'Meara
- School of Science and Computing, Waterford Institute of Technology, Ireland
| | - Poppy Pescod
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | | | - Jennifer E. Stockdale
- School of Biosciences, University of Cardiff, UK
- School of Life Sciences, University of Nottingham, UK
| | | | | | - Susan L. Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Michael D. Wood
- School of Science, Engineering and Environment, University of Salford, UK
| | - Rachael E. Antwis
- School of Science, Engineering and Environment, University of Salford, UK
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163
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Bodawatta KH, Hird SM, Grond K, Poulsen M, Jønsson KA. Avian gut microbiomes taking flight. Trends Microbiol 2021; 30:268-280. [PMID: 34393028 DOI: 10.1016/j.tim.2021.07.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important - but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska, Anchorage, AK, USA
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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164
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Kim PS, Shin NR, Lee JB, Kim MS, Whon TW, Hyun DW, Yun JH, Jung MJ, Kim JY, Bae JW. Host habitat is the major determinant of the gut microbiome of fish. MICROBIOME 2021; 9:166. [PMID: 34332628 PMCID: PMC8325807 DOI: 10.1186/s40168-021-01113-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. RESULTS We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). CONCLUSIONS Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
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Affiliation(s)
- Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Jae-Bong Lee
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Gijang-eup, Busan, 46083 Republic of Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Joon Yong Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
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165
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Presley SJ, Graf J, Hassan AF, Sjodin AR, Willig MR. Effects of Host Species Identity and Diet on the Biodiversity of the Microbiota in Puerto Rican Bats. Curr Microbiol 2021; 78:3526-3540. [PMID: 34318342 DOI: 10.1007/s00284-021-02607-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/02/2021] [Indexed: 11/30/2022]
Abstract
Microbiota perform vital functions for their mammalian hosts, making them potential drivers of host evolution. Understanding effects of environmental factors and host characteristics on the composition and biodiversity of the microbiota may provide novel insights into the origin and maintenance of these symbiotic relationships. Our goals were to (1) characterize biodiversity of oral and rectal microbiota in bats from Puerto Rico; and (2) determine the effects of geographic location and host characteristics on that biodiversity. We collected bats and their microbiota from three sites, and used four metrics (species richness, Shannon diversity, Camargo evenness, Berger-Parker dominance) to characterize biodiversity. We quantified the relative importance of site, host sex, host species-identity, and host foraging-guild on biodiversity of the microbiota. Microbe biodiversity was highly variable among conspecifics. Geographical location exhibited consistent effects, whereas host sex did not. Within each host guild, host species exhibited consistent differences in biodiversity of oral microbiota and of rectal microbiota. Oral microbe biodiversity was indistinguishable between guilds, whereas rectal microbe biodiversity was significantly greater in carnivores than in herbivores. The high intraspecific and spatial variation in microbe biodiversity necessitate a relatively large number of samples to statistically isolate the effects of environmental or host characteristics on the microbiota. Species-specific biodiversity of oral microbiota suggests these communities are structured by direct interactions with the host immune system via epithelial receptors. In contrast, the number of microbial taxa that a host gut supports may be driven by host diet-diversity or composition.
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Affiliation(s)
- Steven J Presley
- Institute of the Environment, Center for Environmental Sciences & Engineering, and Department of Ecology & Evolutionary Biology, University of Connecticut, 3107 Horsebarn Hill Road, Storrs, CT, 06269-4210, USA.
| | - Joerg Graf
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA
| | - Ahmad F Hassan
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA
| | - Anna R Sjodin
- Institute of the Environment, Center for Environmental Sciences & Engineering, and Department of Ecology & Evolutionary Biology, University of Connecticut, 3107 Horsebarn Hill Road, Storrs, CT, 06269-4210, USA.,Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Michael R Willig
- Institute of the Environment, Center for Environmental Sciences & Engineering, and Department of Ecology & Evolutionary Biology, University of Connecticut, 3107 Horsebarn Hill Road, Storrs, CT, 06269-4210, USA
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166
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Alessandri G, Rizzo SM, Ossiprandi MC, van Sinderen D, Ventura M. Creating an atlas to visualize the biodiversity of the mammalian gut microbiota. Curr Opin Biotechnol 2021; 73:28-33. [PMID: 34280701 DOI: 10.1016/j.copbio.2021.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/22/2022]
Abstract
Given the fundamental role played by the intestinal microbial community in influencing host health, it is not surprising that recent decades have been marked by increased efforts to determine the taxonomic composition of the human gut microbiota and its associated functions. Despite their generally accepted importance, these large-scale human-centered studies prevent an exhaustive overview of those mechanisms and factors that contribute to the mammalian gut microbiota assembly. However, Next-Generation Sequencing techniques and associated bioinformatic tools provide an exciting opportunity to rapidly expand our knowledge on the intestinal microbial communities associated with members of the Mammalia class. These non-human-focused studies established that dietary, host phylogeny, host physiology and anthropogenic influences represent the main factors driving the selection of a specific gut microbial consortium in mammals. The current review is aimed at providing a comprehensive overview on the impact that the above-mentioned factors exert on the assembly of the mammalian gut microbiota.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sonia M Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Maria C Ossiprandi
- Department of Veterinary Medical Science, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, Parma, Italy.
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167
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Pekarsky S, Corl A, Turjeman S, Kamath PL, Getz WM, Bowie RCK, Markin Y, Nathan R. Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation. Mol Ecol 2021; 30:4723-4739. [PMID: 34260783 DOI: 10.1111/mec.16079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/14/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022]
Abstract
Human activities shape resources available to wild animals, impacting diet and probably altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS-tracking) over three periods of their migratory cycle, and by analysing the effect of artificially supplemented food provided as part of a crane-agriculture management programme. We sampled faecal droppings in Russia (nonsupplemented, premigration) and in Israel in late autumn (nonsupplemented, postmigration) and winter (supplemented and nonsupplemented, wintering). As supplemented food is typically homogenous, we predicted lower microbiota diversity and different composition in birds relying on supplementary feeding. We did not observe changes in microbial diversity with food supplementation, as diversity differed only in samples from nonsupplemented wintering sites. However, both food supplementation and season affected bacterial community composition and led to increased abundance of specific genera (mostly Firmicutes). Cranes from the nonsupplemented groups spent most of their time in agricultural fields, probably feeding on residual grain when available, while food-supplemented cranes spent most of their time at the feeding station. Thus, nonsupplemented and food-supplemented diets probably diverge only in winter, when crop rotation and depletion of anthropogenic resources may lead to a more variable diet in nonsupplemented sites. Our results support the role of diet in structuring bacterial communities and show that they undergo both seasonal and human-induced shifts. Movement analyses provide important clues regarding host diet and behaviour towards understanding how human-induced changes shape the gut microbiota in wild animals.
