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Jurburg SD, Blowes SA, Shade A, Eisenhauer N, Chase JM. Synthesis of recovery patterns in microbial communities across environments. MICROBIOME 2024; 12:79. [PMID: 38711157 DOI: 10.1186/s40168-024-01802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/25/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. RESULTS To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. CONCLUSIONS This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany.
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany.
| | - Shane A Blowes
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
| | - Ashley Shade
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Universite Claude Bernard Lyon 1, 69622, Villeurbanne, France
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
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Sha H, Lu J, Chen J, Xiong J. Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis. NPJ Biofilms Microbiomes 2024; 10:40. [PMID: 38605016 PMCID: PMC11009345 DOI: 10.1038/s41522-024-00509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Mullens N, Hendrycks W, Bakengesa J, Kabota S, Tairo J, Svardal H, Majubwa R, Mwatawala M, De Meyer M, Virgilio M. Anna Karenina as a promoter of microbial diversity in the cosmopolitan agricultural pest Zeugodacus cucurbitae (Diptera, Tephritidae). PLoS One 2024; 19:e0300875. [PMID: 38568989 PMCID: PMC10990204 DOI: 10.1371/journal.pone.0300875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Gut microbial communities are critical in determining the evolutive success of fruit fly phytophagous pests (Diptera, Tephritidae), facilitating their adaptation to suboptimal environmental conditions and to plant allelochemical defences. An important source of variation for the microbial diversity of fruit flies is represented by the crop on which larvae are feeding. However, a "crop effect" is not always the main driver of microbial patterns, and it is often observed in combination with other and less obvious processes. In this work, we aim at verifying if environmental stress and, by extension, changing environmental conditions, can promote microbial diversity in Zeugodacus cucurbitae (Coquillett), a cosmopolitan pest of cucurbit crops. With this objective, 16S rRNA metabarcoding was used to test differences in the microbial profiles of wild fly populations in a large experimental setup in Eastern Central Tanzania. The analysis of 2,973 unique ASV, which were assigned to 22 bacterial phyla, 221 families and 590 putative genera, show that microbial α diversity (as estimated by Abundance Coverage Estimator, Faith's Phylogenetic Diversity, Shannon-Weiner and the Inverse Simpson indexes) as well as β microbial diversity (as estimated by Compositional Data analysis of ASVs and of aggregated genera) significantly change as the species gets closer to its altitudinal limits, in farms where pesticides and agrochemicals are used. Most importantly, the multivariate dispersion of microbial patterns is significantly higher in these stressful environmental conditions thus indicating that Anna Karenina effects contribute to the microbial diversity of Z. cucurbitae. The crop effect was comparably weaker and detected as non-consistent changes across the experimental sites. We speculate that the impressive adaptive potential of polyphagous fruit flies is, at least in part, related to the Anna Karenina principle, which promotes stochastic changes in the microbial diversity of fly populations exposed to suboptimal environmental conditions.
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Affiliation(s)
- Nele Mullens
- Royal Museum for Central Africa, Biology Department, Tervuren, Belgium
- University of Antwerp, Department of Biology, Antwerp, Belgium
| | - Wouter Hendrycks
- Royal Museum for Central Africa, Biology Department, Tervuren, Belgium
- University of Antwerp, Department of Biology, Antwerp, Belgium
| | - Jackline Bakengesa
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Biology, University of Dodoma (UDOM), Dodoma, Tanzania
| | - Sija Kabota
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
- National Sugar Institute, Academic, Research and Consultancy Section, Morogoro, Tanzania
| | - Jenipher Tairo
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Hannes Svardal
- University of Antwerp, Department of Biology, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Ramadhani Majubwa
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Maulid Mwatawala
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Marc De Meyer
- Royal Museum for Central Africa, Biology Department, Tervuren, Belgium
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Jernfors T, Lavrinienko A, Vareniuk I, Landberg R, Fristedt R, Tkachenko O, Taskinen S, Tukalenko E, Mappes T, Watts PC. Association between gut health and gut microbiota in a polluted environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169804. [PMID: 38184263 DOI: 10.1016/j.scitotenv.2023.169804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, digestion of otherwise undigestible foodstuffs, and impacts on host behaviour. Exposure to stressors, such as environmental pollution, parasites, and/or predators, can alter the composition of the gut microbiome, potentially affecting host-microbiome interactions that can be manifest in the host as, for example, metabolic dysfunction or inflammation. However, whether a change in gut microbiota in wild animals associates with a change in host condition is seldom examined. Thus, we quantified whether wild bank voles inhabiting a polluted environment, areas where there are environmental radionuclides, exhibited a change in gut microbiota (using 16S amplicon sequencing) and concomitant change in host health using a combined approach of transcriptomics, histological staining analyses of colon tissue, and quantification of short-chain fatty acids in faeces and blood. Concomitant with a change in gut microbiota in animals inhabiting contaminated areas, we found evidence of poor gut health in the host, such as hypotrophy of goblet cells and likely weakened mucus layer and related changes in Clca1 and Agr2 gene expression, but no visible inflammation in colon tissue. Through this case study we show that inhabiting a polluted environment can have wide reaching effects on the gut health of affected animals, and that gut health and other host health parameters should be examined together with gut microbiota in ecotoxicological studies.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland.
