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Takahashi K, Kuwahara H, Horikawa Y, Izawa K, Kato D, Inagaki T, Yuki M, Ohkuma M, Hongoh Y. Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade. THE ISME JOURNAL 2023; 17:1895-1906. [PMID: 37653056 PMCID: PMC10579323 DOI: 10.1038/s41396-023-01502-0] [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: 03/26/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.
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Affiliation(s)
- Kazuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
| | - Hirokazu Kuwahara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yutaro Horikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kazuki Izawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Daiki Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Tatsuya Inagaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan.
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Tongununui P, Kuriya Y, Murata M, Sawada H, Araki M, Nomura M, Morioka K, Ichie T, Ikejima K, Adachi K. Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling. PLoS One 2022; 16:e0261654. [PMID: 34972143 PMCID: PMC8719709 DOI: 10.1371/journal.pone.0261654] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022] Open
Abstract
Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.
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Affiliation(s)
- Prasert Tongununui
- Department of Marine Science and Environment, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Tambon Maifad, Amphur Sikao, Trang, Thailand
| | - Yuki Kuriya
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masahiro Murata
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Hideki Sawada
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Maizuru, Kyoto, Japan
| | - Michihiro Araki
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Mika Nomura
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Katsuji Morioka
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Tomoaki Ichie
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Kou Ikejima
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Kohsuke Adachi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
- * E-mail:
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Bayen S, Roy S, Chakraborti D, Mukhopadhyay A, Hazarika LK, Pramanik P, Borchetia S, Mukherjee S. Mutualistic relation of termites with associated microbes for their harmonious survival. Symbiosis 2021. [DOI: 10.1007/s13199-021-00809-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Campanini EB, Pedrino M, Martins LA, Athaide Neta OS, Carazzolle MF, Ciancaglini I, Malavazi I, Costa-Leonardo AM, de Melo Freire CC, Nunes FMF, da Cunha AF. Expression profiles of neotropical termites reveal microbiota-associated, caste-biased genes and biotechnological targets. INSECT MOLECULAR BIOLOGY 2021; 30:152-164. [PMID: 33247845 DOI: 10.1111/imb.12684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/21/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Termites are well recognized by their complex development trajectories, involving dynamic differentiation process between non-reproductive castes, workers and soldiers. These insects are associated with endosymbiotic microorganisms, which help in lignocellulose digestion and nitrogen metabolism. Aiming to identify genes harbouring biotechnological potential, we analyzed workers and soldiers RNA-Seq data of three neotropical termites: Heterotermes tenuis (Isoptera: Rhinotermitidae), Velocitermes heteropterus (Isoptera: Termitidae) and Cornitermes cumulans (Isoptera: Termitidae). We observed differences in the microbiota associated with each termite family, and found protists' genes in both Termitidae species. We found an opposite pattern of caste-biased gene expression between H. tenuis and the termitids studied. Moreover, the two termitids are considerably different concerning the number of differentially expressed genes (DEGs). Functional annotation indicated considerable differences in caste-biased gene content between V. heteropterus and C. cumulans, even though they share similar diet and biological niche. Among the most DEGs, we highlighted those involved in caste differentiation and cellulose digestion, which are attractive targets for studying more efficient technologies for termite control, biomass digestion and other biotechnological applications.
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Affiliation(s)
- E B Campanini
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - M Pedrino
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L A Martins
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - O S Athaide Neta
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - M F Carazzolle
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - I Ciancaglini
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - I Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A M Costa-Leonardo
- Laboratório de Cupins, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), campus de Rio Claro, Rio Claro, Brazil
| | - C C de Melo Freire
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - F M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A F da Cunha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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Yao L, Li X, Zhou Z, Shi D, Li Z, Li S, Yao H, Yang J, Yu H, Xiao Y. Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey ( Rhinopithecus roxellana hubeiensis). BIOMED RESEARCH INTERNATIONAL 2021; 2021:6667715. [PMID: 33778078 PMCID: PMC7979289 DOI: 10.1155/2021/6667715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/08/2021] [Accepted: 02/28/2021] [Indexed: 11/18/2022]
Abstract
The gut microbiota represents a source of genetic and metabolic diversity of a complex polymicrobial ecosystem within its host. To investigate age-based variations of the gut microbiota among Shennongjia golden snub-nosed monkeys (Rhinopithecus roxellana hubeiensis), we characterized the microbial species in fecal samples from 18 Shennongjia golden snub-nosed monkeys evenly pooled into 3 aged groups (Group 1, 1-3 years; Group 2, 5-8 years; Group 3, above 12 years) in Shennongjia, Hubei Province, China. Genomic DNA was extracted from fecal samples, and the 16S rRNA gene V4 region was sequenced using the Illumina high-throughput MiSeq platform PE250. A total of 28 microbial phyla were identified in the gut microbiome of these monkeys with the ten most abundant phyla (i.e., Firmicutes, Bacteroidetes, Verrucomicrobia, Spirochaetes, Tenericutes, Proteobacteria, Planctomycetes, Fibrobacteres, Cyanobacteria, and Euryarchaeota). A total of 1,469 (of 16 phyla and 166 genera), 1,381 (of 16 phyla and 157 genera), and 1,931 (of 19 phyla and 190 genera) operational taxonomic units (OTUs) were revealed in Groups 1, 2, and 3, respectively, with Group 3 containing the most diverse groups of OTUs as revealed by the species relative abundance clustering analysis. These results suggest that the gut microbiota in these monkeys maintain a dynamic status, starting from the early developmental stages of life with the species relative abundance increasing with age. This is the first study to comprehensively characterize the gut microbiota and provide valuable information for monitoring the health and nutritional needs of this endangered primate at different ages.