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Affiliation(s)
- Sasha Pekarsky
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
| | - Sondra Turjeman
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Wayne M Getz
- Department of Environmental Science, Policy & Management, University of California, Berkeley, California, USA.,School Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Yuri Markin
- Oksky State Reserve, pos. Brykin Bor, Spassky raion, Ryazanskaya oblast, Russia
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution & Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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168
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Boukerb AM, Noël C, Quenot E, Cadiou B, Chevé J, Quintric L, Cormier A, Dantan L, Gourmelon M. Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach. Front Microbiol 2021; 12:697553. [PMID: 34335529 PMCID: PMC8317174 DOI: 10.3389/fmicb.2021.697553] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/14/2021] [Indexed: 12/28/2022] Open
Abstract
Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R2 = 0.13, p = 10–4, Adonis R2 = 0.11, p = 10–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.
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Affiliation(s)
- Amine M Boukerb
- IFREMER, RBE-SGMM-LSEM, Laboratoire Santé Environnement Microbiologie, Plouzané, France
| | - Cyril Noël
- IFREMER - PDG-IRSI-SEBIMER, Plouzané, France
| | - Emmanuelle Quenot
- IFREMER, RBE-SGMM-LSEM, Laboratoire Santé Environnement Microbiologie, Plouzané, France
| | | | - Julien Chevé
- IFREMER, ODE-UL-LERBN, Laboratoire Environnement Ressource Bretagne Nord, Dinard, France
| | | | | | - Luc Dantan
- IFREMER, RBE-SGMM-LSEM, Laboratoire Santé Environnement Microbiologie, Plouzané, France
| | - Michèle Gourmelon
- IFREMER, RBE-SGMM-LSEM, Laboratoire Santé Environnement Microbiologie, Plouzané, France
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169
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Abstract
Animal (human) gut microbiomes have been coevolving with their hosts for many millions of years. Understanding how the coevolution shapes the processes of microbiome assembly and diversity maintenance is important but rather challenging. An effort may start with the understanding of how and why animals and humans may differ in their microbiome neutrality (stochasticity) levels. Here, we attempted to perform layered comparative stochasticity analyses across animal species (including humans), class, and kingdom scales, corresponding to microbial metacommunity, landscape, and global-landscape scales. By analyzing 4,903 microbiome samples from 274 animal species covering 4 major invertebrate classes and all 6 vertebrate classes and including 1,787 human gut microbiome samples, we discovered the following: (i) at the microbial metacommunity (animal species) scale, although the general trend of stochasticity (measured in the relationships between fundamental biodiversity/dispersal numbers of Hubbell’s neutral theory and host species phylogenetic timeline) seems continuous, there seems to be a turning point from animals to humans in the passing rate of neutrality tests (12% to 45% versus 100%). We postulate that it should be the human experiences from agricultural/industrial activities (e.g., diet effects) and frequent social/familial contacts that are responsible for the dramatically rising stochastic neutrality in human gut microbiomes. (ii) At the microbial landscape (animal class) and global landscape (animal kingdom) scales, neutrality is not detectable, suggesting that the landscape is niche differentiated—animal species may possess “home niches” for their coadapted microbiomes. We further analyze the reliabilities of our findings by using variable P value thresholds (type I error) and performing power analysis (type II error) of neutrality tests. IMPORTANCE Understanding how the coevolution (evolutionary time scale) and/or the interactions (ecological time scale) between animal (human) gut microbiomes and their hosts shape the processes of the microbiome assembly and diversity maintenance is important but rather challenging. An effort may start with the understanding of how and why animals and humans may differ in their microbiome neutrality (stochasticity) levels. Here, we attempted to perform layered comparative stochasticity analyses across animal species (including humans), class, and kingdom scales, corresponding to microbial metacommunity, landscape, and global-landscape scales by analyzing 4,903 microbiome samples from 274 animal species covering 4 major invertebrate classes and all 6 vertebrate classes, and including 1,787 human gut microbiome samples. The analyses were implemented by fitting the multisite neutral model and further augmented by checking false-positive and false-negative errors, respectively. It appears that there is a turning (tipping) point in the neutrality level from animal to human microbiomes.
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170
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Hoppe MI, Meloro C, Edwards MS, Codron D, Clauss M, Duque-Correa MJ. Less need for differentiation? Intestinal length of reptiles as compared to mammals. PLoS One 2021; 16:e0253182. [PMID: 34214090 PMCID: PMC8253402 DOI: 10.1371/journal.pone.0253182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/28/2021] [Indexed: 11/18/2022] Open
Abstract
Although relationships between intestinal morphology between trophic groups in reptiles are widely assumed and represent a cornerstone of ecomorphological narratives, few comparative approaches actually tested this hypothesis on a larger scale. We collected data on lengths of intestinal sections of 205 reptile species for which either body mass (BM), snout-vent-length (SVL) or carapax length (CL) was recorded, transforming SVL or CL into BM if the latter was not given, and analyzed scaling patterns with BM and SVL, accounting for phylogeny, comparing three trophic guilds (faunivores, omnivores, herbivores), and comparing with a mammal dataset. Length-BM relationships in reptiles were stronger for the small than the large intestine, suggesting that for the latter, additional factors might be relevant. Adding trophic level did not consistently improve model fit; only when controlling for phylogeny, models indicated a longer large intestine in herbivores, due to a corresponding pattern in lizards. Trophic level effects were highly susceptible to sample sizes, and not considered strong. Models that linked BM to intestine length had better support than models using SVL, due to the deviating body shape of snakes. At comparable BM, reptiles had shorter intestines than mammals. While the latter finding corresponds to findings of lower tissue masses for the digestive tract and other organs in reptiles as well as our understanding of differences in energetic requirements between the classes, they raise the hitherto unanswered question what it is that reptiles of similar BM have more than mammals. A lesser effect of trophic level on intestine lengths in reptiles compared to mammals may stem from lesser selective pressures on differentiation between trophic guilds, related to the generally lower food intake and different movement patterns of reptiles, which may not similarly escalate evolutionary arms races tuned to optimal agility as between mammalian predators and prey.