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Igor Vareniuk
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Rikard Fristedt
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Olena Tkachenko
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Sara Taskinen
- Department of Mathematics and Statistics, University of Jyväskylä, FI-40014, Finland
| | - Eugene Tukalenko
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, 020000, Ukraine
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
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5
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Jones I, Marsh K, Handby TM, Hopkins K, Slezacek J, Bearhop S, Harrison XA. The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird. PeerJ 2023; 11:e16682. [PMID: 38130921 PMCID: PMC10734429 DOI: 10.7717/peerj.16682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Gut-associated microbial communities are known to play a vital role in the health and fitness of their hosts. Though studies investigating the factors associated with among-individual variation in microbiome structure in wild animal species are increasing, knowledge of this variation at the individual level is scarce, despite the clear link between microbiome and nutritional status uncovered in humans and model organisms. Here, we combine detailed observational data on life history and foraging preference with 16S rRNA profiling of the faecal microbiome to investigate the relationship between diet, microbiome stability and rates of body mass gain in a migratory capital-breeding bird, the light-bellied Brent goose (Branta bernicla hrota). Our findings suggest that generalist feeders have microbiomes that are intermediate in diversity and composition between two foraging specialisms, and also show higher within-individual plasticity. We also suggest a link between foraging phenotype and the rates of mass gain during the spring staging of a capital breeder. This study offers rare insight into individual-level temporal dynamics of the gut microbiome of a wild host. Further work is needed to uncover the functional link between individual dietary choices, gut microbiome structure and stability, and the implications this has for the reproductive success of this capital breeder.
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Affiliation(s)
- Isabelle Jones
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Kirsty Marsh
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Tess M. Handby
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Kevin Hopkins
- Institute of Zoology, Zoological Socety of London, London, United Kingdom
| | - Julia Slezacek
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Stuart Bearhop
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Xavier A. Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
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6
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Askenazi EM, Lazar EA, Grinberg I. Identification of High-Reliability Regions of Machine Learning Predictions Based on Materials Chemistry. J Chem Inf Model 2023; 63:7350-7362. [PMID: 37983482 DOI: 10.1021/acs.jcim.3c01684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Progress in the application of machine learning (ML) methods to materials design is hindered by the lack of understanding of the reliability of ML predictions, in particular, for the application of ML to small data sets often found in materials science. Using ML prediction for transparent conductor oxide formation energy and band gap, dilute solute diffusion, and perovskite formation energy, band gap, and lattice parameter as examples, we demonstrate that (1) construction of a convex hull in feature space that encloses accurately predicted systems can be used to identify regions in feature space for which ML predictions are highly reliable; (2) analysis of the systems enclosed by the convex hull can be used to extract physical understanding; and (3) materials that satisfy all well-known chemical and physical principles that make a material physically reasonable are likely to be similar and show strong relationships between the properties of interest and the standard features used in ML. We also show that similar to the composition-structure-property relationships, inclusion in the ML training data set of materials from classes with different chemical properties will not be beneficial for the accuracy of ML prediction and that reliable results likely will be obtained by ML model for narrow classes of similar materials even in the case where the ML model will show large errors on the data set consisting of several classes of materials.