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Affiliation(s)
- Lijuan Yao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zutao Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Deshi Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Zili Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Shangfei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Hui Yao
- Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Hubei Conservation and Research Center for the Golden Monkey, Muyu, Shennongjia, 442411 Hubei, China
| | - Jingyuan Yang
- Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Hubei Conservation and Research Center for the Golden Monkey, Muyu, Shennongjia, 442411 Hubei, China
| | - Huiliang Yu
- Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Hubei Conservation and Research Center for the Golden Monkey, Muyu, Shennongjia, 442411 Hubei, China
| | - Yuncai Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
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Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes. Sci Rep 2020; 10:3864. [PMID: 32123275 PMCID: PMC7052144 DOI: 10.1038/s41598-020-60850-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/24/2019] [Indexed: 11/08/2022] Open
Abstract
In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.
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Hervé V, Liu P, Dietrich C, Sillam-Dussès D, Stiblik P, Šobotník J, Brune A. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ 2020; 8:e8614. [PMID: 32095380 PMCID: PMC7024585 DOI: 10.7717/peerj.8614] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
"Higher" termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, for example, Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.
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Affiliation(s)
- Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Pengfei Liu
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology EA 4443, Université Paris 13, Villetaneuse, France
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jan Šobotník
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota. Sci Rep 2019; 9:16329. [PMID: 31705042 PMCID: PMC6841923 DOI: 10.1038/s41598-019-52843-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.
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Diouf M, Miambi E, Mora P, Frechault S, Robert A, Rouland-Lefèvre C, Hervé V. Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes. FEMS Microbiol Lett 2019; 365:4904115. [PMID: 29579215 DOI: 10.1093/femsle/fny046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/22/2018] [Indexed: 12/19/2022] Open
Abstract
There are multiple forms of interactions between termites and bacteria. In addition to their gut microbiota, which has been intensively studied, termites host intracellular symbionts such as Wolbachia. These distinct symbioses have been so far approached independently and mostly in adult termites. We addressed the dynamics of Wolbachia and the microbiota of the eggs and gut for various life stages and castes of the wood-feeding termite, Nasutitermes arborum, using deep-sequencing of the 16S rRNA gene. Wolbachia was dominant in eggs as expected. Unexpectedly, it persisted in the gut of nearly all stages and castes, indicating a wide somatic distribution in termites. Wolbachia-related sequences clustered into few operational taxonomic units, but these were within the same genotype, acquired maternally. Wolbachia was largely dominant in DNA extracts from the guts of larvae and pre-soldiers (59.1%-99.1% of reads) where gut-resident lineages were less represented and less diverse. The reverse was true for the adult castes. This is the first study reporting the age-dependency of the relative abundance of Wolbachia in the termite gut and its negative correlation with the diversity of the microbiota. The possible mechanisms underlying this negative interaction are discussed.
