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Scheelings TF, Kodikara S, Beale DJ, Van TTH, Moore RJ, Skerratt LF. Pondering Ponds: Exploring Correlations Between Cloacal Microbiota and Blood Metabolome in Freshwater Turtles. MICROBIAL ECOLOGY 2025; 88:50. [PMID: 40404904 PMCID: PMC12098208 DOI: 10.1007/s00248-025-02556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Accepted: 05/15/2025] [Indexed: 05/24/2025]
Abstract
The gut microbiota of vertebrates significantly influences host physiology, yet little is known about how habitat factors shape microbiotas in non-human species, especially freshwater turtles. This study explores the relationship between cloacal microbiota and serum metabolome in eastern longneck turtles (Chelodina longicollis), marking the first such investigation in chelonians. By comparing microbiotas from two distinct pond environments, we applied a multi-omics approach combining 16S rRNA sequencing and metabolomic profiling. Results showed that location influenced microbial composition and metabolic profiles, with dominant bacterial phyla Pseudomonadota, Actinomycetota, and Bacillota, and distinct families linked to differences in microbial diversity. Notably, turtles from one pond displayed an unusually high proportion of Actinomycetota. We also found a clear connection between microbiota diversity and metabolome, suggesting certain bacterial combinations impact host physiology. These findings offer important insights into the complex interaction between microbial communities and metabolism in freshwater turtles, a highly threatened group. This research emphasises the value of integrating microbiota and metabolomic data in conservation strategies and highlights the need for further longitudinal studies to explore the dynamic host-microbiota relationship in these understudied species.
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Affiliation(s)
- T Franciscus Scheelings
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, 3030, Australia.
| | - Saritha Kodikara
- School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Parkville, 3052, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, 4102, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, 3083, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, 3083, Australia
| | - Lee F Skerratt
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, 3030, Australia
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2
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Rehermann B, Graham AL, Masopust D, Hamilton SE. Integrating natural commensals and pathogens into preclinical mouse models. Nat Rev Immunol 2025; 25:385-397. [PMID: 39562646 DOI: 10.1038/s41577-024-01108-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2024] [Indexed: 11/21/2024]
Abstract
Fundamental discoveries in many aspects of mammalian physiology have been made using laboratory mice as research models. These studies have been facilitated by the genetic tractability and inbreeding of such mice, the large set of immunological reagents that are available, and the establishment of environmentally controlled, high-throughput facilities. Such facilities typically include barriers to keep the mouse colonies free of pathogens and the frequent re-derivation of the mice severely limits their commensal flora. Because humans have co-evolved with microorganisms and are exposed to a variety of pathogens, a growing community of researchers posits that preclinical disease research can be improved by studying mice in the context of the microbiota and pathogens that they would encounter in the natural world. Here, we provide a perspective of how these different approaches can be combined and integrated to improve existing mouse models to enhance our understanding of disease mechanisms and develop new therapies for humans. We also propose that the term 'mice with natural microbiota' is more appropriate for describing these models than existing terms such as 'dirty mice'.
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Affiliation(s)
- Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Andrea L Graham
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - David Masopust
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Sara E Hamilton
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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3
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Pallen MJ, Ponsero AJ, Telatin A, Moss CJ, Baker D, Heavens D, Davidson GL. Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity. Access Microbiol 2025; 7:000910.v3. [PMID: 40302838 PMCID: PMC12038002 DOI: 10.1099/acmi.0.000910.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 04/14/2025] [Indexed: 05/02/2025] Open
Abstract
Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.
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Affiliation(s)
- Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Cara-Jane Moss
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ UK
| | - Gabrielle L. Davidson
- University of East Anglia, Norwich Research Park, Norwich, UK
- University of Cambridge, Downing Street, Cambridge, CB2 3EB, UK
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Degregori S, Wang X, Kommala A, Schulhof N, Moradi S, MacDonald A, Eblen K, Jukovich S, Smith E, Kelleher E, Suzuki K, Hall Z, Knight R, Amato KR. Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices. Biol Rev Camb Philos Soc 2025; 100:748-763. [PMID: 39530277 PMCID: PMC11885713 DOI: 10.1111/brv.13161] [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: 02/07/2024] [Revised: 10/20/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]
Abstract
Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.
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Affiliation(s)
- Samuel Degregori
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Xiaolin Wang
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Akhil Kommala
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Noah Schulhof
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Sadaf Moradi
- Department of Ecology and Evolutionary BiologyUniversity of California621 Young Drive SouthLos AngelesCA90095USA
| | - Allison MacDonald
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Kaitlin Eblen
- Department of Ecology and Evolutionary BiologyUniversity of California621 Young Drive SouthLos AngelesCA90095USA
| | - Sophia Jukovich
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Emma Smith
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Emily Kelleher
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Kota Suzuki
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Zoey Hall
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Rob Knight
- Department of PediatricsUniversity of CaliforniaSan DiegoLa JollaCA92093USA
| | - Katherine Ryan Amato
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
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Tingga RCT, Mohd-Ridwan AR, Denel A, Md-Zain BM. Profiling the Gut Microbiome of Hylobatidae and Cercopithecinae: Insights Into the Health of Primates in Captivity. J Med Primatol 2025; 54:e70008. [PMID: 39994494 DOI: 10.1111/jmp.70008] [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: 10/23/2024] [Revised: 12/18/2024] [Accepted: 02/04/2025] [Indexed: 02/26/2025]
Abstract
BACKGROUND A healthy gut microbiome is essential for digestion in primates, for developing the gut immune system, and for defense against pathogen invasion. Next-generation sequencing allows for determining the microbiome composition and enables the continuous monitoring of primate health. METHODS To comprehensively analyze the gut microbiome diversity of three endangered primate species at Matang Wildlife Centre-Hylobates abbotti, Macaca fascicularis, and Macaca nemestrina, using high-throughput sequencing of the 16S rRNA gene. RESULTS A total of 18 phyla, 84 families, 188 genera, and 46 species were successfully classified. H. abbotti exhibited the highest microbial diversity with a distinct microbiome profile from the Macaca species. The presence of Treponema (nonpallidum), Bifidobacterium, and Faecalibacterium prausnitzii is critical for gut health, promoting digestion and maintaining the microbial balance. CONCLUSION This study highlights the importance of monitoring microbial diversity in captive primates to better understand their health and facilitate the early detection of potential pathogens. This also offers insights into microbiome-based strategies for improving overall animal welfare.
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Affiliation(s)
- Roberta Chaya Tawie Tingga
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | | | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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6
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Heidrich V, Valles-Colomer M, Segata N. Human microbiome acquisition and transmission. Nat Rev Microbiol 2025:10.1038/s41579-025-01166-x. [PMID: 40119155 DOI: 10.1038/s41579-025-01166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2025] [Indexed: 03/24/2025]
Abstract
As humans, we host personal microbiomes intricately connected to our biology and health. Far from being isolated entities, our microbiomes are dynamically shaped by microbial exchange with the surroundings, in lifelong microbiome acquisition and transmission processes. In this Review, we explore recent studies on how our microbiomes are transmitted, beginning at birth and during interactions with other humans and the environment. We also describe the key methodological aspects of transmission inference, based on the uniqueness of the building blocks of the microbiome - single microbial strains. A better understanding of human microbiome transmission will have implications for studies of microbial host regulation, of microbiome-associated diseases, and for effective microbiome-targeting strategies. Besides exchanging strains with other humans, there is also preliminary evidence we acquire microorganisms from animals and food, and thus a complete understanding of microbiome acquisition and transmission can only be attained by adopting a One Health perspective.
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Affiliation(s)
| | | | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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7
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Sprockett DD, Dillard BA, Landers AA, Sanders JG, Moeller AH. Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice. Nat Commun 2025; 16:2218. [PMID: 40044678 PMCID: PMC11883045 DOI: 10.1038/s41467-025-57435-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 02/19/2025] [Indexed: 03/09/2025] Open
Abstract
Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice but whose evolutionary histories are unclear. Here, we show that laboratory mice have retained gut bacterial lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that laboratory-mouse gut microbiota (LGM) strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past ~ 120 years of captivity. Compared to closely related wild-mouse gut microbiota (WGM) strains, co-diversified LGM strains displayed significantly faster genome-wide rates of nonsynonymous substitutions, indicating elevated genetic drift-a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.