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Affiliation(s)
- Evan M Askenazi
- Department of Chemistry, Bar-Ilan University, Ramat, Gan 52900, Israel
| | - Emanuel A Lazar
- Department of Mathematics, Bar-Ilan University, Ramat, Gan 52900, Israel
| | - Ilya Grinberg
- Department of Chemistry, Bar-Ilan University, Ramat, Gan 52900, Israel
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7
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Lu J, Mao J, Qi X, Chen J, Xiong J. The assembly of gut microbiota implicates shrimp acute hepatopancreas necrosis disease progression. Appl Microbiol Biotechnol 2023; 107:7489-7500. [PMID: 37768346 DOI: 10.1007/s00253-023-12810-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Ample evidence shows dysbiosis in the gut microbiota when comparing healthy shrimp with those affected by severe acute hepatopancreatic necrosis disease (AHPND). However, the static comparison used in available studies leads to the uncertainties regarding how and to what extent the gut microbiota responds to the progressive severity of AHPND. In addition, shrimp AHPND is featured by rapid and massive mortality, thus the initiation of AHPND must be diagnosed for preemptive therapy. For these reasons, we explored the ecological assembly of gut microbiota over shrimp AHPND progression. Increasing AHPND severity was associated with linear increase in the copies of pirAB genes, relative abundance of gut Vibrio and potentially pathogenic, and reduction in the gut bacterial diversity, stability, and relative abundance of Bdellovibrio. Negative and significant association between gut Vibrio and Bdellovibrio were noted, indicating that compromised predation exerts a role in AHPND progression. Notably, the extents of departure to the healthy shrimp gut microbiota were positively coupled with the increasing severity of AHPND. After controlling the temporal variation in the gut microbiota as healthy shrimp age, we constructed a diagnosis model that accurately diagnosed the initial, progressed or moribund stages of AHPND, with an overall accuracy of 86.5%. Shrimp AHPND induced more stochastic gut microbiotas as a consequence of the attenuated ability of diseased shrimp to select their commensals, resulting in convergent bacterial communities between gut and rearing water over AHPND progression. Collectively, our findings provide important step toward the ecological assembly of gut microbiota implicating in AHPND etiology and in diagnosing AHPND stages. KEY POINTS: • The departure of shrimp gut microbiota positively linked with AHPND severity. • The diagnosis model accurately diagnosed the stages of AHPND. • Shrimp AHPND induced more stochastic gut microbiota.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiangning Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xuejing Qi
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Dai X, Han YX, Shen QY, Tang H, Cheng LZ, Yang FP, Wei WH, Yang SM. Effect of Food Restriction on Food Grinding in Brandt's Voles. Animals (Basel) 2023; 13:3424. [PMID: 37958179 PMCID: PMC10647212 DOI: 10.3390/ani13213424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Food grinding is supposed to be influenced by multiple factors. However, how those factors affecting this behavior remain unclear. In this study, we investigated the effect of food restriction on food grinding in Brandt's voles (Lasiopodomys brandtii), as well as the potential role of the gut microbiota in this process, through a comparison of the variations between voles with different food supplies. Food restriction reduced the relative amount of ground food to a greater extent than it lowered the relative food consumption, and altered the abundance of Staphylococcus, Aerococcus, Jeotgalicoccus, and Un--s-Clostridiaceae bacterium GM1. Fecal acetate content for the 7.5 g-food supply group was lower than that for the 15 g-food supply group. Our study indicated that food restriction could effectively inhibit food grinding. Further, Un--s-Clostridiaceae bacterium GM1 abundance, Aerococcus abundance, and acetate content were strongly related to food grinding. Variations in gut microbial abundance and short-chain fatty acid content induced by food restriction likely promote the inhibition of food grinding. These results could potentially provide guidance for reducing food waste during laboratory rodent maintenance.
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Affiliation(s)
- Xin Dai
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Yu-Xuan Han
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Qiu-Yi Shen
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Hao Tang
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Li-Zhi Cheng
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Feng-Ping Yang
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Wan-Hong Wei
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Sheng-Mei Yang
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
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Florkowski MR, Hamer SA, Yorzinski JL. Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad096. [PMID: 37586886 DOI: 10.1093/femsec/fiad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.