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Affiliation(s)
- Michel Diouf
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Edouard Miambi
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Philippe Mora
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Sophie Frechault
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Alain Robert
- Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). Centre IRD France Nord, 32 Avenue Henri Varagnat, 93143 Bondy, France
| | - Corinne Rouland-Lefèvre
- Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). Centre IRD France Nord, 32 Avenue Henri Varagnat, 93143 Bondy, France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
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Grieco MB, Lopes FAC, Oliveira LS, Tschoeke DA, Popov CC, Thompson CC, Gonçalves LC, Constantino R, Martins OB, Kruger RH, de Souza W, Thompson FL. Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim. Curr Microbiol 2019; 76:687-697. [DOI: 10.1007/s00284-019-01662-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/22/2019] [Indexed: 01/04/2023]
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Luo C, Li Y, Chen Y, Fu C, Long W, Xiao X, Liao H, Yang Y. Bamboo lignocellulose degradation by gut symbiotic microbiota of the bamboo snout beetle Cyrtotrachelus buqueti. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:70. [PMID: 30976320 PMCID: PMC6442426 DOI: 10.1186/s13068-019-1411-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/15/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Gut symbiotic microbiota plays a critical role in nutrient supply, digestion, and absorption. The bamboo snout beetle, Cyrtotrachelus buqueti, a common pest of several bamboo species, exhibits high lignocellulolytic enzyme activity and contains various CAZyme genes. However, to date, no studies have evaluated the role of gut symbiotic microbiota of the snout beetle on bamboo lignocellulose degradation. Therefore, the present study investigated the role of gut symbiotic microbiota of C. buqueti on bamboo lignocellulose degradation. RESULTS Gut symbiotic microbiota of female (CCJ), male (XCJ), and larvae (YCJ) beetles was used to treat bamboo shoot particles (BSPs) in vitro for 6 days. Scanning electron microscopy (SEM) revealed significant destruction of the lignocellulose structure after treatment, which was consistent with the degradation efficiencies of CCJ, XCJ, and YCJ for cellulose (21.11%, 17.58% and 18.74%, respectively); hemicellulose (22.22%, 27.18% and 34.20%, respectively); and lignin (19.83%, 24.30% and 32.97%, respectively). Gut symbiotic microbiota of adult and larvae beetles was then identified using 16sRNA sequencing, which revealed that four microbes: Lactococcus, Serratia, Dysgonomonas and Enterococcus, comprise approximately 84% to 94% of the microbiota. Moreover, the genomes of 45 Lactococcus, 72 Serratia, 86 Enterococcus and 4 Dysgonomonas microbes were used to analyse resident CAZyme genes. These results indicated that gut symbiotic microbiota of adult and larvae C. buqueti is involved in the lignocellulose degradation traits shown by the host. CONCLUSIONS This study shows that the gut symbiotic microbiota of C. buqueti participates in bamboo lignocellulose degradation, providing innovative findings for bamboo lignocellulose bioconversion. Furthermore, the results of this study will allow us to further isolate lignocellulose-degrading microbiota for use in bamboo lignocellulose bioconversion.
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Affiliation(s)
- Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
| | - Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039 Sichuan China
| | - Ying Chen
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039 Sichuan China
| | - Chun Fu
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
| | - Wencong Long
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
| | - Ximeng Xiao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039 Sichuan China
| | - Hong Liao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
| | - Yaojun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 Sichuan China
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12
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Utami YD, Kuwahara H, Igai K, Murakami T, Sugaya K, Morikawa T, Nagura Y, Yuki M, Deevong P, Inoue T, Kihara K, Lo N, Yamada A, Ohkuma M, Hongoh Y. Genome analyses of uncultured TG2/ZB3 bacteria in 'Margulisbacteria' specifically attached to ectosymbiotic spirochetes of protists in the termite gut. THE ISME JOURNAL 2019; 13:455-467. [PMID: 30287885 PMCID: PMC6331581 DOI: 10.1038/s41396-018-0297-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022]
Abstract
We investigated the phylogenetic diversity, localisation and metabolism of an uncultured bacterial clade, Termite Group 2 (TG2), or ZB3, in the termite gut, which belongs to the candidate phylum 'Margulisbacteria'. We performed 16S rRNA amplicon sequencing analysis and detected TG2/ZB3 sequences in 40 out of 72 termite and cockroach species, which exclusively constituted a monophyletic cluster in the TG2/ZB3 clade. Fluorescence in situ hybridisation analysis in lower termites revealed that these bacteria are specifically attached to ectosymbiotic spirochetes of oxymonad gut protists. Draft genomes of four TG2/ZB3 phylotypes from a small number of bacterial cells were reconstructed, and functional genome analysis suggested that these bacteria hydrolyse and ferment cellulose/cellobiose to H2, CO2, acetate and ethanol. We also assembled a draft genome for a partner Treponema spirochete and found that it encoded genes for reductive acetogenesis from H2 and CO2. We hypothesise that the TG2/ZB3 bacteria we report here are commensal or mutualistic symbionts of the spirochetes, exploiting the spirochetes as H2 sinks. For these bacteria, we propose a novel genus, 'Candidatus Termititenax', which represents a hitherto uncharacterised class-level clade in 'Margulisbacteria'. Our findings add another layer, i.e., cellular association between bacteria, to the multi-layered symbiotic system in the termite gut.
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Affiliation(s)
- Yuniar Devi Utami
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Hirokazu Kuwahara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Katsura Igai
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Takumi Murakami
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kaito Sugaya
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Takahiro Morikawa
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yuichi Nagura
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Pinsurang Deevong
- Department of Microbiology, Kasetsart University, Bangkok, 10900, Thailand
| | - Tetsushi Inoue
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Kumiko Kihara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Akinori Yamada
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan.