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Affiliation(s)
- Monika I. Hoppe
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carlo Meloro
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Mark S. Edwards
- California Polytechnic State University, San Luis Obispo, California, United States of America
| | - Daryl Codron
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Marcus Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- * E-mail:
| | - María J. Duque-Correa
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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171
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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus). Ecol Evol 2021; 11:9472-9488. [PMID: 34306636 PMCID: PMC8293786 DOI: 10.1002/ece3.7767] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.
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Affiliation(s)
- Alexandra L. DeCandia
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kira A. Cassidy
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Daniel R. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Erin A. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
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172
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De Schepper S, Crowley G, Hong S. Understanding microglial diversity and implications for neuronal function in health and disease. Dev Neurobiol 2021; 81:507-523. [PMID: 32757416 PMCID: PMC8438703 DOI: 10.1002/dneu.22777] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/21/2020] [Accepted: 07/31/2020] [Indexed: 12/22/2022]
Abstract
Genetic data implicate microglia as central players in brain health and disease, urging the need to better understand what microglia do in the brain. Microglia are critical partners in neuronal wiring and function during development and disease. Emerging literature suggests that microglia have diverse functional roles, raising the intriguing question of which functions of microglia become impaired in disease to undermine proper neuronal function. It is also becoming increasingly clear that microglia exist in heterogeneous cell states. Microglial cell states appear context-dependent, that is, age, sex, location, and health of their microenvironment; these are further influenced by external signaling factors including gut microbiota and lipid metabolites. These data altogether suggest that microglia exist in functional clusters that impact, and are impacted by, surrounding neuronal microenvironment. However, we still lack understanding of how we can translate microglia cell states into function. Here, we summarize the state-of-the-art on the diverse functions of microglia in relation to neuronal health. Then, we discuss heterogeneity during developing, healthy adult and diseased brains, and whether this may be predetermined by origin and/or regulated by local milieu. Finally, we propose that it is critical to gain high-resolution functional discernment into microglia-neuron interactions while preserving the spatial architecture of the tissue. Such insight will reveal specific targets for biomarker and therapeutic development toward microglia-neuron crosstalk in disease.
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Affiliation(s)
| | - Gerard Crowley
- UK Dementia Research InstituteUniversity College LondonLondonUK
| | - Soyon Hong
- UK Dementia Research InstituteUniversity College LondonLondonUK
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173
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Fu H, Zhang L, Fan C, Liu C, Li W, Cheng Q, Zhao X, Jia S, Zhang Y. Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals. Microb Biotechnol 2021; 14:1300-1315. [PMID: 33369229 PMCID: PMC8313255 DOI: 10.1111/1751-7915.13687] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/07/2020] [Indexed: 02/01/2023] Open
Abstract
The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.
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Affiliation(s)
- Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Shangang Jia
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
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174
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Huang K, Wang J, Huang J, Zhang S, Vogler AP, Liu Q, Li Y, Yang M, Li Y, Zhou X. Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects. Front Microbiol 2021; 12:633075. [PMID: 34239504 PMCID: PMC8260032 DOI: 10.3389/fmicb.2021.633075] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.
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Affiliation(s)
- Kuanguan Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Jie Wang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Junhao Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shouke Zhang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London Silwood Park, Ascot, United Kingdom
| | - Quanquan Liu
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Maowei Yang
- Institute of Forestry Investigation and Planning of Guangning, Guangning, China
| | - You Li
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, United States
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175
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O'Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, Bourne DG. Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Mol Ecol 2021; 30:3768-3782. [PMID: 34060182 DOI: 10.1111/mec.16006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Qld, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia
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176
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Martinson VG, Strand MR. Diet-Microbiota Interactions Alter Mosquito Development. Front Microbiol 2021; 12:650743. [PMID: 34168624 PMCID: PMC8217444 DOI: 10.3389/fmicb.2021.650743] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/28/2021] [Indexed: 12/27/2022] Open
Abstract
Gut microbes and diet can both strongly affect the biology of multicellular animals, but it is often difficult to disentangle microbiota–diet interactions due to the complex microbial communities many animals harbor and the nutritionally variable diets they consume. While theoretical and empirical studies indicate that greater microbiota diversity is beneficial for many animal hosts, there have been few tests performed in aquatic invertebrates. Most mosquito species are aquatic detritivores during their juvenile stages that harbor variable microbiotas and consume diets that range from nutrient rich to nutrient poor. In this study, we produced a gnotobiotic model that allowed us to examine how interactions between specific gut microbes and diets affect the fitness of Aedes aegypti, the yellow fever mosquito. Using a simplified seven-member community of bacteria (ALL7) and various laboratory and natural mosquito diets, we allowed larval mosquitoes to develop under different microbial and dietary conditions and measured the resulting time to adulthood and adult size. Larvae inoculated with the ALL7 or a more complex community developed similarly when fed nutrient-rich rat chow or fish food laboratory diets, whereas larvae inoculated with individual bacterial members of the ALL7 community exhibited few differences in development when fed a rat chow diet but exhibited large differences in performance when fed a fish food diet. In contrast, the ALL7 community largely failed to support the growth of larvae fed field-collected detritus diets unless supplemented with additional protein or yeast. Collectively, our results indicate that mosquito development and fitness are strongly contingent on both diet and microbial community composition.
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Affiliation(s)
- Vincent G Martinson
- Department of Entomology, University of Georgia, Athens, GA, United States.,Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, GA, United States
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177
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Host Species and Geography Differentiate Honeybee Gut Bacterial Communities by Changing the Relative Contribution of Community Assembly Processes. mBio 2021; 12:e0075121. [PMID: 34061602 PMCID: PMC8262996 DOI: 10.1128/mbio.00751-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Honeybee gut microbiota modulates the health and fitness of honeybees, the ecologically and economically important pollinators and honey producers. However, which processes drive the assembly and shift of honeybee gut microbiota remains unknown. To explore the patterns of honeybee gut bacterial communities across host species and geographical sites and the relative contribution of different processes (i.e., homogeneous selection, variable selection, homogeneous dispersal, dispersal limitation, and an undominated process) in driving the patterns, two honeybee species (Apis cerana and Apis mellifera) were sampled from five geographically distant sites along a latitudinal gradient, followed by gut bacterial 16S rRNA gene sequencing. The gut bacterial communities differed significantly between A. cerana and A. mellifera, which was driven by the interhost dispersal limitation associated with the long-term coevolution between hosts and their prokaryotic symbionts. A. mellifera harbored more diverse but less varied gut bacterial communities than A. cerana due to the dominant role of homogeneous selection in converging A. mellifera intestinal communities. For each honeybee species, the gut bacterial communities differed across geographical sites, with individuals from lower latitudes harboring higher diversity; also, there was significant decay of gut community similarity against geographic distance. The geographical variation of honeybee gut bacterial communities was mainly driven by an undominated process (e.g., stochastic drift) rather than variable selection or dispersal limitation. This study elucidates that variations in host and geography alter the relative contribution of different processes in assembling honeybee gut microbiota and, thus, provides insights into the mechanisms underlying honeybee gut microbial shifts across evolutionary time.