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Affiliation(s)
- Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Brian A Dillard
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Abigail A Landers
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08540, USA.
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8
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Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O'Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RMT, Thinnes CC, Thiele I. A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. Cell Syst 2025; 16:101196. [PMID: 39947184 DOI: 10.1016/j.cels.2025.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 10/04/2024] [Accepted: 01/15/2025] [Indexed: 02/19/2025]
Abstract
Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland; Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Timothy Otto Hulshof
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Arianna Basile
- School of Medicine, University of Galway, Galway, Ireland; Department of Biology, University of Padova, Padova, Italy
| | | | | | | | | | | | - Ian Lalor
- University of Galway, Galway, Ireland
| | | | | | | | | | | | | | | | | | | | - Cyrille C Thinnes
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland; Division of Microbiology, University of Galway, Galway, Ireland; APC Microbiome Ireland, Cork, Ireland.
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9
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Heidrich V, Fackelmann G, Malesevic M, Armanini F, Dey H, Mengoni C, Stanisavljevic N, Vukotic G, Segata N. Newly identified species from the dog dental plaque microbiome highlight little overlap with humans. NPJ Biofilms Microbiomes 2025; 11:30. [PMID: 39966419 PMCID: PMC11836392 DOI: 10.1038/s41522-025-00665-2] [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: 10/03/2024] [Accepted: 02/08/2025] [Indexed: 02/20/2025] Open
Abstract
Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.
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Affiliation(s)
- Vitor Heidrich
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Gloria Fackelmann
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Hrituraj Dey
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Claudia Mengoni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Nemanja Stanisavljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Goran Vukotic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- European Institute of Oncology, Scientific Institute for Research, Hospitalization and Healthcare, Milan, Italy.
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Bhosle A, Jackson MI, Walsh AM, Franzosa EA, Badri DV, Huttenhower C. Response of the gut microbiome and metabolome to dietary fiber in healthy dogs. mSystems 2025; 10:e0045224. [PMID: 39714168 PMCID: PMC11748496 DOI: 10.1128/msystems.00452-24] [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: 03/28/2024] [Accepted: 10/21/2024] [Indexed: 12/24/2024] Open
Abstract
Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects. IMPORTANCE Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.
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Affiliation(s)
- Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Aaron M. Walsh
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric A. Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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11
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Dmitrijeva M, Ruscheweyh HJ, Feer L, Li K, Miravet-Verde S, Sintsova A, Mende DR, Zeller G, Sunagawa S. The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities. Nucleic Acids Res 2025; 53:D797-D805. [PMID: 39526369 PMCID: PMC11701688 DOI: 10.1093/nar/gkae1004] [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: 08/15/2024] [Revised: 10/03/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024] Open
Abstract
Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communities. However, genome-resolved microbial diversity on Earth remains undersampled, and accessing the genomic context of taxa detected during taxonomic profiling remains a challenging task. Here, we present the mOTUs online database (mOTUs-db), which is consistent with and interfaces with the mOTUs taxonomic profiling tool. It comprises 2.83 million metagenome-assembled genomes (MAGs) and 919 090 single-cell and isolate genomes from 124 295 species-level taxonomic units. In addition to being one of the largest prokaryotic genome resources to date, all MAGs in the mOTUs-db were reconstructed de novo in 117 902 individual samples by abundance correlation of scaffolds across multiple samples for improved quality metrics. The database complements the Genome Taxonomy Database, with over 50% of its species-level taxonomic groups being unique. It also offers interactive querying, enabling users to explore and download genomes at various taxonomic levels. The mOTUs-db is accessible at https://motus-db.org.
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Affiliation(s)
- Marija Dmitrijeva
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Lilith Feer
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Kang Li
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Samuel Miravet-Verde
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Anna Sintsova
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Daniel R Mende
- Medical Microbiology and Infection Prevention (MMI), Amsterdam University Medical Center, 1105AZ Amsterdam, The Netherlands
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, 2333ZA Leiden, The Netherlands
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, 2333ZA Leiden, Netherlands
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
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12
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Lee CZ, Worsley SF, Davies CS, Silan E, Burke T, Komdeur J, Hildebrand F, Dugdale HL, Richardson DS. Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance. ISME COMMUNICATIONS 2025; 5:ycaf008. [PMID: 39968350 PMCID: PMC11833318 DOI: 10.1093/ismeco/ycaf008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 01/15/2025] [Accepted: 01/22/2025] [Indexed: 02/20/2025]
Abstract
Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.
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Affiliation(s)
- Chuen Zhang Lee
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR47TJ, United Kingdom
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR47TJ, United Kingdom
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR47TJ, United Kingdom
| | - Ece Silan
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR47UQ, United Kingdom
| | - Terry Burke
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S102TN, United Kingdom
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9718 BG, Groningen, The Netherlands
| | - Falk Hildebrand
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR47UQ, United Kingdom
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9718 BG, Groningen, The Netherlands
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR47TJ, United Kingdom
- Nature Seychelles, Roche Caiman, Mahé, 1310, Republic of Seychelles, Seychelles
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13
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Coba-Males MA, Díaz M, Molina CA, Medrano-Vizcaíno P, Brito-Zapata D, Martin-Solano S, Ocaña-Mayorga S, Carrillo-Bilbao GA, Narváez W, Arrivillaga-Henríquez J, González-Suárez M, Enríquez S, Poveda A. Gut bacterial communities in roadkill animals: A pioneering study of two species in the Amazon region in Ecuador. PLoS One 2024; 19:e0313263. [PMID: 39775386 PMCID: PMC11684718 DOI: 10.1371/journal.pone.0313263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 10/21/2024] [Indexed: 01/11/2025] Open
Abstract
Studying the microbial communities within the gastrointestinal tract of vertebrate species can provide insights into biodiversity, disease ecology, and conservation. Currently, we have very limited understanding of the composition of endogenous microbiota in wildlife, particularly in high biodiversity tropical areas. Knowledge is limited by the logistical and ethical challenges of obtaining samples for free-living animals. Roadkill carcasses offer a largely untapped source for biological material, including endogenous gut microbiota. These animals that have died on roads due to collisions with vehicles are suitable for accessible, opportunistic sampling. Here, we used metabarcoding for the V3-V4 region of the 16S rRNA gene in gut samples of nine roadkill samples collected from a road in Ecuador representing two vertebrate species: the speckled worm lizard (Amphisbaena bassleri) and the smooth-billed ani (Crotophaga ani). We successfully identify microbial phyla in both samples including Firmicutes, Bacteroidetes, and Proteobacteria for A. bassleri, and Firmicutes and Actinobacteria for C. ani. Our study provides the first description of the gut microbiota for these two vertebrates, and demonstrates the feasibility of studying endogenous microbial communities from roadkill material that can be opportunistically collected and preserved in biobanks.