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Affiliation(s)
- Melanie R Florkowski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
| | - Sarah A Hamer
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Schubot Center for Avian Health, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 701 Farm to Market Service Road, College Station, TX 77840, United States
| | - Jessica L Yorzinski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Department of Ecology and Conservation Biology, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
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10
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Fernandes A, Oliveira A, Soares R, Barata P. The Effects of Ionizing Radiation on Gut Microbiota: What Can Animal Models Tell Us?-A Systematic Review. Curr Issues Mol Biol 2023; 45:3877-3910. [PMID: 37232718 DOI: 10.3390/cimb45050249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/16/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The gut microbiota is relatively stable; however, various factors can precipitate an imbalance that is known to be associated with various diseases. We aimed to conduct a systematic literature review of studies reporting the effects of ionizing radiation on the composition, richness, and diversity of the gut microbiota of animals. METHODS A systematic literature search was performed in PubMed, EMBASE, and Cochrane library databases. The standard methodologies expected by Cochrane were utilized. RESULTS We identified 3531 non-duplicated records and selected twenty-nine studies after considering the defined inclusion criteria. The studies were found to be heterogeneous, with significant differences in the chosen populations, methodologies, and outcomes. Overall, we found evidence of an association between ionizing radiation exposure and dysbiosis, with a reduction of microbiota diversity and richness and alterations in the taxonomic composition. Although differences in taxonomic composition varied across studies, Proteobacteria, Verrucomicrobia, Alistipes, and Akkermancia most consistently reported to be relatively more abundant after ionizing radiation exposure, whereas Bacteroidetes, Firmicutes, and Lactobacillus were relatively reduced. CONCLUSIONS This review highlights the effect of ionizing exposure on gut microbiota diversity, richness, and composition. It paves the way for further studies on human subjects regarding gastrointestinal side effects in patients submitted to treatments with ionizing radiation and the development of potential preventive, therapeutic approaches.
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Affiliation(s)
- Ana Fernandes
- Department Nuclear Medicine, Centro Hospitalar e Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Ana Oliveira
- Department Nuclear Medicine, Centro Hospitalar e Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Raquel Soares
- i3S-Institute for Research and Innovation in Health, Universidade do Porto, 4200-135 Porto, Portugal
- Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Pedro Barata
- i3S-Institute for Research and Innovation in Health, Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal
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11
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Dysbiotic microbiome variation in colorectal cancer patients is linked to lifestyles and metabolic diseases. BMC Microbiol 2023; 23:33. [PMID: 36709262 PMCID: PMC9883847 DOI: 10.1186/s12866-023-02771-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/12/2023] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Differences in the composition and diversity of the gut microbial communities among individuals are influenced by environmental factors. However, there is limited research on factors affecting microbiome variation in colorectal cancer patients, who display lower inter-individual variations than that of healthy individuals. In this study, we examined the association between modifiable factors and the microbiome variation in colorectal cancer patients. METHODS A total of 331 colorectal cancer patients who underwent resection surgery at the Department of Surgery, Seoul National University Hospital between October 2017 and August 2019 were included. Fecal samples from colorectal cancer patients were collected prior to the surgery. Variations in the gut microbiome among patients with different lifestyles and metabolic diseases were examined through the network analysis of inter-connected microbial abundance, the assessment of the Anna Karenina principle effect for microbial stochasticity, and the identification of the enriched bacteria using linear discrimination analysis effect size. Associations of dietary diversity with microbiome variation were investigated using the Procrustes analysis. RESULTS We found stronger network connectivity of microbial communities in non-smokers, non-drinkers, obese individuals, hypertensive subjects, and individuals without diabetes than in their counterparts. The Anna Karenina principle effect was found for history of smoking, alcohol consumption, and diabetes (with significantly greater intra-sample similarity index), whereas obesity and hypertension showed the anti-Anna Karenina principle effect (with significantly lower intra-sample similarity index). We found certain bacterial taxa to be significantly enriched in patients of different categories of lifestyles and metabolic diseases using linear discrimination analysis. Diversity of food and nutrient intake did not shape the microbial diversity between individuals (pProcrustes>0.05). CONCLUSIONS Our findings suggested an immune dysregulation and a reduced ability of the host and its microbiome in regulating the community composition. History of smoking, alcohol consumption, and diabetes were shown to affect partial individuals in shifting new microbial communities, whereas obesity and history of hypertension appeared to affect majority of individuals and shifted to drastic reductions in microbial compositions. Understanding the contribution of modifiable factors to microbial stochasticity may provide insights into how the microbiome regulates effects of these factors on the health outcomes of colorectal cancer patients.