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178
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Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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179
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Abstract
Opportunistic feeding and multiple other environment factors can modulate the gut microbiome, and bias conclusions, when wild animals are used for studying the influence of phylogeny and diet on their gut microbiomes. Here, we controlled for these other confounding factors in our investigation of the magnitude of the effect of diet on the gut microbiome assemblies of nonpasserine birds. We collected fecal samples, at one point in time, from 35 species of birds in a single zoo as well as 6 species of domestic poultry from farms in Guangzhou city to minimize the influences from interfering factors. Specifically, we describe 16S rRNA amplicon data from 129 fecal samples obtained from 41 species of birds, with additional shotgun metagenomic sequencing data generated from 16 of these individuals. Our data show that diets containing native starch increase the abundance of Lactobacillus in the gut microbiome, while those containing plant-derived fiber mainly enrich the level of Clostridium Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, the metagenome functions of the microbes (such as lipid metabolism and amino acid synthesis) were adapted to the different food types to achieve a beneficial state for the host. In conclusion, the covariation of diet and gut microbiome identified in our study demonstrates a modulation of the gut microbiome by dietary diversity and helps us better understand how birds live based on diet-microbiome-host interactions.IMPORTANCE Our study identified food source, rather than host phylogeny, as the main factor modulating the gut microbiome diversity of nonpasserine birds, after minimizing the effects of other complex interfering factors such as weather, season, and geography. Adaptive evolution of microbes to food types formed a dietary-microbiome-host interaction reciprocal state. The covariation of diet and gut microbiome, including the response of microbiota assembly to diet in structure and function, is important for health and nutrition in animals. Our findings help resolve the major modulators of gut microbiome diversity in nonpasserine birds, which had not previously been well studied. The diet-microbe interactions and cooccurrence patterns identified in our study may be of special interest for future health assessment and conservation in birds.
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180
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Antwis RE, Beresford NA, Jackson JA, Fawkes R, Barnett CL, Potter E, Walker L, Gaschak S, Wood MD. Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone. J Anim Ecol 2021; 90:2172-2187. [PMID: 33901301 DOI: 10.1111/1365-2656.13507] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/11/2021] [Indexed: 12/19/2022]
Abstract
Environmental impacts of the 1986 Chernobyl Nuclear Power Plant accident are much debated, but the effects of radiation on host microbiomes have received little attention to date. We present the first analysis of small mammal gut microbiomes from the Chernobyl Exclusion Zone in relation to total absorbed dose rate, including both caecum and faeces samples. We provide novel evidence that host species determines fungal community composition, and that associations between microbiome (both bacterial and fungal) communities and radiation exposure vary between host species. Using ambient versus total weighted absorbed dose rates in analyses produced different results, with the latter more robust for interpreting microbiome changes at the individual level. We found considerable variation between results for faecal and gut samples of bank voles, suggesting faecal samples are not an accurate indicator of gut composition. Associations between radiation exposure and microbiome composition of gut samples were not robust against geographical variation, although we identified families of bacteria (Lachnospiraceae and Muribaculaceae) and fungi (Steccherinaceae and Strophariaceae) in the guts of bank voles that may serve as biomarkers of radiation exposure. Further studies considering a range of small mammal species are needed to establish the robustness of these potential biomarkers.
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Affiliation(s)
- Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nicholas A Beresford
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Joseph A Jackson
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ross Fawkes
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Catherine L Barnett
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Elaine Potter
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Lee Walker
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Sergey Gaschak
- Chornobyl Center for Nuclear Safety, Radioactive Waste and Radioecology, International Radioecology Laboratory, Slavutych, Ukraine
| | - Michael D Wood
- School of Science, Engineering and Environment, University of Salford, Salford, UK
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181
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Maturana JL, Cárdenas JP. Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages. Front Microbiol 2021; 12:660920. [PMID: 33981291 PMCID: PMC8107234 DOI: 10.3389/fmicb.2021.660920] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/25/2021] [Indexed: 12/02/2022] Open
Abstract
Blautia, a genus established in 2008, is a relevantly abundant taxonomic group present in the microbiome of human and other mammalian gastrointestinal (GI) tracts. Several described (or proposed) Blautia species are available at this date. However, despite the increasing level of knowledge about Blautia, its diversity is still poorly understood. The increasing availability of Blautia genomic sequences in the public databases opens the possibility to study this genus from a genomic perspective. Here we report the pangenome analysis and the phylogenomic study of 225 Blautia genomes available in RefSeq. We found 33 different potential species at the genomic level, 17 of them previously undescribed; we also confirmed by genomic standards the status of 4 previously proposed new Blautia species. Comparative genomic analyses suggest that the Blautia pangenome is open, with a relatively small core genome (∼ 700-800 gene families). Utilizing a set of representative genomes, we performed a gene family gain/loss model for the genus, showing that despite terminal nodes suffered more massive gene gain events than internal nodes (i.e., predicted ancestors), some ancestors were predicted to have gained an important number of gene families, some of them associated with the possible acquisition of metabolic abilities. Gene loss events remained lower than gain events in most cases. General aspects regarding pangenome composition and gene gain/loss events are discussed, as well as the proposition of changes in the taxonomic assignment of B. coccoides TY and the proposition of a new species, "B. pseudococcoides.".
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Affiliation(s)
- José Luis Maturana
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Juan P. Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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182
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Rojas CA, Ramírez-Barahona S, Holekamp KE, Theis KR. Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales. Anim Microbiome 2021; 3:33. [PMID: 33892813 PMCID: PMC8063394 DOI: 10.1186/s42523-021-00094-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/04/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.