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Affiliation(s)
- Manuel Alejandro Coba-Males
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Magdalena Díaz
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - C. Alfonso Molina
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Pablo Medrano-Vizcaíno
- Ecology and Evolutionary Biology, School of Biological Sciences, University of Reading, Reading, United Kingdom
- Grupo de Investigación Población y Ambiente, Universidad Regional Amazónica IKIAM, Tena, Ecuador
- Red Ecuatoriana para el Monitoreo de Fauna Atropellada – REMFA, Quito, Ecuador
| | - David Brito-Zapata
- Red Ecuatoriana para el Monitoreo de Fauna Atropellada – REMFA, Quito, Ecuador
- Museo de Zoología & Laboratorio de Zoología Terrestre, Instituto iBIOTROP, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sarah Martin-Solano
- Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas—ESPE, Sangolquí, Ecuador
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, CISeAL Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Gabriel Alberto Carrillo-Bilbao
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Wilmer Narváez
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Jazzmín Arrivillaga-Henríquez
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Manuela González-Suárez
- Ecology and Evolutionary Biology, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Sandra Enríquez
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Ana Poveda
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Facultad de Ciencias Químicas (FCQ), Facultad de Ingeniería Química (FIQ), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
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14
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Jia X, Li Q, Yang X, Li D, Jin Z. Comparative analysis of the gut microbiota composition and diversity in Erinaceus amurensis from the Wandashan Mountain range area based on metagenomics. Front Microbiol 2024; 15:1479352. [PMID: 39703701 PMCID: PMC11656159 DOI: 10.3389/fmicb.2024.1479352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 11/12/2024] [Indexed: 12/21/2024] Open
Abstract
This study aimed to preliminarily explore the composition and diversity of intestinal bacteria in Erinaceus amurensis during breeding period, aiding in the field rescue and population conservation efforts of Erinaceus amurensis. This also provides foundational data for further research on the prevention and screening of Emerging Zoonotic Infectious Diseases and the experimental animalization of wild Erinaceus amurensis. Between April and July 2023, we collected 13 fresh fecal samples from Erinaceus amurensis at the Sishan Forest Farm in Jidong County, Heilongjiang Province, situated within the Wandashan Mountain range. Utilizing metagenomic sequencing technology, we conducted a comparative analysis of the gut microbiota composition and diversity in wild Erinaceus amurensis across different genders and between adult and fetal individuals within the same habitat. Our results revealed significant differences (P < 0.01) in the classification and diversity of gut microbiota between genders and between adult and fetal Erinaceus amurensis. Specifically, the dominant bacterial groups in the gut of Erinaceus amurensis were Pseudomonas, Proteobacteria, and Enterobacteriaceae. In male and female Erinaceus amurensis, the dominant bacterial groups were Pseudomonas, Bacteroides, and Firmicutes, with variations in bacterial abundance and diversity. While male and female Erinaceus amurensis exhibited similar microbial compositions, they displayed significant differences in specific bacterial classifications. The dominant bacterial group in fetal Erinaceus amurensis was Proteobacteria, which demonstrated lower diversity and abundance compared to the adult group. Furthermore, the types and abundance of pathogenic or opportunistic pathogens in the gut of fetal Erinaceus amurensis and male Erinaceus amurensis were higher than those in female Erinaceus amurensis. The analysis of experimental results indicates that Erinaceus amurensis in this region either have or are at risk of developing inflammation related to the intestinal and urinary tracts, as well as skin-related issues. Consequently, it is advised that forestry and wildlife conservation personnel in this area prioritize treatment against these specific pathogens when conducting rescue operations for Erinaceus amurensis in the wild.
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Affiliation(s)
| | | | | | | | - Zhimin Jin
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
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15
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Pinto Y, Bhatt AS. Sequencing-based analysis of microbiomes. Nat Rev Genet 2024; 25:829-845. [PMID: 38918544 DOI: 10.1038/s41576-024-00746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/27/2024]
Abstract
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA sequencing, improved long-read sequencing and innovative computational analysis methods. These advances are providing a deeper understanding of microbiomes at the genomic, transcriptional and translational level, generating insights into their function and composition at resolutions beyond the species level.
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Affiliation(s)
- Yishay Pinto
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA.
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16
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Nickols WA, McIver LJ, Walsh A, Zhang Y, Nearing JT, Asnicar F, Punčochář M, Segata N, Nguyen LH, Hartmann EM, Franzosa EA, Huttenhower C, Thompson KN. Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.08.622677. [PMID: 39574575 PMCID: PMC11580994 DOI: 10.1101/2024.11.08.622677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.
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Affiliation(s)
- William A. Nickols
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J. McIver
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron Walsh
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yancong Zhang
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob T. Nearing
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Long H. Nguyen
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Medicine/Division of Pulmonary Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric A. Franzosa
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Kelsey N. Thompson
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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17
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Zhu F, Sun K, Zhang H, Lu J, Guo P, Zhang J, Xu Y, Lyu B. Comparative Analyses of Lycodon rufozonatus and Lycodon rosozonatus Gut Microbiota in Different Regions. Ecol Evol 2024; 14:e70480. [PMID: 39440211 PMCID: PMC11495892 DOI: 10.1002/ece3.70480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 09/27/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024] Open
Abstract
The interactions between hosts and the gut microbiota are intricate and can significantly affect the ecology and evolution of both parties. Various host traits, including taxonomy, diet, social behaviour, and external factors such as prey availability and the local environment, all play an important role in shaping composition and diversity of the gut microbiogta. In this study, we explored the impact of intestinal microorganisms on the host in adapting to their respective ecological niches in two species of snakes. We collected feces from Lycodon rufozonatus and Lycodon rosozonatus from different geographical locations and used 16S rRNA gene sequencing technology to sequence the v3-v4 region. The results revealed that there was no significant difference in the alpha diversity of intestinal microorganisms between L. rufozonatus and L. rosozonatus. The gut microbiota of all individuals comprised four main phyla: Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. At the genus level, the genus Salmonella dominated the enterobacterial microbiota in the samples from Hainan, while there was no obvious dominant genus in the enterobacterial microbiota of the samples from the other four localities. Comparative analysis of enzyme families annotated to the gut microbiota between L. rufozonatus and L. rosozonatus from the four sampling regions by CAZy carbohydrate annotation revealed that nine enzyme families differed significantly in terms of glycoside hydrolases (GHs). In addition, we compared the composition of gut microbial communities between L. rufozonatus and L. rosozonatus and investigated the impact of the differences on their functions. Our results will provide insights into the coevolution of host and gut microbes.
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Affiliation(s)
- Fei Zhu
- School of Life SciencesGuizhou Normal UniversityGuiyangGuizhouChina
| | - Ke Sun
- School of Life SciencesGuizhou Normal UniversityGuiyangGuizhouChina
| | - He Zhang
- Guizhou Academy of ForestryGuiyangGuizhouChina
| | - Jing Lu
- School of Life SciencesGuizhou Normal UniversityGuiyangGuizhouChina
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinSichuanChina
| | - Jiaqi Zhang
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinSichuanChina
| | - Yu Xu
- School of Life SciencesGuizhou Normal UniversityGuiyangGuizhouChina
| | - Bing Lyu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinSichuanChina
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18
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Li Q, Ruscheweyh HJ, Østergaard LH, Libertella M, Simonsen KS, Sunagawa S, Scoma A, Schwab C. Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores. MICROBIOME 2024; 12:178. [PMID: 39300575 DOI: 10.1186/s40168-024-01863-4] [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: 02/24/2024] [Accepted: 06/25/2024] [Indexed: 09/22/2024]
Abstract
BACKGROUND Microbial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity. RESULTS Fecal levels of the glycerol transformation product 1,3-propanediol (1,3-PD) were higher in hindgut than foregut fermenters. Gene-based analyses indicated that pduC harboring taxa are common feature of captive wild animal fecal microbiota that occur more frequently and at higher abundance in hindgut fermenters. Phylogenetic analysis of genomes reconstructed from metagenomic sequences identified captive wild animal fecal microbiota as taxonomically rich with a total of 4150 species and > 1800 novel species but pointed at only 56 species that at least partially harbored pdu and cbi-cob-hem. While taxonomic diversity was highest in fecal samples of foregut-fermenting herbivores, higher pduC abundance and higher diversity of pdu/cbi-cob-hem related to higher potential for glycerol and 1,2-PD utilization of the less diverse microbiota of hindgut-fermenting carnivores in vitro. CONCLUSION Our approach combining metabolite and gene biomarker analysis with metagenomics and phenotypic characterization identified Pdu as a common function of fecal microbiota of captive wild animals shared by few taxa and stratified the potential of fecal microbiota for glycerol/1,2-PD utilization and cobalamin synthesis depending on diet and physiology of the host. This trait-based study suggests that the ability to utilize glycerol/1,2-PD is a key function of hindgut-fermenting carnivores, which does not relate to overall community diversity but links to the potential for cobalamin formation. Video Abstract.
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Affiliation(s)
- Qing Li
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Arhus, Denmark
- Present address: National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Lærke Hartmann Østergaard
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Arhus, Denmark
| | - Micael Libertella
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Arhus, Denmark
| | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Alberto Scoma
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Arhus, Denmark
| | - Clarissa Schwab
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Arhus, Denmark.