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13
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Tokuda G, Mikaelyan A, Fukui C, Matsuura Y, Watanabe H, Fujishima M, Brune A. Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites. Proc Natl Acad Sci U S A 2018; 115:E11996-E12004. [PMID: 30504145 PMCID: PMC6304966 DOI: 10.1073/pnas.1810550115] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.
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Affiliation(s)
- Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan;
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan
| | - Aram Mikaelyan
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27607
| | - Chiho Fukui
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan
| | - Yu Matsuura
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan
| | - Hirofumi Watanabe
- Biomolecular Mimetics Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8634 Ibaraki, Japan
| | - Masahiro Fujishima
- Department of Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida 1677-1, 753-8512 Yamaguchi, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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14
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Noda S, Sakamoto M, Aihara C, Yuki M, Katsuhara M, Ohkuma M. Lactococcus termiticola sp. nov., isolated from the gut of the wood-feeding higher termite Nasutitermes takasagoensis. Int J Syst Evol Microbiol 2018; 68:3832-3836. [DOI: 10.1099/ijsem.0.003068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Satoko Noda
- 1Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Mitsuo Sakamoto
- 3PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- 2Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Chihiro Aihara
- 1Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Masahiro Yuki
- 2Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Megumi Katsuhara
- 1Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Moriya Ohkuma
- 2Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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15
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Chew YM, Lye S, Md. Salleh M, Yahya A. 16S rRNA metagenomic analysis of the symbiotic community structures of bacteria in foregut, midgut, and hindgut of the wood-feeding termite Bulbitermes sp. Symbiosis 2018. [DOI: 10.1007/s13199-018-0544-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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16
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Suzuki K, Asano S, Iijima K, Ogata T, Kitagawa Y, Ikeda T. Effects of Beer Adaptation on Culturability of Beer-Spoilage Dekkera/Brettanomyces Yeasts. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2008-0917-01] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Koji Suzuki
- Research Laboratories of Brewing Technology, Asahi Breweries Ltd., Moriya-shi, Ibaraki, Japan
| | - Shizuka Asano
- Research Laboratories of Brewing Technology, Asahi Breweries Ltd., Moriya-shi, Ibaraki, Japan
| | - Kazumaru Iijima
- Research Laboratories of Brewing Technology, Asahi Breweries Ltd., Moriya-shi, Ibaraki, Japan
| | - Tomoo Ogata
- Research Laboratories of Brewing Technology, Asahi Breweries Ltd., Moriya-shi, Ibaraki, Japan
| | - Yasushi Kitagawa
- Research Laboratories of Brewing Technology, Asahi Breweries Ltd., Moriya-shi, Ibaraki, Japan
| | - Tsunehiro Ikeda
- Research Laboratories for Food Safety Chemistry, Asahi Breweries Ltd., Moriya-shi, Ibaraki, Japan
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17
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Auer L, Lazuka A, Sillam-Dussès D, Miambi E, O'Donohue M, Hernandez-Raquet G. Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors. Front Microbiol 2017; 8:2623. [PMID: 29312279 PMCID: PMC5744482 DOI: 10.3389/fmicb.2017.02623] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/15/2017] [Indexed: 11/16/2022] Open
Abstract
Termites are xylophages, being able to digest a wide variety of lignocellulosic biomass including wood with high lignin content. This ability to feed on recalcitrant plant material is the result of complex symbiotic relationships, which involve termite-specific gut microbiomes. Therefore, these represent a potential source of microorganisms for the bioconversion of lignocellulose in bioprocesses targeting the production of carboxylates. In this study, gut microbiomes of four termite species were studied for their capacity to degrade wheat straw and produce carboxylates in controlled bioreactors. All of the gut microbiomes successfully degraded lignocellulose and up to 45% w/w of wheat straw degradation was observed, with the Nasutitermes ephratae gut-microbiome displaying the highest levels of wheat straw degradation, carboxylate production and enzymatic activity. Comparing the 16S rRNA gene diversity of the initial gut inocula to the bacterial communities in lignocellulose degradation bioreactors revealed important changes in community diversity. In particular, taxa such as Spirochaetes and Fibrobacteres that were highly abundant in the initial gut inocula were replaced by Firmicutes and Proteobacteria at the end of incubation in wheat straw bioreactors. Overall, this study demonstrates that termite-gut microbiomes constitute a reservoir of lignocellulose-degrading bacteria that can be harnessed in artificial conditions for biomass conversion processes that lead to the production of useful molecules.