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Affiliation(s)
- Connie A. Rojas
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Santiago Ramírez-Barahona
- Departament of Botany, Institute of Biology, Universidad Nacional Autónoma de México, Mexico City, MX Mexico
| | - Kay E. Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Kevin R. Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI USA
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183
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Bodawatta KH, Koane B, Maiah G, Sam K, Poulsen M, Jønsson KA. Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications. Proc Biol Sci 2021; 288:20210446. [PMID: 33878920 DOI: 10.1098/rspb.2021.0446] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host-microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Bonny Koane
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Gibson Maiah
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Branisovska 31, 37005, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Branisovska 1760, 37005, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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184
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Walke JB, Becker MH, Krinos A, Chang EAB, Santiago C, Umile TP, Minbiole KPC, Belden LK. Seasonal changes and the unexpected impact of environmental disturbance on skin bacteria of individual amphibians in a natural habitat. FEMS Microbiol Ecol 2021; 97:6024676. [PMID: 33278302 DOI: 10.1093/femsec/fiaa248] [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] [Received: 07/10/2020] [Accepted: 12/02/2020] [Indexed: 01/16/2023] Open
Abstract
Amphibians host diverse skin bacteria that have a role in pathogen defense, but these skin communities could change over time and impact this function. Here, we monitored individual Eastern red-spotted newts (Notophthalmus viridescens; N = 17) for 2 years in a field pond enclosure and assessed the effects of season and disturbance on skin bacterial community dynamics. We created disturbances by adding additional pond substrate to the enclosure at two timepoints. We planned to sample the skin bacterial community and metabolite profiles of each newt every 6 weeks; we ultimately sampled eight individuals at least six times. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities and HPLC-MS for metabolite profiling. We found that disturbance had a dramatic effect on skin bacterial communities and metabolite profiles, while season had an effect only using select metrics. There were seven core bacterial taxa (97% OTUs) that were found on all newts in all seasons, pre- and post-disturbance. Lastly, there was a correlation between bacterial and metabolite profiles post-disturbance, which was not observed pre-disturbance. This longitudinal study suggests that environmental disturbances can have lasting effects on skin bacterial communities that overwhelm seasonal changes, although the core bacteria remain relatively consistent over time.
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Affiliation(s)
- Jenifer B Walke
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Matthew H Becker
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Arianna Krinos
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Celina Santiago
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
| | - Thomas P Umile
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
| | | | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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185
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Affiliation(s)
- Abigail L Lind
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA, USA
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186
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Diet and gut microbiome enterotype are associated at the population level in African buffalo. Nat Commun 2021; 12:2267. [PMID: 33859184 PMCID: PMC8050287 DOI: 10.1038/s41467-021-22510-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/02/2021] [Indexed: 12/19/2022] Open
Abstract
Studies in humans and laboratory animals link stable gut microbiome “enterotypes” with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease. There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.
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187
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Couch CE, Wise BL, Scurlock BM, Rogerson JD, Fuda RK, Cole EK, Szcodronski KE, Sepulveda AJ, Hutchins PR, Cross PC. Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem. PLoS One 2021; 16:e0249521. [PMID: 33831062 PMCID: PMC8031386 DOI: 10.1371/journal.pone.0249521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 03/19/2021] [Indexed: 12/27/2022] Open
Abstract
Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of the gut microbiome for extracting and synthesizing nutrients, modulating host immunity, and many other vital host functions, but these relationships can be disrupted by dietary perturbation. The well-described interplay between diet, the microbiome, and host health in laboratory and human systems highlights the need to understand the consequences of supplemental feeding on the microbiomes of free-ranging animal populations. This study describes changes to the gut microbiomes of wild elk under different supplemental feeding regimes. We demonstrated significant cross-sectional variation between elk at different feeding locations and identified several relatively low-abundance bacterial genera that differed between fed versus unfed groups. In addition, we followed four of these populations through mid-season changes in supplemental feeding regimes and demonstrated a significant shift in microbiome composition in a single population that changed from natural forage to supplementation with alfalfa pellets. Some of the taxonomic shifts in this population mirrored changes associated with ruminal acidosis in domestic livestock. We discerned no significant changes in the population that shifted from natural forage to hay supplementation, or in the populations that changed from one type of hay to another. Our results suggest that supplementation with alfalfa pellets alters the native gut microbiome of elk, with potential implications for population health.
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Affiliation(s)
- Claire E. Couch
- Department of Fisheries & Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Benjamin L. Wise
- Wyoming Game & Fish Department, Jackson, Wyoming, United States of America
| | | | - Jared D. Rogerson
- Wyoming Game & Fish Department, Pinedale, Wyoming, United States of America
| | - Rebecca K. Fuda
- Oregon Department of Fish & Wildlife, Prineville, Oregon, United States of America
| | - Eric K. Cole
- U.S. Fish & Wildlife Service, National Elk Refuge, Jackson, Wyoming, United States of America
| | - Kimberly E. Szcodronski
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
| | - Adam J. Sepulveda
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
| | - Patrick R. Hutchins
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
| | - Paul C. Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
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188
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Ortega VA, Mercer EM, Giesbrecht GF, Arrieta MC. Evolutionary Significance of the Neuroendocrine Stress Axis on Vertebrate Immunity and the Influence of the Microbiome on Early-Life Stress Regulation and Health Outcomes. Front Microbiol 2021; 12:634539. [PMID: 33897639 PMCID: PMC8058197 DOI: 10.3389/fmicb.2021.634539] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Stress is broadly defined as the non-specific biological response to changes in homeostatic demands and is mediated by the evolutionarily conserved neuroendocrine networks of the hypothalamus-pituitary-adrenal (HPA) axis and the sympathetic nervous system. Activation of these networks results in transient release of glucocorticoids (cortisol) and catecholamines (epinephrine) into circulation, as well as activation of sympathetic fibers innervating end organs. These interventions thus regulate numerous physiological processes, including energy metabolism, cardiovascular physiology, and immunity, thereby adapting to cope with the perceived stressors. The developmental trajectory of the stress-axis is influenced by a number of factors, including the gut microbiome, which is the community of microbes that colonizes the gastrointestinal tract immediately following birth. The gut microbiome communicates with the brain through the production of metabolites and microbially derived signals, which are essential to human stress response network development. Ecological perturbations to the gut microbiome during early life may result in the alteration of signals implicated in developmental programming during this critical window, predisposing individuals to numerous diseases later in life. The vulnerability of stress response networks to maladaptive development has been exemplified through animal models determining a causal role for gut microbial ecosystems in HPA axis activity, stress reactivity, and brain development. In this review, we explore the evolutionary significance of the stress-axis system for health maintenance and review recent findings that connect early-life microbiome disturbances to alterations in the development of stress response networks.