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19
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Deyaert S, Poppe J, Dai Vu L, Baudot A, Bubeck S, Bayne T, Krishnan K, Giusto M, Moltz S, Van den Abbeele P. Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo. Metabolites 2024; 14:497. [PMID: 39330504 PMCID: PMC11433953 DOI: 10.3390/metabo14090497] [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: 08/10/2024] [Revised: 09/07/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024] Open
Abstract
GoodBiome™ Foods are functional foods containing a probiotic (Bacillus subtilis HU58™) and prebiotics (mainly inulin). Their effects on the human gut microbiota were assessed using ex vivo SIFR® technology, which has been validated to provide clinically predictive insights. GoodBiome™ Foods (BBM/LCM/OSM) were subjected to oral, gastric, and small intestinal digestion/absorption, after which their impact on the gut microbiome of four adults was assessed (n = 3). All GoodBiome™ Foods boosted health-related SCFA acetate (+13.1/14.1/13.8 mM for BBM/LCM/OSM), propionate (particularly OSM; +7.4/7.5/8.9 mM for BBM/LCM/OSM) and butyrate (particularly BBM; +2.6/2.1/1.4 mM for BBM/LCM/OSM). This is related to the increase in Bifidobacterium species (B. catenulatum, B. adolescentis, B. pseudocatenulatum), Coprococcus catus and Bacteroidetes members (Bacteroides caccae, Phocaeicola dorei, P. massiliensis), likely mediated via inulin. Further, the potent propionogenic potential of OSM related to increased Bacteroidetes members known to ferment oats (s key ingredient of OSM), while the butyrogenic potential of BBM related to a specific increase in Anaerobutyricum hallii, a butyrate producer specialized in the fermentation of erythritol (key ingredient of BBM). In addition, OSM/BBM suppressed the pathogen Clostridioides difficile, potentially due to inclusion of HU58™ in GoodBiome™ Foods. Finally, all products enhanced a spectrum of metabolites well beyond SCFA, including vitamins (B3/B6), essential amino acids, and health-related metabolites such as indole-3-propionic acid. Overall, the addition of specific ingredients to complex foods was shown to specifically modulate the gut microbiome, potentially contributing to health benefits. Noticeably, our findings contradict a recent in vitro study, underscoring the critical role of employing a physiologically relevant digestion/absorption procedure for a more accurate evaluation of the microbiome-modulating potential of complex foods.
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Affiliation(s)
- Stef Deyaert
- Cryptobiotix, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (S.D.)
| | - Jonas Poppe
- Cryptobiotix, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (S.D.)
| | - Lam Dai Vu
- Cryptobiotix, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (S.D.)
| | - Aurélien Baudot
- Cryptobiotix, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (S.D.)
| | - Sarah Bubeck
- Bubeck Scientific Communications, 194 Rainbow Drive #9418, Livingston, TX 77399, USA
| | - Thomas Bayne
- Microbiome Labs, 101 E Town Pl, Saint Augustine, FL 92092, USA
| | - Kiran Krishnan
- Microbiome Labs, 101 E Town Pl, Saint Augustine, FL 92092, USA
| | - Morgan Giusto
- Microbiome Labs, 101 E Town Pl, Saint Augustine, FL 92092, USA
| | - Samuel Moltz
- Novonesis, Biologiens Vej 2, 2800 Lyngby, Denmark
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20
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Liu C, Tang Z, Li L, Kang Y, Teng Y, Yu Y. Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes. Chin Med J (Engl) 2024; 137:2092-2098. [PMID: 38934052 PMCID: PMC11374256 DOI: 10.1097/cm9.0000000000003182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics, environmental microbiology, and biodiversity. As sequencing technologies evolve, this task becomes increasingly challenging due to the intricate nature of microbial communities and the vast amount of data generated. Especially in intensive care units (ICUs), infections caused by antibiotic-resistant bacteria are increasingly prevalent among critically ill patients, significantly impacting the effectiveness of treatments and patient prognoses. Therefore, obtaining timely and accurate information about infectious pathogens is of paramount importance for the treatment of patients with severe infections, which enables precisely targeted anti-infection therapies, and a tool that can extract microbial genomic sequences from metagenomic dataset would be of help. METHODS We developed MetaGeneMiner to help with retrieving specific microbial genomic sequences from metagenomes using a k-mer-based approach. It facilitates the rapid and accurate identification and analysis of pathogens. The tool is designed to be user-friendly and efficient on standard personal computers, allowing its use across a wide variety of settings. We validated MetaGeneMiner using eight metagenomic samples from ICU patients, which demonstrated its efficiency and accuracy. RESULTS The software extensively retrieved coding sequences of pathogens Acinetobacter baumannii and herpes simplex virus type 1 and detected a variety of resistance genes. All documentation and source codes for MetaGeneMiner are freely available at https://gitee.com/sculab/MetaGeneMiner . CONCLUSIONS It is foreseeable that MetaGeneMiner possesses the potential for applications across multiple domains, including clinical diagnostics, environmental microbiology, gut microbiome research, as well as biodiversity and conservation biology. Particularly in ICU settings, MetaGeneMiner introduces a novel, rapid, and precise method for diagnosing and treating infections in critically ill patients. This tool is capable of efficiently identifying infectious pathogens, guiding personalized and precise treatment strategies, and monitoring the development of antibiotic resistance, significantly impacting the diagnosis and treatment of severe infections.
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Affiliation(s)
- Chang Liu
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zizhen Tang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Linzhu Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Yan Kang
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
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21
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Fan J, Kang H, Lv M, Zhai Y, Jia Y, Yang Z, Shi C, Zhou C, Diao L, Li J, Jin X, Liu S, Kristiansen K, Zhang P, Chen J, Li S. Taxonomic composition and functional potentials of gastrointestinal microbiota in 12 wild-stranded cetaceans. Front Microbiol 2024; 15:1394745. [PMID: 39268538 PMCID: PMC11390675 DOI: 10.3389/fmicb.2024.1394745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024] Open
Abstract
Cetaceans play a crucial role in marine ecosystems; however, research on their gastrointestinal microbiota remains limited due to sampling constraints. In this study, we collected hindgut samples from 12 stranded cetaceans and performed 16S rRNA gene amplicon sequencing to investigate microbial composition and functional potentials. Analysis of ZOTUs profiles revealed that the phyla Firmicutes, Proteobacteria, and Bacteroidetes dominated all hindgut samples. However, unique microbial profiles were observed among different cetacean species, with significant separation of gut microbiota communities according to biological evolutionary lineages. Different genera that contain pathogens were observed distinguishing delphinids from physeteroids/ziphiids. Delphinid samples exhibited higher abundances of Vibrio, Escherichia, and Paeniclostridium, whereas physeteroid and ziphiid samples showed higher abundances of Pseudomonas, Enterococcus, and Intestinimonas. Functional analysis indicated convergence in the gut microbiota among all cetaceans, with shared bacterial infection pathways across hindgut samples. In addition, a comparison of the gastrointestinal microbial composition between a stranded short-finned pilot whale (Globicephala macrorhynchus) and a stranded rough-toothed dolphin (Steno bredanensis) using 16S rRNA gene sequencing revealed distinct microbial community structures and functional capacities. To the best of our knowledge, this study represents the first report on the gastrointestinal microbiota of the pantropical spotted dolphin (Stenella attenuata), Blainville's beaked whale (Mesoplodon densirostris), and rough-toothed dolphin, with various comparisons conducted among different cetacean species. Our findings enhance the understanding of microbial composition and diversity in cetacean gastrointestinal microbiota, providing new insights into co-evolution and complex interactions between cetacean microbes and hosts.
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Affiliation(s)
- Jie Fan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Qingdao, China
| | - Hui Kang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Yuhuan Zhai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Zixin Yang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | | | | | | | - Xiaowei Jin
- China National Environmental Monitoring Centre, Beijing, China
| | | | - Karsten Kristiansen
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jianwei Chen
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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22
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Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell 2024; 187:4554-4570.e18. [PMID: 38981480 DOI: 10.1016/j.cell.2024.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 02/23/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.