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12
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Arnault G, Mony C, Vandenkoornhuyse P. Plant microbiota dysbiosis and the Anna Karenina Principle. TRENDS IN PLANT SCIENCE 2023; 28:18-30. [PMID: 36127241 DOI: 10.1016/j.tplants.2022.08.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/19/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.
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Affiliation(s)
- Gontran Arnault
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
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13
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Li J, Bates KA, Hoang KL, Hector TE, Knowles SCL, King KC. Experimental temperatures shape host microbiome diversity and composition. GLOBAL CHANGE BIOLOGY 2023; 29:41-56. [PMID: 36251487 PMCID: PMC10092218 DOI: 10.1111/gcb.16429] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/20/2022] [Indexed: 05/10/2023]
Abstract
Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms-especially in marine habitats-experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.
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Affiliation(s)
- Jingdi Li
- Department of BiologyUniversity of OxfordOxfordUK
| | | | - Kim L. Hoang
- Department of BiologyUniversity of OxfordOxfordUK
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14
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Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits. THE ISME JOURNAL 2022; 16:2610-2621. [PMID: 35974086 PMCID: PMC9563048 DOI: 10.1038/s41396-022-01295-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/08/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations belonging to the bacteria and archaea domains show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns that exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global challenges of food security and sustainability.
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15
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Hanhimäki E, Watts PC, Koskela E, Koteja P, Mappes T, Hämäläinen AM. Evolved high aerobic capacity has context-specific effects on gut microbiota. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.934164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota is expected to coevolve with the host's physiology and may play a role in adjusting the host's energy metabolism to suit the host's environment. To evaluate the effects of both evolved host metabolism and the environmental context in shaping the gut microbiota, we used a unique combination of (1) experimental evolution to create selection lines for a fast metabolism and (2) a laboratory-to-field translocation study. Mature bank voles Myodes glareolus from lines selected for high aerobic capacity (A lines) and from unselected control (C lines) were released into large (0.2 ha) outdoor enclosures for longitudinal monitoring. To examine whether the natural environment elicited a similar or more pronounced impact on the gut microbiota of the next generation, we also sampled the field-reared offspring. The gut microbiota were characterized using 16S rRNA amplicon sequencing of fecal samples. The artificial selection for fast metabolism had minimal impact on the gut microbiota in laboratory conditions but in field conditions, there were differences between the selection lines (A lines vs. C lines) in the diversity, community, and resilience of the gut microbiota. Notably, the selection lines differed in the less abundant bacteria throughout the experiment. The lab-to-field transition resulted in an increase in alpha diversity and an altered community composition in the gut microbiota, characterized by a significant increase in the relative abundance of Actinobacteria and a decrease of Patescibacteria. Also, the selection lines showed different temporal patterns in changes in microbiota composition, as the average gut microbiota alpha diversity of the C lines, but not A lines, was temporarily reduced during the initial transition to the field. In surviving young voles, the alpha diversity of gut microbiota was significantly higher in A-line than C-line voles. These results indicate that the association of host metabolism and gut microbiota is context-specific, likely mediated by behavioral or physiological modifications in response to the environment.