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Affiliation(s)
- Van A Ortega
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, Cumming School of Medicine, Health Sciences Centre, University of Calgary, Calgary, AB, Canada
| | - Emily M Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, Cumming School of Medicine, Health Sciences Centre, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, University of Calgary, Calgary, AB, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada.,Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada.,Owerko Centre, The Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, Cumming School of Medicine, Health Sciences Centre, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, University of Calgary, Calgary, AB, Canada
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189
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Kumar S, Khan MA, Beijer E, Liu J, Lowe KK, Young W, Mills DA, Moon CD. Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation. Anim Microbiome 2021; 3:27. [PMID: 33795026 PMCID: PMC8017768 DOI: 10.1186/s42523-021-00088-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/02/2022] Open
Abstract
Background The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, the influence of different types of milk feeds, and their allowances, on the calf hindgut microbiota is not well understood. In this study, faecal samples from 199 calves raised on three different allowances of milk replacer: 10% of initial bodyweight (LA), 20% of initial bodyweight (HA), and ad libitum (ADLIB), were collected just prior to weaning. Bacterial community structures and fermentation products were analysed, and their relationships with calf growth and health parameters were examined to identify potential interactions between diet, gut microbiota and calf performance. Results Differences in the total concentrations of short-chain fatty acids were not observed, but higher milk replacer allowances increased the concentrations of branched short-chain fatty acids and decreased acetate to propionate ratios. The bacterial communities were dominated by Ruminococcaceae, Lachnospiraceae and Bacteroides, and the bacterial diversity of the ADLIB diet group was greater than that of the other diet groups. Faecalibacterium was over three times more abundant in the ADLIB compared to the LA group, and its abundance correlated strongly with girth and body weight gains. Milk replacer intake correlated strongly with Peptococcus and Blautia, which also correlated with body weight gain. Bifidobacterium averaged less than 1% abundance, however its levels, and those of Clostridium sensu stricto 1, correlated strongly with initial serum protein levels, which are an indicator of colostrum intake and passive transfer of immunoglobulins in early life. Conclusions Higher milk replacer intakes in calves increased hindgut bacterial diversity and resulted in bacterial communities and short chain fatty acid profiles associated with greater protein fermentation. Increased abundances of beneficial bacteria such as Faecalibacterium, were also observed, which may contribute to development and growth. Moreover, correlations between microbial taxa and initial serum protein levels suggest that colostrum intake in the first days of life may influence microbiota composition at pre-weaning. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00088-2.
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Affiliation(s)
- Sandeep Kumar
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - M Ajmal Khan
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Emma Beijer
- Animal Nutrition Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Jinxin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.,Foods for Health Institute, University of California, Davis, California, One Shields Ave, Davis, CA, 95616, USA
| | - Katherine K Lowe
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wayne Young
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - David A Mills
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.,Foods for Health Institute, University of California, Davis, California, One Shields Ave, Davis, CA, 95616, USA.,Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, California, One Shields Ave, Davis, CA, 95616, USA
| | - Christina D Moon
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
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190
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Sharma V, Hecker N, Walther F, Stuckas H, Hiller M. Convergent Losses of TLR5 Suggest Altered Extracellular Flagellin Detection in Four Mammalian Lineages. Mol Biol Evol 2021; 37:1847-1854. [PMID: 32145026 DOI: 10.1093/molbev/msaa058] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Toll-like receptors (TLRs) play an important role for the innate immune system by detecting pathogen-associated molecular patterns. TLR5 encodes the major extracellular receptor for bacterial flagellin and frequently evolves under positive selection, consistent with coevolutionary arms races between the host and pathogens. Furthermore, TLR5 is inactivated in several vertebrates and a TLR5 stop codon polymorphism is widespread in human populations. Here, we analyzed the genomes of 120 mammals and discovered that TLR5 is convergently lost in four independent lineages, comprising guinea pigs, Yangtze river dolphin, pinnipeds, and pangolins. Validated inactivating mutations, absence of protein-coding transcript expression, and relaxed selection on the TLR5 remnants confirm these losses. PCR analysis further confirmed the loss of TLR5 in the pinniped stem lineage. Finally, we show that TLR11, encoding a second extracellular flagellin receptor, is also absent in these four lineages. Independent losses of TLR5 and TLR11 suggest that a major pathway for detecting flagellated bacteria is not essential for different mammals and predicts an impaired capacity to sense extracellular flagellin.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,CRTD-DFG Center for Regenerative Therapies Dresden, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden; German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Felix Walther
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
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191
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Levin D, Raab N, Pinto Y, Rothschild D, Zanir G, Godneva A, Mellul N, Futorian D, Gal D, Leviatan S, Zeevi D, Bachelet I, Segal E. Diversity and functional landscapes in the microbiota of animals in the wild. Science 2021; 372:science.abb5352. [PMID: 33766942 DOI: 10.1126/science.abb5352] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.
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Affiliation(s)
| | | | | | - Daphna Rothschild
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | | | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10065, USA
| | - Ido Bachelet
- Wild Biotech, Rehovot, Israel.,Augmanity, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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192
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Reese AT, Chadaideh KS, Diggins CE, Schell LD, Beckel M, Callahan P, Ryan R, Emery Thompson M, Carmody RN. Effects of domestication on the gut microbiota parallel those of human industrialization. eLife 2021; 10:60197. [PMID: 33755015 PMCID: PMC7987347 DOI: 10.7554/elife.60197] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Domesticated animals experienced profound changes in diet, environment, and social interactions that likely shaped their gut microbiota and were potentially analogous to ecological changes experienced by humans during industrialization. Comparing the gut microbiota of wild and domesticated mammals plus chimpanzees and humans, we found a strong signal of domestication in overall gut microbial community composition and similar changes in composition with domestication and industrialization. Reciprocal diet switches within mouse and canid dyads demonstrated the critical role of diet in shaping the domesticated gut microbiota. Notably, we succeeded in recovering wild-like microbiota in domesticated mice through experimental colonization. Although fundamentally different processes, we conclude that domestication and industrialization have impacted the gut microbiota in related ways, likely through shared ecological change. Our findings highlight the utility, and limitations, of domesticated animal models for human research and the importance of studying wild animals and non-industrialized humans for interrogating signals of host-microbial coevolution.