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Affiliation(s)
- Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Hanseul Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alberto Arrè
- Department CIBIO, University of Trento, Trento, Italy; Zoe Ltd, London, UK
| | - Kate M Bermingham
- Zoe Ltd, London, UK; Department of Nutritional Sciences, King's College London, London, UK
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | | | - Emily R Leeming
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Monia Lobina
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tim D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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23
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Shi Z, Yao F, Chen Q, Chen Y, Zhang J, Guo J, Zhang S, Zhang C. More deterministic assembly constrains the diversity of gut microbiota in freshwater snails. Front Microbiol 2024; 15:1394463. [PMID: 39040899 PMCID: PMC11260827 DOI: 10.3389/fmicb.2024.1394463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 07/24/2024] Open
Abstract
Growing evidence has suggested a strong link between gut microbiota and host fitness, yet our understanding of the assembly mechanisms governing gut microbiota remains limited. Here, we collected invasive and native freshwater snails coexisting at four independent sites in Guangdong, China. We used high-throughput sequencing to study the assembly processes of their gut microbiota. Our results revealed significant differences in the diversity and composition of gut microbiota between invasive and native snails. Specifically, the gut microbiota of invasive snails exhibited lower alpha diversity and fewer enriched bacteria, with a significant phylogenetic signal identified in the microbes that were enriched or depleted. Both the phylogenetic normalized stochasticity ratio (pNST) and the phylogenetic-bin-based null model analysis (iCAMP) showed that the assembly process of gut microbiota in invasive snails was more deterministic compared with that in native snails, primarily driven by homogeneous selection. The linear mixed-effects model revealed a significant negative correlation between deterministic processes (homogeneous selection) and alpha diversity of snail gut microbiota, especially where phylogenetic diversity explained the most variance. This indicates that homogeneous selection acts as a filter by the host for specific microbial lineages, constraining the diversity of gut microbiota in invasive freshwater snails. Overall, our study suggests that deterministic assembly-mediated lineage filtering is a potential mechanism for maintaining the diversity of gut microbiota in freshwater snails.
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Affiliation(s)
- Zhaoji Shi
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Fucheng Yao
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Qi Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Yingtong Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Jiaen Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Jing Guo
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Shaobin Zhang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Chunxia Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
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24
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Liu Y, Kou C, Chen J, Li Y, Li J. The Response of the Gut Physiological Function and Microbiome of a Wild Freshwater Fish ( Megalobrama terminalis) to Alterations in Reproductive Behavior. Int J Mol Sci 2024; 25:7425. [PMID: 39000530 PMCID: PMC11242598 DOI: 10.3390/ijms25137425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
The fish gut microbiome is well known for its role in degrading nutrients to improve the host's digestion and absorption efficiency. In this study, we focused on the core physiological adaptability during the various reproductive stages of the black Amur bream (Megalobrama terminalis) to explore the interaction mechanisms among the fish host gut mucosal structure, gut enzyme activity, and gut microbial metabolism in the course of the host's reproductive cycle. Our findings showed that M. terminalis exhibited locomotion metabolic type (aids in sporting) in the reproductive stage, and a change to visceral metabolic type (aids in digestion) during non-reproductive and post-reproductive stage phases. The impact of metabolic type selection and energy demand during various reproductive stages on fish nutrition strategy and digestive function was substantial. Our resulted showed that mitochondria in intestinal epithelial cells of reproductive M. terminalis appeared autophagy phenomenon, and the digestive enzyme activities in the intestines of reproductive M. terminalis were lower than those in the non-reproductive and post-reproductive individuals. Moreover, these differences in nutrition strategy have a prominent impact on the gut microbiome of reproductive M. terminalis, compared to non-reproductive and post-reproductive samples. Our findings showed that reproductive females had lower levels of alpha diversity compared to non-reproductive and post-reproductive females. Our results also showed a greater functional variety and an increase in functional genes related to carbohydrate, lipid, amino acid, cofactors, and vitamin metabolic pathways in the NRS and PRS group. It is noteworthy that an enrichment of genes encoding putative enzymes implicated in the metabolism of taurine and hypotaurine was observed in the RS samples. Our findings illustrated that the stability and resilience of the gut bacterial community could be shaped in the wild fish host-microbiome interactions during reproductive life history.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (C.K.); (Y.L.)
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Chunni Kou
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (C.K.); (Y.L.)
| | - Jiayue Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (C.K.); (Y.L.)
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (C.K.); (Y.L.)
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (C.K.); (Y.L.)
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
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25
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Wang Q, Zhan PC, Han XL, Lu T. Metagenomic and culture-dependent analysis of Rhinopithecius bieti gut microbiota and characterization of a novel genus of Sphingobacteriaceae. Sci Rep 2024; 14:13819. [PMID: 38879636 PMCID: PMC11180105 DOI: 10.1038/s41598-024-64727-9] [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: 03/18/2024] [Accepted: 06/12/2024] [Indexed: 06/19/2024] Open
Abstract
Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009T, formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009T and its most closely related strains S. kitahiroshimense 10CT, S. pakistanense NCCP-246T and S. faecium DSM 11690T were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009T represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009T = CCTCC AA 2021153T = KCTC 82941T) are proposed.
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Affiliation(s)
- Qiong Wang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
- Center for Pharmaceutical Sciences, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, PR China
| | - Peng-Chao Zhan
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
| | - Xiu-Lin Han
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
| | - Tao Lu
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
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Coubris C, Duchatelet L, Delroisse J, Bayaert WS, Parise L, Eloy MC, Pels C, Mallefet J. Maintain the light, long-term seasonal monitoring of luminous capabilities in the brittle star Amphiura filiformis. Sci Rep 2024; 14:13238. [PMID: 38853171 PMCID: PMC11163003 DOI: 10.1038/s41598-024-64010-x] [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: 03/19/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
The European brittle star Amphiura filiformis emits blue light, via a Renilla-like luciferase, which depends on the dietary acquisition of coelenterazine. Questions remain regarding luciferin availability across seasons and the persistence of luminous capabilities after a single boost of coelenterazine. To date, no study has explored the seasonal, long-term monitoring of these luminous capabilities or the tracking of luciferase expression in photogenic tissues. Through multidisciplinary analysis, we demonstrate that luminous capabilities evolve according to the exogenous acquisition of coelenterazine throughout adult life. Moreover, no coelenterazine storage forms are detected within the arms tissues. Luciferase expression persists throughout the seasons, and coelenterazine's presence in the brittle star diet is the only limiting factor for the bioluminescent reaction. No seasonal variation is observed, involving a continuous presence of prey containing coelenterazine. The ultrastructure description provides a morphological context to investigate the green autofluorescence signal attributed to coelenterazine during luciferin acquisition. Finally, histological analyses support the hypothesis of a pigmented sheath leading light to the tip of the spine. These insights improve our understanding of the bioluminescence phenomenon in this burrowing brittle star.
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Affiliation(s)
- Constance Coubris
- Marine Biology Laboratory, Earth and Life Institute, UCLouvain, Croix du Sud 3, 1348, Louvain-la-Neuve, Belgium.
| | - Laurent Duchatelet
- Marine Biology Laboratory, Earth and Life Institute, UCLouvain, Croix du Sud 3, 1348, Louvain-la-Neuve, Belgium
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, UMONS, 23 Place du Parc, 7000, Mons, Belgium
- Laboratory of Cellular and Molecular Biology, GIGA Institute, 4000, Liège, Belgium
| | - Wendy Shirley Bayaert
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Laura Parise
- Marine Biology Laboratory, Earth and Life Institute, UCLouvain, Croix du Sud 3, 1348, Louvain-la-Neuve, Belgium
| | - Marie Christine Eloy
- Institut des Sciences de la Vie, UCLouvain, Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Christophe Pels
- Marine Biology Laboratory, Earth and Life Institute, UCLouvain, Croix du Sud 3, 1348, Louvain-la-Neuve, Belgium
| | - Jérôme Mallefet
- Marine Biology Laboratory, Earth and Life Institute, UCLouvain, Croix du Sud 3, 1348, Louvain-la-Neuve, Belgium
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27
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Zhang K, He C, Wang L, Suo L, Guo M, Guo J, Zhang T, Xu Y, Lei Y, Liu G, Qian Q, Mao Y, Kalds P, Wu Y, Cuoji A, Yang Y, Brugger D, Gan S, Wang M, Wang X, Zhao F, Chen Y. Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization. MICROBIOME 2024; 12:104. [PMID: 38845047 PMCID: PMC11155115 DOI: 10.1186/s40168-024-01806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/03/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database. RESULTS A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host's species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation. CONCLUSIONS By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins. Video Abstract.