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Affiliation(s)
- Lucas Auer
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - Adèle Lazuka
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - David Sillam-Dussès
- Laboratoire d'Éthologie Expérimentale et Comparée, Université Paris 13 - Sorbonne Paris Cité, Villetaneuse, France
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Institut de Recherche Pour le Développement – Sorbonne Universités, Bondy, France
| | - Edouard Miambi
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Université Paris-Est Créteil, Créteil, France
| | - Michael O'Donohue
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - Guillermina Hernandez-Raquet
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
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18
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Evidence from the gut microbiota of swarming alates of a vertical transmission of the bacterial symbionts in Nasutitermes arborum (Termitidae, Nasutitermitinae). Antonie van Leeuwenhoek 2017; 111:573-587. [DOI: 10.1007/s10482-017-0978-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
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19
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Izawa K, Kuwahara H, Sugaya K, Lo N, Ohkuma M, Hongoh Y. Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:411-418. [PMID: 28556617 DOI: 10.1111/1758-2229.12549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/19/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The genus Endomicrobium is a dominant bacterial group in the gut of lower termites, and most phylotypes are intracellular symbionts of gut protists. Here we report the discovery of Endomicrobium ectosymbionts of termite gut protists. We found that bristle-like Endomicrobium cells attached to the surface of spirotrichosomid protist cells inhabiting the termite Stolotermes victoriensis. Transmission electron microscopy revealed that a putative Endomicrobium cell likely attached to the protist surface via a protrusion from the tip of the bacterium. A phylotype, sharing 98.9% 16S rRNA sequence identity with the Endomicrobium ectosymbionts of the spirotrichosomid protists, was also found on the cell surface of the protist Trichonympha magna in the gut of the termite Porotermes adamsoni. We propose the novel species 'Candidatus Endomicrobium superficiale' for these bacteria. T. magna simultaneously harboured another Endomicrobium ectosymbiont that shared 93.5-94.2% 16S rRNA sequence identities with 'Ca. Endomicrobium superficiale'. Furthermore, Spirotrichonympha-like protists in P. adamsoni guts were associated with an Endomicrobium phylotype that possibly attached to the host flagella. A phylogenetic analysis suggested that these ectosymbiotic lineages have evolved multiple times from free-living Endomicrobium lineages and are relatively distant from the endosymbionts. Our results provide novel insights into the ecology and evolution of the Endomicrobium.
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Affiliation(s)
- Kazuki Izawa
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Hirokazu Kuwahara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kaito Sugaya
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Moriya Ohkuma
- RIKEN BioResource Center, Japan Collection of Microorganisms, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- RIKEN BioResource Center, Japan Collection of Microorganisms, Tsukuba, 305-0074, Japan
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20
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Xia X, Gurr GM, Vasseur L, Zheng D, Zhong H, Qin B, Lin J, Wang Y, Song F, Li Y, Lin H, You M. Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory. Front Microbiol 2017; 8:663. [PMID: 28491055 PMCID: PMC5405146 DOI: 10.3389/fmicb.2017.00663] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/31/2017] [Indexed: 01/18/2023] Open
Abstract
Herbivore specialists adapt to feed on a specific group of host plants by evolving various mechanisms to respond to plant defenses. Insects also possess complex gut microbiotas but their potential role in adaptation is poorly understood. Our previous study of the genome of diamondback moth, Plutella xylostella, revealed an intrinsic capacity to detoxify plant defense compounds, which is an important factor in its success as a pest. Here we expand on that work with a complete taxonomic and functional profile of the P. xylostella gut microbiota obtained by metagenomic sequencing. Gene enrichment in the metagenome, accompanied by functional identification, revealed an important role of specific gut bacteria in the breakdown of plant cell walls, detoxification of plant phenolics, and synthesis of amino acids. Microbes participating in these pathways mainly belonged to three highly abundant bacteria: Enterobacter cloacae, Enterobacter asburiae, and Carnobacterium maltaromaticum. Results show that while the gut microbial community may be complex, a small number of functionally active species can be disproportionally important. The presence of specific enzymes in the microbiota community, such as supporting amino acid synthesis, digestion and detoxification functions, demonstrates the beneficial interactions between P. xylostella and its gut microbiota. These interactions can be potential targets for manipulation to provide novel pest management approaches.
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Affiliation(s)
- Xiaofeng Xia
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Graham Centre, Charles Sturt UniversityOrange, NSW, Australia
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Department of Biological Sciences, Brock UniversitySt. Catharines, ON, Canada
| | - Dandan Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | | | | | - Junhan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yue Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - FengQin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yong Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Hailan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of AgricultureFuzhou, China
- Fujian-Taiwan Joint Innovation Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry UniversityFuzhou, China
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Samoilova ES, Kostina NV, Striganova BR. Microbial population of the digestive tract of click beetle larvae (Elateridae, Coleoptera). BIOL BULL+ 2016. [DOI: 10.1134/s1062359016050083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Sorokin DY, Rakitin AL, Gumerov VM, Beletsky AV, Sinninghe Damsté JS, Mardanov AV, Ravin NV. Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres. Front Microbiol 2016; 7:407. [PMID: 27065971 PMCID: PMC4814513 DOI: 10.3389/fmicb.2016.00407] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5–10.5 and total Na+ concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia; Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Vadim M Gumerov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and and Utrecht UniversityUtrecht, Netherlands; Geochemistry, Department of Earth Sciences, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol 2016; 6:1469. [PMID: 26779135 PMCID: PMC4704652 DOI: 10.3389/fmicb.2015.01469] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022] Open
Abstract
The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.