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Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States.,Society of Fellows, Harvard University, Cambridge, MA, United States
| | - Katia S Chadaideh
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Caroline E Diggins
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Laura D Schell
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Mark Beckel
- Wildlife Science Center, Stacy, MN, United States
| | | | - Roberta Ryan
- Wildlife Science Center, Stacy, MN, United States
| | | | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
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193
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Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans. mBio 2021; 12:mBio.03581-20. [PMID: 33758084 PMCID: PMC8092312 DOI: 10.1128/mbio.03581-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
There has been considerable interest in the impact of short-chain fatty acids (SCFAs) on inflammatory effects related to the microbiome. Here, we present evidence that SCFAs may also be important in disease by providing an energy source or disease-associated cue for colonizing pathogens. Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. Aggregatibacter actinomycetemcomitans (Aa) is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of Aa isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the Catarrhini, the lineage that includes Old World monkeys (OWM) and humans. Further genomic analysis showed a strong association with the presence of a short-chain fatty acid (SCFA) catabolism locus (atoRDAEB) in many human isolates that was absent in almost all nonhuman OWM isolates. We show that this locus was likely acquired through horizontal gene transfer. When grown under conditions that are similar to those at the subgingival site of periodontitis (anaerobic, SCFA replete), Aa strains with atoRDAEB formed robust biofilms and showed upregulation of genes involved in virulence, colonization, and immune evasion. Both an isogenic deletion mutant and nonhuman primate isolates lacking the ato locus failed to grow in a robust biofilm under these conditions, but grew well under the carbohydrate-rich conditions similar to those found above the gumline. We propose that the acquisition of the ato locus was a key evolutionary step allowing Aa to utilize SCFAs, adapt, and modulate subgingival disease.
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194
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Sottas C, Schmiedová L, Kreisinger J, Albrecht T, Reif J, Osiejuk TS, Reifová R. Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance. BMC Ecol Evol 2021; 21:41. [PMID: 33691625 PMCID: PMC7948333 DOI: 10.1186/s12862-021-01773-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that divergence in the gut microbiota composition between incipient species could contribute to their reproductive isolation. Nevertheless, empirical evidence for the role of gut microbiota in speciation is scarce. Moreover, it is still largely unknown to what extent closely related species in the early stages of speciation differ in their gut microbiota composition, especially in non-mammalian taxa, and which factors drive the divergence. Here we analysed the gut microbiota in two closely related passerine species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). The ranges of these two species overlap in a secondary contact zone, where both species occasionally hybridize and where interspecific competition has resulted in habitat use differentiation. Results We analysed the gut microbiota from the proximal, middle and distal part of the small intestine in both sympatric and allopatric populations of the two nightingale species using sequencing of bacterial 16S rRNA. We found small but significant differences in the microbiota composition among the three gut sections. However, the gut microbiota composition in the two nightingale species did not differ significantly between either sympatric or allopatric populations. Most of the observed variation in the gut microbiota composition was explained by inter-individual differences. Conclusions To our knowledge, this is the first attempt to assess the potential role of the gut microbiota in bird speciation. Our results suggest that neither habitat use, nor geographical distance, nor species identity have strong influence on the nightingale gut microbiota composition. This suggests that changes in the gut microbiota composition are unlikely to contribute to reproductive isolation in these passerine birds. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01773-1.
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Affiliation(s)
- Camille Sottas
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Jiří Reif
- Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Tomasz S Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
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195
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Díez-Sainz E, Lorente-Cebrián S, Aranaz P, Riezu-Boj JI, Martínez JA, Milagro FI. Potential Mechanisms Linking Food-Derived MicroRNAs, Gut Microbiota and Intestinal Barrier Functions in the Context of Nutrition and Human Health. Front Nutr 2021; 8:586564. [PMID: 33768107 PMCID: PMC7985180 DOI: 10.3389/fnut.2021.586564] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules from 18 to 24 nucleotides that are produced by prokaryote and eukaryote organisms, which play a crucial role in regulating gene expression through binding to their mRNA targets. MiRNAs have acquired special attention for their potential in cross kingdom communication, notably food-derived microRNAs (xenomiRs), which could have an impact on microorganism and mammal physiology. In this review, we mainly aim to deal with new perspectives on: (1) The mechanism by which food-derived xenomiRs (mainly dietary plant xenomiRs) could be incorporated into humans through diet, in a free form, associated with proteins or encapsulated in exosome-like nanoparticles. (2) The impact of dietary plant-derived miRNAs in modulating gut microbiota composition, which in turn, could regulate intestinal barrier permeability and therefore, affect dietary metabolite, postbiotics or food-derived miRNAs uptake efficiency. Individual gut microbiota signature/composition could be also involved in xenomiR uptake efficiency through several mechanisms such us increasing the bioavailability of exosome-like nanoparticles miRNAs. (3) Gut microbiota dysbiosis has been proposed to contribute to disease development by affecting gut epithelial barrier permeability. For his reason, the availability and uptake of dietary plant xenomiRs might depend, among other factors, on this microbiota-related permeability of the intestine. We hypothesize and critically review that xenomiRs-microbiota interaction, which has been scarcely explored yet, could contribute to explain, at least in part, the current disparity of evidences found dealing with dietary miRNA uptake and function in humans. Furthermore, dietary plant xenomiRs could be involved in the establishment of the multiple gut microenvironments, in which microorganism would adapt in order to optimize the resources and thrive in them. Additionally, a particular xenomiR could preferentially accumulate in a specific region of the gastrointestinal tract and participate in the selection and functions of specific gut microbial communities.
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Affiliation(s)
- Ester Díez-Sainz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Silvia Lorente-Cebrián
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Paula Aranaz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - José I. Riezu-Boj
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - J. Alfredo Martínez
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Fermín I. Milagro
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
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196
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Eckert EM, Anicic N, Fontaneto D. Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment. Mol Ecol 2021; 30:1545-1558. [PMID: 33484584 DOI: 10.1111/mec.15815] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 12/17/2022]
Abstract
The association with microbes in plants and animals is known to be beneficial for host's survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the pattern could be due to co-evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species-specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of "core" microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co-evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host-microbiome association to originate and persist.