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Affiliation(s)
- Ke Zhang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chong He
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Lei Wang
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Langda Suo
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850009, China
- Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, 850009, China
| | - Mengmeng Guo
- College of Animal Engineering, Yangling Vocational and Technical College, Yangling, 712100, China
| | - Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611100, China
| | - Ting Zhang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangbin Xu
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Lei
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Gongwei Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quan Qian
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yunrui Mao
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Peter Kalds
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yujiang Wu
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850009, China
- Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, 850009, China
| | - Awang Cuoji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850009, China
- Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, 850009, China
| | - Yuxin Yang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Daniel Brugger
- Institute of Animal Nutrition and Dietetics, Vetsuisse-Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Shangquan Gan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Meili Wang
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
- School of Future Technology On Bio-Breeding, Northwest A&F University, Yangling, 712100, China.
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 102206, China.
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
- School of Future Technology On Bio-Breeding, Northwest A&F University, Yangling, 712100, China.
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Zhang B, Xiao L, Lyu L, Zhao F, Miao M. Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists. MICROBIOME 2024; 12:96. [PMID: 38790063 PMCID: PMC11127453 DOI: 10.1186/s40168-024-01809-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates. RESULTS To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range. CONCLUSIONS As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.
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Affiliation(s)
- Bing Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Liwen Xiao
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Miao Miao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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Wang Y, Zhai J, Tang B, Dong Y, Sun S, He S, Zhao W, Lancuo Z, Jia Q, Wang W. Metagenomic comparison of gut communities between wild and captive Himalayan griffons. Front Vet Sci 2024; 11:1403932. [PMID: 38784654 PMCID: PMC11112026 DOI: 10.3389/fvets.2024.1403932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. Methods In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Results Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). Discussion In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.
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Affiliation(s)
- You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yonggang Dong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Shengzhen Sun
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Qiangqiang Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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30
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Cao B, Wang X, Yin W, Gao Z, Xia B. The human microbiota is a beneficial reservoir for SARS-CoV-2 mutations. mBio 2024; 15:e0318723. [PMID: 38530031 PMCID: PMC11237538 DOI: 10.1128/mbio.03187-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/14/2024] [Indexed: 03/27/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging. In particular, beneficial mutations in the spike (S) protein, which can either make a person more infectious or enable immunological escape, are providing a significant obstacle to the prevention and treatment of pandemics. However, how the virus acquires a high number of beneficial mutations in a short time remains a mystery. We demonstrate here that variations of concern may be mutated due in part to the influence of the human microbiome. We searched the National Center for Biotechnology Information database for homologous fragments (HFs) after finding a mutation and the six neighboring amino acids in a viral mutation fragment. Among the approximate 8,000 HFs obtained, 61 mutations in S and other outer membrane proteins were found in bacteria, accounting for 62% of all mutation sources, which is 12-fold higher than the natural variable proportion. A significant proportion of these bacterial species-roughly 70%-come from the human microbiota, are mainly found in the lung or gut, and share a composition pattern with COVID-19 patients. Importantly, SARS-CoV-2 RNA-dependent RNA polymerase replicates corresponding bacterial mRNAs harboring mutations, producing chimeric RNAs. SARS-CoV-2 may collectively pick up mutations from the human microbiota that change the original virus's binding sites or antigenic determinants. Our study clarifies the evolving mutational mechanisms of SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging, in particular advantageous mutations in the spike (S) protein, which either increase transmissibility or lead to immune escape and are posing a major challenge to pandemic prevention and treatment. However, how the virus acquires a high number of advantageous mutations in a short time remains a mystery. Here, we provide evidence that the human microbiota is a reservoir of advantageous mutations and aids mutational evolution and host adaptation of SARS-CoV-2. Our findings demonstrate a conceptual breakthrough on the mutational evolution mechanisms of SARS-CoV-2 for human adaptation. SARS-CoV-2 may grab advantageous mutations from the widely existing microorganisms in the host, which is undoubtedly an "efficient" manner. Our study might open a new perspective to understand the evolution of virus mutation, which has enormous implications for comprehending the trajectory of the COVID-19 pandemic.
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Affiliation(s)
- Birong Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Guangya High School, Guangzhou, China
| | - Xiaoxi Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wanchao Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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Wang Y, Qu M, Bi Y, Liu WJ, Ma S, Wan B, Hu Y, Zhu B, Zhang G, Gao GF. The multi-kingdom microbiome catalog of the chicken gastrointestinal tract. BIOSAFETY AND HEALTH 2024; 6:101-115. [PMID: 40078943 PMCID: PMC11894977 DOI: 10.1016/j.bsheal.2024.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2025] Open
Abstract
Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries. We found that 812 and 240 MAGs in our dataset were putative novel species and genera, respectively, far beyond what was previously reported. The newly unclassified MAGs were predominant in Phyla Firmicutes_A (n = 263), followed by Firmicutes (n = 126), Bacteroidota (n = 121), and Proteobacteria (n = 87). Most of the classified species-level viral operational taxonomic units belong to Caudovirales. Approximately, 63.24 % of chicken gut viromes are predicted to infect two or more hosts, including complete circular viruses. Moreover, we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses. Together, our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date, functional insights into the chicken gastrointestinal tract microbiota, and paves the way for microbial interventions for better chicken health and productivity.
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Affiliation(s)
- Yanan Wang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Longhu Laboratory, Zhengzhou 450046, China
| | - Mengqi Qu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - William J. Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bo Wan
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- Longhu Laboratory, Zhengzhou 450046, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaiping Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- Longhu Laboratory, Zhengzhou 450046, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Buck CB, Welch N, Belford AK, Varsani A, Pastrana DV, Tisza MJ, Starrett GJ. Widespread Horizontal Gene Transfer Among Animal Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586562. [PMID: 38712252 PMCID: PMC11071296 DOI: 10.1101/2024.03.25.586562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
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Affiliation(s)
| | - Nicole Welch
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: L.E.K. Consulting, Boston, MA, USA
| | - Anna K. Belford
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Varsani
- Arizona State University, Tempe, AZ, USA
- University of Cape Town, South Africa
| | | | - Michael J. Tisza
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: Baylor College of Medicine, Houston, TX, USA
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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [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: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [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: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Ning R, Li C, Xia M, Zhang Y, Gan Y, Huang Y, Zhang T, Song H, Zhang S, Guo W. Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda ( Ailuropoda melanoleuca). Microbiol Spectr 2024; 12:e0381923. [PMID: 38305171 PMCID: PMC10913395 DOI: 10.1128/spectrum.03819-23] [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: 11/02/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism. IMPORTANCE Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.
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Affiliation(s)
- Ruihong Ning
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Maohua Xia
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, Beijing, P.R. China
| | - Yu Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yunong Gan
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Tianyou Zhang
- Chimelong Safari Park in Guangdong Province, Guangzhou, China
| | - Haitao Song
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Siyuan Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Wei Guo
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [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: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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Hu J, Chen J, Ma L, Hou Q, Zhang Y, Kong X, Huang X, Tang Z, Wei H, Wang X, Yan X. Characterizing core microbiota and regulatory functions of the pig gut microbiome. THE ISME JOURNAL 2024; 18:wrad037. [PMID: 38366194 PMCID: PMC10873858 DOI: 10.1093/ismejo/wrad037] [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: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/23/2023] [Indexed: 02/18/2024]
Abstract
Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.
