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Zhu Y, Shang J, Peng C, Sun Y. Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Front Microbiol 2022; 13:1032186. [PMID: 36590402 PMCID: PMC9800612 DOI: 10.3389/fmicb.2022.1032186] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.
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2
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Bhardwaj K, Garg A, Pandey AD, Sharma H, Kumar M, Vrati S. Insights into the human gut virome by sampling a population from the Indian subcontinent. J Gen Virol 2022; 103. [PMID: 35951476 DOI: 10.1099/jgv.0.001774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.
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Affiliation(s)
- Kanchan Bhardwaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India.,Manav Rachna International Institute of Research and Studies, Sector-43, Aravali hills, Faridabad-121 004, Haryana, India
| | - Anjali Garg
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Abhay Deep Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Himani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
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3
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Hunter ES, Literman R, Handy SM. Utilizing Big Data to Identify Tiny Toxic Components: Digitalis. Foods 2021; 10:1794. [PMID: 34441571 PMCID: PMC8391216 DOI: 10.3390/foods10081794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022] Open
Abstract
The botanical genus Digitalis is equal parts colorful, toxic, and medicinal, and its bioactive compounds have a long history of therapeutic use. However, with an extremely narrow therapeutic range, even trace amounts of Digitalis can cause adverse effects. Using chemical methods, the United States Food and Drug Administration traced a 1997 case of Digitalis toxicity to a shipment of Plantago (a common ingredient in dietary supplements marketed to improve digestion) contaminated with Digitalis lanata. With increased accessibility to next generation sequencing technology, here we ask whether this case could have been cracked rapidly using shallow genome sequencing strategies (e.g., genome skims). Using a modified implementation of the Site Identification from Short Read Sequences (SISRS) bioinformatics pipeline with whole-genome sequence data, we generated over 2 M genus-level single nucleotide polymorphisms in addition to species-informative single nucleotide polymorphisms. We simulated dietary supplement contamination by spiking low quantities (0-10%) of Digitalis whole-genome sequence data into a background of commonly used ingredients in products marketed for "digestive cleansing" and reliably detected Digitalis at the genus level while also discriminating between Digitalis species. This work serves as a roadmap for the development of novel DNA-based assays to quickly and reliably detect the presence of toxic species such as Digitalis in food products or dietary supplements using genomic methods and highlights the power of harnessing the entire genome to identify botanical species.
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Affiliation(s)
| | | | - Sara M. Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD 20740, USA; (E.S.H.); (R.L.)
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4
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Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. Appl Environ Microbiol 2021; 87:AEM.02914-20. [PMID: 33452030 PMCID: PMC8091602 DOI: 10.1128/aem.02914-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/07/2021] [Indexed: 01/04/2023] Open
Abstract
Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator amplicon sequence variants (ASVs) of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes. Wastewater management in the Canadian Arctic is challenging due to climate extremes, small population sizes, and lack of conventional infrastructure for wastewater treatment. Although many northern communities use waste stabilization ponds (WSPs) as their primary form of wastewater treatment, few studies have explored WSP microbial communities and assessed effluent impacts on receiving waters from a microbiological perspective. Here, we used 16S rRNA gene and metagenome sequencing to characterize WSP and receiving water microbial communities for two time points bracketing the spring WSP thaw in Baker Lake (Nunavut) and compared these results to other Nunavut WSPs in Cambridge Bay and Kugluktuk. Most amplicon sequence variants (ASVs) recovered from these WSP samples belonged to the phylum Proteobacteria, with considerable variation between the three locations and only six ASVs shared among the WSPs at >0.2% relative abundance. Wastewater indicator ASVs for the Baker Lake WSP were identified, and few indicator ASVs were detected in samples originating from other upstream or downstream sites. The metagenomic data revealed a strong enrichment of antibiotic resistance genes for WSP samples relative to downstream and reference samples, especially for genes associated with macrolide resistance. Together, our results provide a baseline characterization for WSP microbial communities, demonstrate how indicator ASVs can be used to monitor attenuation and dilution of effluent microorganisms, and reveal that WSPs can serve as hot spots for antibiotic resistance genes. IMPORTANCE Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator amplicon sequence variants (ASVs) of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes. Given operational and infrastructure changes anticipated for wastewater treatment systems in the Arctic, baseline data such as these are essential for further development of safe and effective wastewater treatment systems.
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5
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Hunter ES, Paight C, Lane CE. Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae. Front Microbiol 2020; 11:580719. [PMID: 33335517 PMCID: PMC7737231 DOI: 10.3389/fmicb.2020.580719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/05/2020] [Indexed: 12/27/2022] Open
Abstract
Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host. Here we present genomic and transcriptomic data from the parasitic sister species to this mutualist, Cardiosporidium cionae, and its associated bacterial endosymbiont. Cardiosporidium cionae and Nephromyces both infect tunicate hosts, localize to similar organs within these hosts, and maintain bacterial endosymbionts. Though many other protists are known to harbor bacterial endosymbionts, these associations are completely unknown in Apicomplexa outside of the Nephromycidae clade. Our data indicate that a vertically transmitted α-proteobacteria has been retained in each lineage since Nephromyces and Cardiosporidium diverged. This α-proteobacterial endosymbiont has highly reduced metabolic capabilities, but contributes the essential amino acid lysine, and essential cofactor lipoic acid to C. cionae. This partnership likely reduces resource competition with the tunicate host. However, our data indicate that the contribution of the single α-proteobacterial endosymbiont in C. cionae is minimal compared to the three taxa of endosymbionts present in the Nephromyces system, and is a potential explanation for the virulence disparity between these lineages.