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16
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Leclaire S, Pineaux M, Blanchard P, White J, Hatch SA. Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird. Mol Ecol 2022; 32:2115-2133. [PMID: 35152516 DOI: 10.1111/mec.16398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Abstract
The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Maxime Pineaux
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Pierrick Blanchard
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Joël White
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
- ENSFEA Castanet‐Tolosan France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation Anchorage AK 99516 USA
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17
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Kivisaari K, Calhim S, Lehmann P, Boratyński Z, Mousseau TA, Møller AP, Mappes T. Chronic Background Radiation Correlates With Sperm Swimming Endurance in Bank Voles From Chernobyl. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.736389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sperm quantity and quality are key features explaining intra- and interspecific variation in male reproductive success. Spermatogenesis is sensitive to ionizing radiation and laboratory studies investigating acute effects of ionizing radiation have indeed found negative effects of radiation on sperm quantity and quality. In nature, levels of natural background radiation vary dramatically, and chronic effects of low-level background radiation exposure on spermatogenesis are poorly understood. The Chernobyl region offers a unique research opportunity for investigating effects of chronic low-level ionizing radiation on reproductive properties of wild organisms. We captured male bank voles (Myodes glareolus) from 24 locations in the Chernobyl exclusion zone in 2011 and 2015 and collected information on sperm morphology and kinetics. The dataset is limited in size and there overall was a relatively weak correlation between background radiation and sperm quality. Still, some correlations are worth discussing. First, mid-piece segments of spermatozoa tended to be smaller in bank vole males from areas with elevated background radiation levels. Second, we demonstrated a significant positive relationship between background radiation dose rates and the proportion of static spermatozoa among males within and among study locations after 10 as well as 60 min of incubation. Our results provide novel evidence of damaging effects of low dose ionizing radiation on sperm performance in wild rodent populations, and highlight that this topic requires further study across the natural gradients of background radiation that exist in nature.
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18
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Abstract
Environmental disasters offer the unique opportunity for landscape-scale ecological and evolutionary studies that are not possible in the laboratory or small experimental plots. The nuclear accident at Chernobyl (1986) allows for rigorous analyses of radiation effects on individuals and populations at an ecosystem scale. Here, the current state of knowledge related to populations within the Chernobyl region of Ukraine and Belarus following the largest civil nuclear accident in history is reviewed. There is now a significant literature that provides contrasting and occasionally conflicting views of the state of animals and how they are affected by this mutagenic stressor. Studies of genetic and physiological effects have largely suggested significant injuries to individuals inhabiting the more radioactive areas of the Chernobyl region. Most population censuses for most species suggest that abundances are reduced in the more radioactive areas.
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Affiliation(s)
- Timothy A. Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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19
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MacLeod KJ, Kohl KD, Trevelline BK, Langkilde T. Context-dependent effects of glucocorticoids on the lizard gut microbiome. Mol Ecol 2021; 31:185-196. [PMID: 34661319 DOI: 10.1111/mec.16229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/19/2021] [Accepted: 10/11/2021] [Indexed: 12/25/2022]
Abstract
The vertebrate gut microbiota (bacterial, archaeal and fungal communities of the gastrointestinal tract) can have profound effects on the physiological processes of their hosts. Although relatively stable, changes in microbiome structure and composition occur due to changes in the environment, including exposure to stressors and associated increases in glucocorticoid hormones. Although a growing number of studies have linked stressor exposure to microbiome changes, few studies have experimentally explored the specific influence of glucocorticoids on the microbiome in wild animals, or across ecologically important processes (e.g., reproductive stages). Here we tested the response of the gut microbiota of adult female Sceloporus undulatus across gestation to ecologically relevant elevations of a stress-relevant glucocorticoid hormone (CORT) in order to determine (i) how experimentally elevated CORT influenced microbiome characteristics, and (ii) whether this relationship was dependent on reproductive context (i.e., whether females were gravid or not, and, in those that were gravid, gestational stage). We show that the effects of CORT on gut microbiota are complex and depend on both gestational state and stage. CORT treatment altered microbial community membership and resulted in an increase in microbiome diversity in late-gestation females, and microbial community membership varied according to treatment. In nongravid females, CORT treatment decreased interindividual variation in microbial communities, but this effect was not observed in late-gestation females. Our results highlight the need for a more holistic understanding of the downstream physiological effects of glucocorticoids, as well as the importance of context (here, gestational state and stage) in interpreting stress effects in ecology.