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Affiliation(s)
- Jun Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Jianwei Chen
- BGI Research, Qingdao, Shandong 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Libao Ma
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Qiliang Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
| | - Yong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiangfeng Kong
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xingguo Huang
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hong Wei
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xianghua Yan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei 430070, China
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38
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Branck T, Hu Z, Nickols WA, Walsh AM, Bhosle A, Short MI, Nearing JT, Asnicar F, McIver LJ, Maharjan S, Rahnavard A, Louyakis AS, Badri DV, Brockel C, Thompson KN, Huttenhower C. Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods. THE ISME JOURNAL 2024; 18:wrae201. [PMID: 39394961 PMCID: PMC11523182 DOI: 10.1093/ismejo/wrae201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 09/19/2024] [Accepted: 10/09/2024] [Indexed: 10/14/2024]
Abstract
The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.
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Affiliation(s)
- Tobyn Branck
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Science and Technology Center, Hill’s Pet Nutrition, Inc., Topeka, KS, United States
| | - Zhiji Hu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - William A Nickols
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Aaron M Walsh
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Amrisha Bhosle
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Meghan I Short
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Jacob T Nearing
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Lauren J McIver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Sagun Maharjan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Artemis S Louyakis
- Science and Technology Center, Hill’s Pet Nutrition, Inc., Topeka, KS, United States
| | - Dayakar V Badri
- Science and Technology Center, Hill’s Pet Nutrition, Inc., Topeka, KS, United States
| | - Christoph Brockel
- Science and Technology Center, Hill’s Pet Nutrition, Inc., Topeka, KS, United States
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, United States
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Mazel F, Guisan A, Parfrey LW. Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes. Mol Ecol 2024; 33:e16862. [PMID: 36786039 DOI: 10.1111/mec.16862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/15/2023]
Abstract
Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.
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Affiliation(s)
- Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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40
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Bhattacharjee AS, Phan D, Zheng C, Ashworth D, Schmidt M, Men Y, Ferreira JFS, Muir G, Hasan NA, Ibekwe AM. Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment. ENVIRONMENT INTERNATIONAL 2024; 183:108374. [PMID: 38101104 DOI: 10.1016/j.envint.2023.108374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Treated municipal wastewater (TMW) can provide a reliable source of irrigation water for crops, which is especially important in arid areas where water resources are limited or prone to drought. Nonetheless, TMW may contain residual antibiotics, potentially exposing the crops to these substances. The goal of this study was to investigate the dissemination of antibiotics resistance genes (ARGs) in the soil-plant-earthworm continuum after irrigation of spinach and radish plants with TMW containing trimethoprim, sulfamethoxazole, and sulfapyridine in a greenhouse experiment, followed by feeding of earthworms with harvested plant materials. Our results showed that antibiotic resistance genes (ARGs) were enriched in the soil-plant-earthworm microbiomes irrigated with TMW and TMW spiked with higher concentrations of antibiotics. The number of ARGs and antibiotic-resistant bacteria (ARB) enrichment varied with plant type, with spinach harboring a significantly higher amount of ARGs and ARB compared to radish. Our data showed that bulk and rhizosphere soils of spinach and radish plants irrigated with MilliQ water, TMW, TMW10, or TMW100 had significant differences in bacterial community (p < 0.001), ARG (p < 0.001), and virulence factor gene (VFG) (p < 0.001) diversities. The abundance of ARGs significantly decreased from bulk soil to rhizosphere to phyllosphere and endosphere. Using metagenome assembled genomes (MAGs), we recovered many bacterial MAGs and a near complete genome (>90 %) of bacterial MAG of genus Leclercia adecarboxylata B from the fecal microbiome of earthworm that was fed harvested radish tubers and spinach leaves grown on TMW10 irrigated waters, and this bacterium has been shown to be an emerging pathogen causing infection in immunocompromised patients that may lead to health complications and death. Therefore, crops irrigated with TMW containing residual antibiotics and ARGs may lead to increased incidences of enrichment of ARB in the soil-plant-earthworm continuum.
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Affiliation(s)
- Ananda S Bhattacharjee
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA; Department of Environmental Sciences, University of California, Riverside, CA 92507, USA
| | - Duc Phan
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA; Department of Environmental Sciences, University of California, Riverside, CA 92507, USA
| | - Chujing Zheng
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92507, USA
| | - Daniel Ashworth
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Michael Schmidt
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92507, USA
| | - Jorge F S Ferreira
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | | | - Nur A Hasan
- EzBiome, Gaithersburg, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Abasiofiok M Ibekwe
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA.
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Dhivahar J, Parthasarathy A, Krishnan K, Kovi BS, Pandian GN. Bat-associated microbes: Opportunities and perils, an overview. Heliyon 2023; 9:e22351. [PMID: 38125540 PMCID: PMC10730444 DOI: 10.1016/j.heliyon.2023.e22351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.
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Affiliation(s)
- J. Dhivahar
- Research Department of Zoology, St. Johns College, Palayamkottai, 627002, India
- Department of Plant Biology and Biotechnology, Laboratory of Microbial Ecology, Loyola College, Chennai, 600034, India
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Anutthaman Parthasarathy
- Department of Chemistry and Biosciences, Richmond Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Kathiravan Krishnan
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Basavaraj S. Kovi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
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Navine AK, Paxton KL, Paxton EH, Hart PJ, Foster JT, McInerney N, Fleischer RC, Videvall E. Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds. Mol Ecol 2023; 32:6659-6670. [PMID: 36281504 DOI: 10.1111/mec.16743] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/30/2022]
Abstract
Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, nine of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum, which is increasing in distribution in Hawai'i as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals has revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawai'i 'amakihi (Chlorodrepanis virens), persists in areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 'amakihi and 172 malaria-resistant warbling white-eyes (Zosterops japonicus) from Hawai'i Island using 16S rRNA gene metabarcoding and quantitative polymerase chain reaction. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp., which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.
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Affiliation(s)
- Amanda K Navine
- Biology Department, University of Hawai'i at Hilo, Hilo, Hawaii, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Kristina L Paxton
- Hawai'i Cooperative Studies Unit, University of Hawai'i at Hilo, Hawai'i National Park, Hawaii, USA
| | - Eben H Paxton
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, Hawaii, USA
| | - Patrick J Hart
- Biology Department, University of Hawai'i at Hilo, Hilo, Hawaii, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Nancy McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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43
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Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 2023; 41:1633-1644. [PMID: 36823356 PMCID: PMC10635831 DOI: 10.1038/s41587-023-01688-w] [Citation(s) in RCA: 412] [Impact Index Per Article: 206.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.
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Affiliation(s)
| | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Lauren J McIver
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kelsey N Thompson
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | - William A Nickols
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | | | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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44
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. MICROBIOME 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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45
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Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O’Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RM, Thinnes CC, Thiele I. APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560573. [PMID: 37873072 PMCID: PMC10592896 DOI: 10.1101/2023.10.02.560573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Computational modelling of microbiome metabolism has proved instrumental to catalyse our understanding of diet-host-microbiome-disease interactions through the interrogation of mechanistic, strain- and molecule-resolved metabolic models. We present APOLLO, a resource of 247,092 human microbial genome-scale metabolic reconstructions spanning 19 phyla and accounting for microbial genomes from 34 countries, all age groups, and five body sites. We explored the metabolic potential of the reconstructed strains and developed a machine learning classifier able to predict with high accuracy the taxonomic strain assignments. We also built 14,451 sample-specific microbial community models, which could be stratified by body site, age, and disease states. Finally, we predicted faecal metabolites enriched or depleted in gut microbiomes of people with Crohn's disease, Parkinson disease, and undernourished children. APOLLO is compatible with the human whole-body models, and thus, provide unprecedented opportunities for systems-level modelling of personalised host-microbiome co-metabolism. APOLLO will be freely available under https://www.vmh.life/.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Timothy Otto Hulshof
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Arianna Basile
- School of Medicine, University of Galway, Galway, Ireland
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | | | | | - Ian Lalor
- University of Galway, Galway, Ireland
| | | | | | | | | | | | | | | | | | | | - Cyrille C. Thinnes
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- Division of Microbiology, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
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46
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Malukiewicz J, D'arc M, Dias CA, Cartwright RA, Grativol AD, Moreira SB, Souza AR, Tavares MCH, Pissinatti A, Ruiz-Miranda CR, Santos AFA. Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools. Sci Rep 2023; 13:15679. [PMID: 37735195 PMCID: PMC10514281 DOI: 10.1038/s41598-023-42059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.