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Affiliation(s)
- Elizabeth Sage Hunter
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Christopher Paight
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Christopher E. Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
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6
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Metwaly A, Dunkel A, Waldschmitt N, Raj ACD, Lagkouvardos I, Corraliza AM, Mayorgas A, Martinez-Medina M, Reiter S, Schloter M, Hofmann T, Allez M, Panes J, Salas A, Haller D. Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism. Nat Commun 2020; 11:4322. [PMID: 32859898 PMCID: PMC7456324 DOI: 10.1038/s41467-020-17956-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Andreas Dunkel
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Abilash Chakravarthy Durai Raj
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Munich, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Ana Maria Corraliza
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Aida Mayorgas
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | | | - Sinah Reiter
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Munich, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Matthieu Allez
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
| | - Julian Panes
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany.
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany.
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7
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Wu R, Chai B, Cole JR, Gunturu SK, Guo X, Tian R, Gu JD, Zhou J, Tiedje JM. Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming. ISME JOURNAL 2020; 14:1651-1662. [PMID: 32221408 PMCID: PMC7305122 DOI: 10.1038/s41396-020-0635-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023]
Abstract
There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.
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Affiliation(s)
- Ruonan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Santosh K Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Xue Guo
- Department of Microbiology & Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Renmao Tian
- Department of Microbiology & Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, USA
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
| | - Jizhong Zhou
- Department of Microbiology & Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. .,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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8
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Mascarenhas R, Ruziska FM, Moreira EF, Campos AB, Loiola M, Reis K, Trindade-Silva AE, Barbosa FAS, Salles L, Menezes R, Veiga R, Coutinho FH, Dutilh BE, Guimarães PR, Assis APA, Ara A, Miranda JGV, Andrade RFS, Vilela B, Meirelles PM. Integrating Computational Methods to Investigate the Macroecology of Microbiomes. Front Genet 2020; 10:1344. [PMID: 32010196 PMCID: PMC6979972 DOI: 10.3389/fgene.2019.01344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 12/09/2019] [Indexed: 12/15/2022] Open
Abstract
Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as “everything is everywhere, but the environment selects”) as well as applied ecological problems, such as those posed by human induced global environmental changes.
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Affiliation(s)
| | - Flávia M Ruziska
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | | | - Amanda B Campos
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Miguel Loiola
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Kaike Reis
- Chemical Engineering Department, Polytechnic School of Federal University of Bahia, Salvador, Brazil
| | - Amaro E Trindade-Silva
- Institute of Biology, Federal University of Bahia, Salvador, Brazil.,Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Lucas Salles
- Institute of Geology, Federal University of Bahia, Salvador, Brazil
| | - Rafael Menezes
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil.,Institute of Physics, Federal University of Bahia, Salvador, Brazil
| | - Rafael Veiga
- Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Brazil
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paulo R Guimarães
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Butantã, Brazil
| | - Ana Paula A Assis
- Department of Ecology, Biosciences Institute, University of Sao Paulo, Butantã, Brazil
| | - Anderson Ara
- Institute of Mathematics, Federal University of Bahia, Salvador, Brazil
| | - José G V Miranda
- Institute of Physics, Federal University of Bahia, Salvador, Brazil
| | - Roberto F S Andrade
- Institute of Physics, Federal University of Bahia, Salvador, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Brazil
| | - Bruno Vilela
- Institute of Biology, Federal University of Bahia, Salvador, Brazil
| | - Pedro Milet Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Brazil.,Department of Ecology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
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9
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Bredon M, Herran B, Bertaux J, Grève P, Moumen B, Bouchon D. Isopod holobionts as promising models for lignocellulose degradation. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:49. [PMID: 32190114 PMCID: PMC7071664 DOI: 10.1186/s13068-020-01683-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/20/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Isopods have colonized all environments, partly thanks to their ability to decompose the organic matter. Their enzymatic repertoire, as well as the one of their associated microbiota, has contributed to their colonization success. Together, these holobionts have evolved several interesting life history traits to degrade the plant cell walls, mainly composed of lignocellulose. It has been shown that terrestrial isopods achieve lignocellulose degradation thanks to numerous and diverse CAZymes provided by both the host and its microbiota. Nevertheless, the strategies for lignocellulose degradation seem more diversified in isopods, in particular in aquatic species which are the least studied. Isopods could be an interesting source of valuable enzymes for biotechnological industries of biomass conversion. RESULTS To provide new features on the lignocellulose degradation in isopod holobionts, shotgun sequencing of 36 metagenomes of digestive and non-digestive tissues was performed from several populations of four aquatic and terrestrial isopod species. Combined to the 15 metagenomes of an additional species from our previous study, as well as the host transcriptomes, this large dataset allowed us to identify the CAZymes in both the host and the associated microbial communities. Analyses revealed the dominance of Bacteroidetes and Proteobacteria in the five species, covering 36% and 56% of the total bacterial community, respectively. The identification of CAZymes and new enzymatic systems for lignocellulose degradation, such as PULs, cellulosomes and LPMOs, highlights the richness of the strategies used by the isopods and their associated microbiota. CONCLUSIONS Altogether, our results show that the isopod holobionts are promising models to study lignocellulose degradation. These models can provide new enzymes and relevant lignocellulose-degrading bacteria strains for the biotechnological industries of biomass conversion.
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Affiliation(s)
- Marius Bredon
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Ecologie et Biologie des Interactions-Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Benjamin Herran
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Ecologie et Biologie des Interactions-Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Joanne Bertaux
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Ecologie et Biologie des Interactions-Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Pierre Grève
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Ecologie et Biologie des Interactions-Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Ecologie et Biologie des Interactions-Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Ecologie et Biologie des Interactions-Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers Cedex 9, France
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