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Affiliation(s)
- Kirsty J MacLeod
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biology, Lund University, Lund, Sweden
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian K Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.,Cornell Laboratory of Ornithology, Cornell University, Ithaca, New York, USA
| | - Tracy Langkilde
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.,Center for Brain, Behavior and Cognition, Pennsylvania State University, University Park, Pennsylvania, USA
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20
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Jernfors T, Danforth J, Kesäniemi J, Lavrinienko A, Tukalenko E, Fajkus J, Dvořáčková M, Mappes T, Watts PC. Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles Myodes glareolus exposed to environmental radionuclides. Ecol Evol 2021; 11:8754-8767. [PMID: 34257925 PMCID: PMC8258220 DOI: 10.1002/ece3.7684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Altered copy number of certain highly repetitive regions of the genome, such as satellite DNA within heterochromatin and ribosomal RNA loci (rDNA), is hypothesized to help safeguard the genome against damage derived from external stressors. We quantified copy number of the 18S rDNA and a pericentromeric satellite DNA (Msat-160) in bank voles (Myodes glareolus) inhabiting the Chernobyl Exclusion Zone (CEZ), an area that is contaminated by radionuclides and where organisms are exposed to elevated levels of ionizing radiation. We found a significant increase in 18S rDNA and Msat-160 content in the genomes of bank voles from contaminated locations within the CEZ compared with animals from uncontaminated locations. Moreover, 18S rDNA and Msat-160 copy number were positively correlated in the genomes of bank voles from uncontaminated, but not in the genomes of animals inhabiting contaminated, areas. These results show the capacity for local-scale geographic variation in genome architecture and are consistent with the genomic safeguard hypothesis. Disruption of cellular processes related to genomic stability appears to be a hallmark effect in bank voles inhabiting areas contaminated by radionuclides.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - John Danforth
- Department of Biochemistry & Molecular BiologyRobson DNA Science CentreArnie Charbonneau Cancer InstituteCumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Jenni Kesäniemi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anton Lavrinienko
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Eugene Tukalenko
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- National Research Center for Radiation Medicine of the National Academy of Medical ScienceKyivUkraine
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
- Laboratory of Functional Genomics and ProteomicsNCBRFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Department of Cell Biology and RadiobiologyInstitute of Biophysics of the Czech Academy of SciencesBrnoCzech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Tapio Mappes
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Phillip C. Watts
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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21
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Boratyński Z, Mousseau TA, Møller AP. Individual quality and phenology mediate the effect of radioactive contamination on body temperature in Chernobyl barn swallows. Ecol Evol 2021; 11:9039-9048. [PMID: 34257943 PMCID: PMC8258232 DOI: 10.1002/ece3.7742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/29/2022] Open
Abstract
Anthropogenic stressors, such as radioactive contaminants released from the Chernobyl and Fukushima Daiichi accidents, deteriorate ecological and evolutionary processes, as evidence for damaging effects of radioactive contamination on wildlife is accumulating. Yet little is known about physiological traits of animals inhabiting contaminated areas, and how those are affected by individual quality and phenology. We investigated variation in body temperature of wild barn swallows, Hirundo rustica, exposed to radioactive contamination from the Chernobyl accident in Ukraine and Belarus. We tested whether exposure to variable levels of radioactive contamination modified core body temperature of birds, and whether individual and phenological characteristics modulated radiosensitivity of body temperature. We showed that barn swallow body temperature varied with exposure to environmental radioactive contamination and that individual characteristics and phenology affected radioactive exposure. Increased radiosensitivity and up-regulation of body temperature were detected in birds of low body condition, high risk of capture, and in animals captured late during the day but early during the season. These results highlight the complex ways that the body temperature of a wild bird is impacted by exposure to increased radioactive contamination in natural habitats. By impacting body temperature, increased radioactive contamination may compromise energetic balance, jeopardize responsiveness to global warming, and increase risk of overheating.
