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Tokuda G. Origin of symbiotic gut spirochetes as key players in the nutrition of termites. Environ Microbiol 2021; 23:4092-4097. [PMID: 34097340 DOI: 10.1111/1462-2920.15625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022]
Abstract
Termites harbour symbiotic spirochetes in their hindguts, which have long been considered treponemes, although they represent separate lines of descent from known species of Treponema. 'Termite gut treponemes' have a mutualistic relationship with the host termites with their physiological properties including CO2 -reductive acetogenesis, from which the resulting acetate fulfils most of the respiratory requirement of the host. Song and co-workers showed that a spirochetal isolate (strain RmG30) from a Madeira cockroach represents the earliest branching lineage of extremely diverse termite (Treponema) cluster I and was a simple homolactic fermenter, suggesting that CO2 -reductive acetogenesis exhibited by some members of termite cluster I originated via horizontal gene transfer. Phylogenomic and 16S rRNA sequence-based phylogenetic analyses indicated a deeply-branched sister clade containing termite cluster I was distinguishable as a family-level lineage. In this context, a new family, 'Termitinemataceae' has been proposed for this clade. Strain RmG30 has been designated as the type strain of Breznakiella homolactica gen. nov. sp. nov. named after John A. Breznak, an American microbiologist distinguished in termite gut microbiology. The study has posed important questions for the future, including the actual roles of the termite spirochetes in each termite lineage and the evolutionary process of their physiological properties.
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Affiliation(s)
- Gaku Tokuda
- Tropical Biosphere Research Center, COMB, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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Ikeda-Ohtsubo W, Strassert JFH, Köhler T, Mikaelyan A, Gregor I, McHardy AC, Tringe SG, Hugenholtz P, Radek R, Brune A. ‘Candidatus
Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria
and a putative homoacetogen. Environ Microbiol 2016; 18:2548-64. [DOI: 10.1111/1462-2920.13234] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/18/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Wakako Ikeda-Ohtsubo
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
| | - Jürgen F. H. Strassert
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
- Institute of Biology/Zoology, Free University of Berlin; Königin-Luise-Strasse 1-3 14195 Berlin Germany
| | - Tim Köhler
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
| | - Aram Mikaelyan
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
| | - Ivan Gregor
- Computational Biology of Infection Research, Helmholtz Center for Infection Research; Inhoffenstraße 7 38124 Braunschweig Germany
- Department of Algorithmic Bioinformatics; Heinrich Heine University Düsseldorf; 40225 Düsseldorf Germany
| | - Alice C. McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research; Inhoffenstraße 7 38124 Braunschweig Germany
- Department of Algorithmic Bioinformatics; Heinrich Heine University Düsseldorf; 40225 Düsseldorf Germany
| | | | - Phil Hugenholtz
- Department of Energy Joint Genome Institute; Walnut Creek; CA 94598 USA
- Australian Centre for Ecogenomics, The University of Queensland; Brisbane QLD 4072 Australia
| | - Renate Radek
- Institute of Biology/Zoology, Free University of Berlin; Königin-Luise-Strasse 1-3 14195 Berlin Germany
| | - Andreas Brune
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
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Brune A, Dietrich C. The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution. Annu Rev Microbiol 2015. [DOI: 10.1146/annurev-micro-092412-155715] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; ,
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; ,
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Baba R, Kimura M, Asakawa S, Watanabe T. Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil. FEMS Microbiol Lett 2013; 350:249-56. [PMID: 24261851 DOI: 10.1111/1574-6968.12335] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 09/03/2013] [Accepted: 11/12/2013] [Indexed: 12/01/2022] Open
Abstract
Hydrogen (H2) is one of the most important intermediates in the anaerobic decomposition of organic matter. Although the microorganisms consuming H2 in anaerobic environments have been well documented, those producing H2 are not well known. In this study, we elucidated potential members of H2 -producing bacteria in a paddy field soil using clone library analysis of [FeFe]-hydrogenase genes. The [FeFe]-hydrogenase is an enzyme involved in H2 metabolism, especially in H2 production. A suitable primer set was selected based on the preliminary clone library analysis performed using three primer sets designed for the [FeFe]-hydrogenase genes. Soil collected in flooded and drained periods was used to examine the dominant [FeFe]-hydrogenase genes in the paddy soil bacteria. In total, 115 and 108 clones were analyzed from the flooded and drained paddy field soils, respectively. Homology and phylogenetic analysis of the clones showed the presence of diverse [FeFe]-hydrogenase genes mainly related to Firmicutes, Deltaproteobacteria, and Chloroflexi. Predominance of Deltaproteobacteria and Chloroflexi suggests that the distinct bacterial community possessed [FeFe]-hydrogenase genes in the paddy field soil. Our study revealed the potential members of H2 -producing bacteria in the paddy field soil based on their genetic diversity and the distinctiveness of the [FeFe]-hydrogenase genes.