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Affiliation(s)
- Nurdyana Abdul Rahman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Advanced Water Management Center, The University of QueenslandBrisbane, QLD, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute Brisbane, QLD, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Genomics and Computational Biology, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
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24
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Rossmassler K, Dietrich C, Thompson C, Mikaelyan A, Nonoh JO, Scheffrahn RH, Sillam-Dussès D, Brune A. Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites. MICROBIOME 2015; 3:56. [PMID: 26607965 PMCID: PMC4660790 DOI: 10.1186/s40168-015-0118-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/28/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. RESULTS Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. CONCLUSION Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.
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Affiliation(s)
- Karen Rossmassler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Present address: Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Claire Thompson
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-Universität Marburg, Marburg, Germany
| | - James O Nonoh
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudolf H Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology, University Paris 13, EA4443, Sorbonne Paris Cité, Villetaneuse, France
- Institute of Research for Development-Sorbonne Universités, Institute of Ecology and Environmental Sciences, U242, Bondy, France
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-Universität Marburg, Marburg, Germany.
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25
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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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26
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Mikaelyan A, Dietrich C, Köhler T, Poulsen M, Sillam-Dussès D, Brune A. Diet is the primary determinant of bacterial community structure in the guts of higher termites. Mol Ecol 2015; 24:5284-95. [PMID: 26348261 DOI: 10.1111/mec.13376] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/20/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
Abstract
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.
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Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tim Köhler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen East, Denmark
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), University of Paris 13, Sorbonne Paris Cité, Villetaneuse, France.,Institute of Ecology and Environmental Sciences - Paris (iEES-Paris), Institute of Research for Development, Sorbonne Universités, Bondy, France
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
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Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing. PLoS One 2015; 10:e0140014. [PMID: 26444989 PMCID: PMC4596844 DOI: 10.1371/journal.pone.0140014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/21/2015] [Indexed: 01/19/2023] Open
Abstract
Previous surveys of the gut microbiota of termites have been limited to the worker caste. Termite gut microbiota has been well documented over the last decades and consists mainly of lineages specific to the gut microbiome which are maintained across generations. Despite this intimate relationship, little is known of how symbionts are transmitted to each generation of the host, especially in higher termites where proctodeal feeding has never been reported. The bacterial succession across life stages of the wood-feeding higher termite Nasutitermes arborum was characterized by 16S rRNA gene deep sequencing. The microbial community in the eggs, mainly affiliated to Proteobacteria and Actinobacteria, was markedly different from the communities in the following developmental stages. In the first instar and last instar larvae and worker caste termites, Proteobacteria and Actinobacteria were less abundant than Firmicutes, Bacteroidetes, Spirochaetes, Fibrobacteres and the candidate phylum TG3 from the last instar larvae. Most of the representatives of these phyla (except Firmicutes) were identified as termite-gut specific lineages, although their relative abundances differed. The most salient difference between last instar larvae and worker caste termites was the very high proportion of Spirochaetes, most of which were affiliated to the Treponema Ic, Ia and If subclusters, in workers. The results suggest that termite symbionts are not transmitted from mother to offspring but become established by a gradual process allowing the offspring to have access to the bulk of the microbiota prior to the emergence of workers, and, therefore, presumably through social exchanges with nursing workers.
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28
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Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb). Syst Appl Microbiol 2015; 38:472-82. [DOI: 10.1016/j.syapm.2015.07.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/13/2015] [Accepted: 07/23/2015] [Indexed: 11/15/2022]
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29
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Butera G, Ferraro C, Alonzo G, Colazza S, Quatrini P. The gut microbiota of the wood-feeding termite Reticulitermes lucifugus (Isoptera; Rhinotermitidae). ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1101-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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30
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Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 2015; 24:2521-36. [PMID: 25809385 DOI: 10.1111/mec.13169] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 12/12/2022]
Abstract
Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.
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Affiliation(s)
- Michael L Yuan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA; Archbold Biological Station, Venus, FL, 33960, USA
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31
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Xu B, Xu W, Li J, Dai L, Xiong C, Tang X, Yang Y, Mu Y, Zhou J, Ding J, Wu Q, Huang Z. Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation. BMC Genomics 2015; 16:174. [PMID: 25887697 PMCID: PMC4369366 DOI: 10.1186/s12864-015-1378-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 02/21/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs. RESULTS In this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen. CONCLUSIONS Metagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.