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Affiliation(s)
- Zbyszek Boratyński
- CIBIO/InBioResearch Centre in Biodiversity and Genetic ResourcesUniversity of PortoPortoPortugal
| | - Timothy A. Mousseau
- Department of Biological SciencesUniversity of South CarolinaColumbiaSCUSA
- SURA/LASSO/NASAISS Utilization and Life Sciences DivisionKennedy Space CenterCape CanaveralFLUSA
| | - Anders Pape Møller
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
- Ecologie Systematique EvolutionCNRSAgroParisTechUniversite Paris‐SaclayOrsayFrance
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22
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Lavrinienko A, Hämäläinen A, Hindström R, Tukalenko E, Boratyński Z, Kivisaari K, Mousseau TA, Watts PC, Mappes T. Comparable response of wild rodent gut microbiome to anthropogenic habitat contamination. Mol Ecol 2021; 30:3485-3499. [PMID: 33955637 DOI: 10.1111/mec.15945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Species identity is thought to dominate over environment in shaping wild rodent gut microbiota, but it remains unknown whether the responses of host gut microbiota to shared anthropogenic habitat impacts are species-specific or if the general gut microbiota response is similar across host species. Here, we compare the influence of exposure to radionuclide contamination on the gut microbiota of four wild mouse species: Apodemus flavicollis, A. sylvaticus, A. speciosus and A. argenteus. Building on the evidence that radiation impacts bank vole (Myodes glareolus) gut microbiota, we hypothesized that radiation exposure has a general impact on rodent gut microbiota. Because we sampled (n = 288) two species pairs of Apodemus mice that occur in sympatry in habitats affected by the Chernobyl and Fukushima nuclear accidents, these comparisons provide an opportunity for a general assessment of the effects of exposure to environmental contamination (radionuclides) on gut microbiota across host phylogeny and geographical areas. In general agreement with our hypothesis, analyses of bacterial 16S rRNA gene sequences revealed that radiation exposure alters the gut microbiota composition and structure in three of the four species of Apodemus mice. The notable lack of an association between the gut microbiota and soil radionuclide contamination in one mouse species from Fukushima (A. argenteus) probably reflects host "radiation escape" through its unique tree-dwelling lifestyle. The finding that host ecology can modulate effects of radiation exposure offers an interesting counterpoint for future analyses into effects of radiation or any other toxic exposure on host and its associated microbiota. Our data show that exposure to radionuclide contamination is linked to comparable gut microbiota responses across multiple species of rodents.
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Affiliation(s)
- Anton Lavrinienko
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anni Hämäläinen
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | | | - Eugene Tukalenko
- Ecology and Genetics, University of Oulu, Oulu, Finland.,National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv, Ukraine
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Kati Kivisaari
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,SURA/LASSO/NASA, ISS Utilization and Life Sciences Division, Kennedy Space Center, Cape Canaveral, FL, USA
| | - Phillip C Watts
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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23
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Antwis R. A boom-or-bust approach-The 'Glass Cannon' hypothesis in host microbiomes. J Anim Ecol 2021; 90:1024-1026. [PMID: 33960407 DOI: 10.1111/1365-2656.13500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/26/2022]
Abstract
In Focus: Dunphy, CM, Vollmer, SV, Gouhier, TC. (2021) Host-microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations. Journal of Animal Ecology, 90, 1044-1057. The importance of symbiotic microbial communities for the functioning of animal hosts is now well-documented; however, the interactions between host microbiomes and stress are less well-understood. Dunphy et al. used a common garden experiment to show that host-microbiomes vary in their resilience across different coral species. The authors then used mathematical modelling to provide novel evidence that species with microbiomes that are regulated by host processes are robust to perturbation from stressors, but that robustness comes at a higher cost to the host. Conversely, species with microbiomes that are regulated by microbial processes are generally much more resilient and cheaper to support, but when disrupted by external stressors, the communities break down entirely-these latter species are termed 'glass cannons'. This novel hypothesis has important implications for how host microbiomes function in a rapidly changing world that exposes animal hosts to multiple biotic and abiotic perturbations.
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Affiliation(s)
- Rachael Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
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24
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Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota. Sci Data 2020; 7:312. [PMID: 32968071 PMCID: PMC7511399 DOI: 10.1038/s41597-020-00656-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022] Open
Abstract
Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents. Measurement(s) | genome • DNA • gut microbiome measurement • metagenomic data | Technology Type(s) | DNA sequencing | Sample Characteristic - Organism | Bacteroidetes • Firmicutes • Spirochaetes • Proteobacteria • Myodes glareolus |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12936797
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