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Affiliation(s)
- Joanna Malukiewicz
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, 37077, Germany.
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Cecilia A Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | - Reed A Cartwright
- School of Life Sciences and the Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | | | - Silvia Bahadian Moreira
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | | | | | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | - Carlos R Ruiz-Miranda
- Laboratorio das Ciencias Ambientais, Centro de Biociencias e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - André F A Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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47
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Zabłotni A, Kaliński A, Glądalski M, Markowski M, Skwarska J, Wawrzyniak J, Bańbura J. Nest Box Bacterial Loads Are Affected by Cavity Use by Secondary Hole Nesters. Animals (Basel) 2023; 13:2989. [PMID: 37760389 PMCID: PMC10526079 DOI: 10.3390/ani13182989] [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: 07/13/2023] [Revised: 08/18/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Among the environmental factors that affect bird nesting in nest boxes, the influence of microbial communities is relatively poorly understood. In this study, nest boxes used for breeding by secondary cavity nesters were sampled before the start of the breeding season to assess the bacterial loads of the nest box in relation to their previous year status. Different parts of the wooden nest box offer variable conditions for the development of bacteria. During the breeding season, the nest box entrance hole is wiped out by birds, delivering bacteria to their bodies, but during winter, it is exposed to unfavourable external conditions. The interior of the nest box, in turn, is also wiped by birds, but the conditions during winter are more stable there. Therefore, samples from the entrance hole and the interior of the nest box were taken at two different study sites: an urban parkland and a natural forest. We predicted that both the occupancy of the nest boxes during the previous breeding season by birds and the nesting sites would influence the bacterial load of the nest box. To verify this prediction, two categories of nest boxes were sampled at both study sites: nest boxes occupied by any of the two tit species (Great Tit or Blue Tit) in the previous season for breeding and nest boxes that had remained empty that year. The interior bacterial load of the nest box was higher in the nest boxes occupied in the previous breeding season, but only in the forest area. Furthermore, the bacterial load of both the entrance hole of the nest box and the interior was significantly higher in the forest study area in both occupied and unoccupied nest boxes. Our results show that the bacterial load of the nest box is positively related to the presence of nests in the previous breeding season and can vary between different sites.
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Affiliation(s)
- Agnieszka Zabłotni
- Laboratory of General Microbiology, Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
| | - Adam Kaliński
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Michał Glądalski
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Marcin Markowski
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Joanna Skwarska
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Jarosław Wawrzyniak
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Jerzy Bańbura
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
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48
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González D, Morales-Olavarria M, Vidal-Veuthey B, Cárdenas JP. Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut. Front Microbiol 2023; 14:1238580. [PMID: 37779688 PMCID: PMC10540074 DOI: 10.3389/fmicb.2023.1238580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.
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Affiliation(s)
- Dámariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Mauricio Morales-Olavarria
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Boris Vidal-Veuthey
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Juan P. Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
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49
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Zhang C, Hu L, Hao J, Cai W, Qin M, Gao Q, Nie M, Qi D, Ma R. Effects of plant-derived protein and rapeseed oil on growth performance and gut microbiomes in rainbow trout. BMC Microbiol 2023; 23:255. [PMID: 37704987 PMCID: PMC10498547 DOI: 10.1186/s12866-023-02998-4] [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: 04/21/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Rainbow trout (Oncorhynchus mykiss) is becoming popular with the increased demand for fish protein. However, the limited resources and expense of fish meal and oil have become restrictive factors for the development of the rainbow trout related industry. To solve this problem, plant-derived proteins and vegetable oils have been developed as alternative resources. The present study focuses on evaluating the effects of two experimental diets, FMR (fish meal replaced with plant-derived protein) and FOR (fish oil replaced with rapeseed oil), through the alteration of the gut microbiota in triploid rainbow trout. The commercial diet was used in the control group (FOM). RESULTS Amplicon sequencing of the 16S and 18S rRNA genes was used to assess the changes in gut bacteria and fungi. Our analysis suggested that the α-diversity of both bacteria and fungi decreased significantly in the FMR and FOR groups, and β-diversity was distinct between FOM/FMR and FOM/FOR based on principal coordinate analysis (PCoA). The abundance of the Planctomycetota phylum increased significantly in the FMR group, while that of Firmicutes and Bacteroidetes decreased. We also found that the fungal phylum Ascomycota was significantly increased in the FMR and FOR groups. At the genus level, we found that the abundance of Citrobacter was the lowest and that of pathogenic Schlesneria, Brevundimonas, and Mycoplasma was highest in the FMR and FOR groups. Meanwhile, the pathogenic fungal genera Verticillium and Aspergillus were highest in the FMR and FOR groups. Furthermore, canonical correspondence analysis (CCA) and network analysis suggested that the relatively low-abundance genera, including the beneficial bacteria Methylobacterium, Enterococcus, Clostridium, Exiguobacterium, Sphingomonas and Bacteroides and the fungi Papiliotrema, Preussia, and Stachybotrys, were positively correlated with plant protein or rapeseed oil. There were more modules that had the above beneficial genera as the hub nodes in the FMR and FOR groups. CONCLUSIONS Our study suggested that the FMR and FOR diets could affect the gut microbiome in rainbow trout, which might offset the effects of the dominant and pathogenic microbial genera. This could be the underlying mechanism of explaining why no significant difference was observed in body weight between the different groups.
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Affiliation(s)
- Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
| | - Lingyong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Jiahui Hao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810001, China
| | - Weijie Cai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810001, China
| | - Minxin Qin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810001, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
| | - Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China
| | - Rui Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810001, China.
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50
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de Morais Nobre ML, Santos LS, de Carvalho Sousa B, Campos MAS, Schwarz DGG, Pinheiro REE, Catenacci LS, Dos Santos Soares MJ. A systematic review of the microbial community in taiassuids: a One Health approach. Braz J Microbiol 2023; 54:2485-2496. [PMID: 37380932 PMCID: PMC10485205 DOI: 10.1007/s42770-023-01046-7] [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: 11/25/2022] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Collared and white-lipped peccaries are sympatric and are distributed in most of South America and in the humid tropical forests of Mexico and Central America. Historically, these species have been used as a source of protein by traditional and/or indigenous human communities, but currently they have been used for legal consumption in different countries. Thus, there has been greater interaction between these wild species and domestic animals and humans, enabling microbial interactions between different niches. The present study presents a systematic review of the literature on the microbial community of collared peccaries and white-lipped peccaries distributed throughout the world, focusing on experimental studies related to the detection of microorganisms as well as the prevalence of the animal species and its characterization of the studied population, in situ or ex situ. Seventy-two studies were selected, mainly in South American countries, related to different species of microorganisms isolated or serologically detected (viruses, bacteria, fungi, and parasites), either as microbiota, pathogens or commensals, many of which are of zoonotic interest, such as Leptospira, Toxoplasma, Brucella, among others. Therefore, these wild mammals are characterized as sentinel agents of anthropic action and require the implementation of studies in relation to their contribution to the spread of microorganisms, being a potential source of amplification and transmission of pathogens.
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Affiliation(s)
- Márcio Leonardo de Morais Nobre
- Federal Institute of Maranhão, IFMA, Caxias, Maranhão, Brazil.
- Postgraduate Program in Technologies Applied to Animals of Regional Interest, Center of Agricultural Science, Federal University of Piauí, UFPI, Teresina, Piauí, Brazil.
| | - Leidiane Sousa Santos
- Department of Veterinary Morphophysiology, Federal University of Piauí, UFPI, Teresina, Piauí, Brazil
| | - Bianca de Carvalho Sousa
- Postgraduate Program in Technologies Applied to Animals of Regional Interest, Center of Agricultural Science, Federal University of Piauí, UFPI, Teresina, Piauí, Brazil
| | | | | | | | - Lilian Silva Catenacci
- Department of Veterinary Morphophysiology, Federal University of Piauí, UFPI, Teresina, Piauí, Brazil
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