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Affiliation(s)
- Bo Xu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Weijiang Xu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Junjun Li
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Liming Dai
- School of Life Science, Yunnan Normal University, Kunming, 650500, China.
| | - Caiyun Xiong
- School of Life Science, Yunnan Normal University, Kunming, 650500, China.
| | - Xianghua Tang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Yunjuan Yang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Yuelin Mu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Junpei Zhou
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Junmei Ding
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Qian Wu
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
| | - Zunxi Huang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China. .,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, 650500, China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, China.
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Bauer E, Lampert N, Mikaelyan A, Köhler T, Maekawa K, Brune A. Physicochemical conditions, metabolites and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae). FEMS Microbiol Ecol 2014; 91:1-14. [PMID: 25764554 DOI: 10.1093/femsec/fiu028] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While the gut microbiota of termites and its role in symbiotic digestion have been studied for decades, little is known about the bacteria colonizing the intestinal tract of the distantly related wood-feeding cockroaches (Blaberidae: Panesthiinae). Here, we show that physicochemical gut conditions and microbial fermentation products in the gut of Panesthia angustipennis resemble that of other cockroaches. Microsensor measurements confirmed that all gut compartments were anoxic at the center and had a slightly acidic to neutral pH and a negative redox potential. While acetate dominated in all compartments, lactate and hydrogen accumulated only in the crop. The high, hydrogen-limited rates of methane emission from living cockroaches were in agreement with the restriction of F420-fluorescent methanogens to the hindgut. The gut microbiota of both P. angustipennis and Salganea esakii differed strongly between compartments, with the highest density and diversity in the hindgut, but similarities between homologous compartments of both cockroaches indicated a specificity of the microbiota for their respective habitats. While some lineages were most closely related to the gut microbiota of omnivorous cockroaches and wood- or litter-feeding termites, others have been encountered also in vertebrates, reinforcing the hypothesis that strong environmental selection drives community structure in the cockroach gut.
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Affiliation(s)
- Eugen Bauer
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Niclas Lampert
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tim Köhler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Kiyoto Maekawa
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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33
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Ransom-Jones E, Jones DL, Edwards A, McDonald JE. Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs. Syst Appl Microbiol 2014; 37:502-9. [DOI: 10.1016/j.syapm.2014.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/10/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
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34
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Affiliation(s)
- Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan
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35
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Li J, Rui J, Pei Z, Sun X, Zhang S, Yan Z, Wang Y, Liu X, Zheng T, Li X. Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure. Appl Microbiol Biotechnol 2014; 98:4771-80. [PMID: 24633443 DOI: 10.1007/s00253-014-5629-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 11/26/2022]
Abstract
Anaerobic co-fermentation of straw and manure is widely used for waste treatment and biogas production. However, the differences between the straw- and slurry-associated prokaryotic communities, their dynamic changes throughout the co-fermentation process, and their correlations with bioreactor performance are not fully understood. To address these questions, we investigated the prokaryotic community compositions and the dynamics of prokaryotes attached to the straw and in the slurry during co-fermentation of wheat straw and swine manure using pyrosequencing technique. The results showed that straw- and slurry-associated prokaryotes were different in their structure and function. Straw-associated prokaryotic communities were overrepresented by the phyla Spirochaetes and Fibrobacteres, while Synergistetes and Euryarchaeota were more abundant in the slurry. The straw-associated candidate class TG3, genera Fibrobacter, Bacteroides, Acetivibrio, Clostridium III, Papillibacter, Treponema, Sedimentibacter, and Lutispora may specialize in substrate hydrolysis. Propionate was the most abundant volatile fatty acid in the slurry, and it was probably degraded through syntrophic oxidation by the genera Pelotomaculum, Methanoculleus, and Methanosaeta. The protein-fermenting bacteria Aminobacterium and Cloacibacillus were much abundant in the slurry, indicating that proteins are important substrates in the co-fermentation. This study provided a better understanding of the anaerobic co-fermentation process that is driven by spatially differentiated microbiota.