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Affiliation(s)
- Ester M Eckert
- MEG- Molecular Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy
| | - Nikoleta Anicic
- MEG- Molecular Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy.,Laboratory of Applied Microbiology, Department of Environment, Construction and Design, University of Applied Sciences and Arts of Southern Switzerland, Bellinzona, Switzerland
| | - Diego Fontaneto
- MEG- Molecular Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy
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197
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Becker AAMJ, Hill KC, Butaye P. Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose ( Urva auropunctata) in the Caribbean. Microorganisms 2021; 9:microorganisms9030465. [PMID: 33668312 PMCID: PMC7996244 DOI: 10.3390/microorganisms9030465] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/13/2021] [Accepted: 02/20/2021] [Indexed: 12/22/2022] Open
Abstract
Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.
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Affiliation(s)
- Anne A. M. J. Becker
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis; (K.H.); (P.B.)
- One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
- Correspondence:
| | - KC Hill
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis; (K.H.); (P.B.)
| | - Patrick Butaye
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis; (K.H.); (P.B.)
- One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
- Department of Pathology, Bacteriology, and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
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198
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Bodawatta KH, Freiberga I, Puzejova K, Sam K, Poulsen M, Jønsson KA. Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets. Anim Microbiome 2021; 3:20. [PMID: 33602335 PMCID: PMC7893775 DOI: 10.1186/s42523-021-00076-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To untangle the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for 4 weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another 4 weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq. Results Initial microbiomes changed significantly with the diet manipulation, but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes in certain bacterial genera. Reverting birds to the standard diet led only to a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundance after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversal Conclusions The gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and the bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species with seasonally changing diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00076-6.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Inga Freiberga
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Katerina Puzejova
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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199
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Davidson GL, Somers SE, Wiley N, Johnson CN, Reichert MS, Ross RP, Stanton C, Quinn JL. A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits. J Anim Ecol 2021; 90:989-1003. [PMID: 33481278 DOI: 10.1111/1365-2656.13428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023]
Abstract
Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore juvenile viability may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits. We collected data on two traits associated with fitness in wild nestling great tits Parus major: weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at Day-8 (D8) and Day-15 (D15) post-hatching. We also explored whether particular microbial taxa were 'indicator species' that reflected whether nestlings survived or not. There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship where weight at D15 was negatively associated with the microbial diversity at D8, controlling for weight at D8, therefore reflecting relative weight gain over the intervening period. Indicator species analysis revealed that specificity values were high and fidelity values were low, suggesting that indicator taxa were primarily detected within either the survived or not survived groups, but not always detected in birds that either survived or died. Therefore these indicator taxa may be sufficient, but not necessary for determining either survival or mortality, perhaps owing to functional overlap in microbiota. We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects may be best investigated longitudinally to detect critical development windows for key microbiota and host traits associated with neonatal weight. Our findings should inform future hypothesis testing to pinpoint which features of the gut microbial community impact on host fitness, and when during development this occurs. Such confirmatory research will shed light on population level processes and could have the potential to support conservation.
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Affiliation(s)
- Gabrielle L Davidson
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Department of Psychology, University of Cambridge, Cambridge, UK
| | - Shane E Somers
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Niamh Wiley
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Ireland
| | - Crystal N Johnson
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Ireland
| | - Michael S Reichert
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Ireland
| | - John L Quinn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
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200
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Hendriks KP, Bisschop K, Kortenbosch HH, Kavanagh JC, Larue AEA, Chee‐Chean P, Bonte D, Duijm EJ, Salles JF, Pigot AL, Richter Mendoza FJ, Schilthuizen M, Anderson MJ, Speksnijder AGCL, Etienne RS. Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails. Ecology 2021; 102:e03237. [PMID: 33098661 PMCID: PMC7900957 DOI: 10.1002/ecy.3237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/14/2020] [Indexed: 01/04/2023]
Abstract
Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co-occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other layers in the food web, or by the environment. Here we show, by studying the relationship between communities of consumers (land snails) and individual diets (from seed plants), that there is in fact no direct, or at most a weak but negative, relationship. However, we found that the diversity of the individual microbiome positively correlates with both consumer community diversity and individual diet diversity in three target species. Moreover, these correlations were affected by various environmental variables, such as anthropogenic activity, habitat island size, and a possibly important nutrient source, guano runoff from nearby caves. Our results suggest that the microbiome and the environment explain the absence of correlations between diet and consumer community diversity. Hence, we advocate that microbiome inventories are routinely added to any community dietary analysis, which our study shows can be done with relatively little extra effort. Our approach presents the tools to quickly obtain an overview of the relationships between consumers and their resources. We anticipate our approach to be useful for ecologists and environmentalists studying different communities in a local food web.
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Affiliation(s)
- Kasper P. Hendriks
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333CRThe Netherlands
- Biology Department, BotanyOsnabrück UniversityBarbarastr. 11Osnabrück49076Germany
| | - Karen Bisschop
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
- Terrestrial Ecology UnitGhent UniversityK.L. Ledeganckstraat 35Ghent9000Belgium
| | - Hylke H. Kortenbosch
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
| | - James C. Kavanagh
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
| | - Anaïs E. A. Larue
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
| | - Phung Chee‐Chean
- Institute for Tropical Biology and ConservationUniversiti Malaysia SabahJalan UMSKota KinabaluSabah88400Malaysia
| | - Dries Bonte
- Terrestrial Ecology UnitGhent UniversityK.L. Ledeganckstraat 35Ghent9000Belgium
| | - Elza J. Duijm
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333CRThe Netherlands
| | - Joana Falcão Salles
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
| | - Alex L. Pigot
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and Environment ResearchUniversity College LondonBloomsburyLondonWC1H 0AGUK
| | - Francisco J. Richter Mendoza
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
| | - Menno Schilthuizen
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333CRThe Netherlands
- Institute for Tropical Biology and ConservationUniversiti Malaysia SabahJalan UMSKota KinabaluSabah88400Malaysia
- Institute for Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
| | - Marti J. Anderson
- New Zealand Institute for Advanced Study (NZIAS)Massey UniversityAlbany Campus, Private Bag 102904, eCentre AL 266Auckland0745New Zealand
| | | | - Rampal S. Etienne
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenP.O. Box 11103Groningen9700 CCThe Netherlands
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