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Affiliation(s)
- Ryuko Baba
- Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
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Zheng H, Bodington D, Zhang C, Miyanaga K, Tanji Y, Hongoh Y, Xing XH. Comprehensive phylogenetic diversity of [FeFe]-hydrogenase genes in termite gut microbiota. Microbes Environ 2013; 28:491-4. [PMID: 24240187 PMCID: PMC4070709 DOI: 10.1264/jsme2.me13082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic diversity of [FeFe]-hydrogenase (HydA) in termite guts was assessed by pyrosequencing PCR amplicons obtained using newly designed primers. Of 8,066 reads, 776 hydA phylotypes, defined with 97% nucleotide sequence identity, were recovered from the gut homogenates of three termite species, Hodotermopsis sjoestedti, Reticulitermes speratus, and Nasutitermes takasagoensis. The phylotype coverage was 92–98%, and the majority shared only low identity with database sequences. It was estimated that 194–745 hydA phylotypes existed in the gut of each termite species. Our results demonstrate that hydA gene diversity in the termite gut microbiota is much higher than previously estimated.
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Affiliation(s)
- Hao Zheng
- Department of Chemical Engineering, Tsinghua University
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He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn RH, Kyrpides NC, Warnecke F, Tringe SG, Hugenholtz P. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One 2013; 8:e61126. [PMID: 23593407 PMCID: PMC3625147 DOI: 10.1371/journal.pone.0061126] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 03/07/2013] [Indexed: 11/19/2022] Open
Abstract
Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the microbial decomposition of biomass with varied chemical profiles, it is important to determine whether termites harbor different microbial symbionts with specialized functionalities geared toward different feeding regimens. In this study, we compared the microbiota in the hindgut paunch of Amitermes wheeleri collected from cow dung and Nasutitermes corniger feeding on sound wood by 16S rRNA pyrotag, comparative metagenomic and metatranscriptomic analyses. We found that Firmicutes and Spirochaetes were the most abundant phyla in A. wheeleri, in contrast to N. corniger where Spirochaetes and Fibrobacteres dominated. Despite this community divergence, a convergence was observed for functions essential to termite biology including hydrolytic enzymes, homoacetogenesis and cell motility and chemotaxis. Overrepresented functions in A. wheeleri relative to N. corniger microbiota included hemicellulose breakdown and fixed-nitrogen utilization. By contrast, glycoside hydrolases attacking celluloses and nitrogen fixation genes were overrepresented in N. corniger microbiota. These observations are consistent with dietary differences in carbohydrate composition and nutrient contents, but may also reflect the phylogenetic difference between the hosts.
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Affiliation(s)
- Shaomei He
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Natalia Ivanova
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edward Kirton
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Martin Allgaier
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Claudia Bergin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, United States of America
| | - Nikos C. Kyrpides
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Falk Warnecke
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Susannah G. Tringe
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Philip Hugenholtz
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail:
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