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Affiliation(s)
- Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, 610041, People's Republic of China
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36
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Mikaelyan A, Strassert JFH, Tokuda G, Brune A. The fibre-associated cellulolytic bacterial community in the hindgut of wood-feeding higher termites (Nasutitermesspp.). Environ Microbiol 2014. [DOI: 10.1111/1462-2920.12425] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Jürgen F. H. Strassert
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Gaku Tokuda
- Tropical Biosphere Research Center; COMB; University of the Ryukyus; Nishihara Okinawa Japan
| | - Andreas Brune
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
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37
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38
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The cockroach origin of the termite gut microbiota: patterns in bacterial community structure reflect major evolutionary events. Appl Environ Microbiol 2014; 80:2261-9. [PMID: 24487532 DOI: 10.1128/aem.04206-13] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Termites digest wood and other lignocellulosic substrates with the help of their intestinal microbiota. While the functions of the symbionts in the digestive process are slowly emerging, the origin of the bacteria colonizing the hindgut bioreactor is entirely unknown. Recently, our group discovered numerous representatives of bacterial lineages specific to termite guts in a closely related omnivorous cockroach, but it remains unclear whether they derive from the microbiota of a common ancestor or were independently selected by the gut environment. Here, we studied the bacterial gut microbiota in 34 species of termites and cockroaches using pyrotag analysis of the 16S rRNA genes. Although the community structures differed greatly between the major host groups, with dramatic changes in the relative abundances of particular bacterial taxa, we found that the majority of sequence reads belonged to bacterial lineages that were shared among most host species. When mapped onto the host tree, the changes in community structure coincided with major events in termite evolution, such as acquisition and loss of cellulolytic protists and the ensuing dietary diversification. UniFrac analysis of the core microbiota of termites and cockroaches and construction of phylogenetic tree of individual genus level lineages revealed a general host signal, whereas the branching order often did not match the detailed phylogeny of the host. It remains unclear whether the lineages in question have been associated with the ancestral cockroach since the early Cretaceous (cospeciation) or are diet-specific lineages that were independently acquired from the environment (host selection).
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Deng Y, Liu J, Li H, Li L, Tu J, Fang H, Chen J, Qian F. An improved plate culture procedure for the rapid detection of beer-spoilage lactic acid bacteria. JOURNAL OF THE INSTITUTE OF BREWING 2014. [DOI: 10.1002/jib.121] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yang Deng
- College of Light Industry and Food Sciences; South China University of Technology; Guangzhou 510640 People's Republic of China
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Junyan Liu
- College of Light Industry and Food Sciences; South China University of Technology; Guangzhou 510640 People's Republic of China
| | - Huiping Li
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Lin Li
- College of Light Industry and Food Sciences; South China University of Technology; Guangzhou 510640 People's Republic of China
| | - Jingxia Tu
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Huijing Fang
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Jiang Chen
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Fei Qian
- Institute of Brewing and Beverage Technology; Centre of Life and Food Sciences, TUM; Germany
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Sorokin DY, Gumerov VM, Rakitin AL, Beletsky AV, Damsté JSS, Muyzer G, Mardanov AV, Ravin NV. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3. Environ Microbiol 2013; 16:1549-65. [PMID: 24112708 DOI: 10.1111/1462-2920.12284] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/29/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6 Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Oktyabrya, bld. 7-2, 117312, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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A phylogenetic analysis of the phylum Fibrobacteres. Syst Appl Microbiol 2013; 36:376-82. [PMID: 23759599 DOI: 10.1016/j.syapm.2013.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/03/2013] [Accepted: 04/19/2013] [Indexed: 11/21/2022]
Abstract
Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.
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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: 111] [Impact Index Per Article: 10.1] [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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Huang XF, Bakker MG, Judd TM, Reardon KF, Vivanco JM. Variations in diversity and richness of gut bacterial communities of termites (Reticulitermes flavipes) fed with grassy and woody plant substrates. MICROBIAL ECOLOGY 2013; 65:531-6. [PMID: 23529653 DOI: 10.1007/s00248-013-0219-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/12/2013] [Indexed: 05/23/2023]
Abstract
Diets shape the animal gut microbiota, although the relationships between diets and the structure of the gut microbial community are not yet well understood. The gut bacterial communities of Reticulitermes flavipes termites fed on four individual plant biomasses with different degrees of recalcitrance to biodegradation were investigated by 16S rRNA pyrosequencing analysis. The termite gut bacterial communities could be differentiated between grassy and woody diets, and among grassy diets (corn stover vs. sorghum). The majority of bacterial taxa were shared across all diets, but each diet significantly enriched some taxa. Interestingly, the diet of corn stover reduced gut bacterial richness and diversity compared to other diets, and this may be related to the lower recalcitrance of this biomass to degradation.
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Affiliation(s)
- Xing-Feng Huang
- Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523-1173, USA
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Boucias DG, Cai Y, Sun Y, Lietze VU, Sen R, Raychoudhury R, Scharf ME. The hindgut lumen prokaryotic microbiota of the termiteReticulitermes flavipesand its responses to dietary lignocellulose composition. Mol Ecol 2013; 22:1836-53. [PMID: 23379767 DOI: 10.1111/mec.12230] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 12/27/2022]
Affiliation(s)
- Drion G. Boucias
- Department of Entomology and Nematology; University of Florida; Gainesville FL 32610-3622 USA
| | - Yunpeng Cai
- Shenzhen Institute of Advanced Technology; Chinese Academy of Science; Shenzhen China
| | - Yijun Sun
- Interdisciplinary Center for Biotechnology Research; University of Florida; Gainesville FL 32610-3622 USA
| | - Verena-Ulrike Lietze
- Department of Entomology and Nematology; University of Florida; Gainesville FL 32610-3622 USA
| | - Ruchira Sen
- Department of Entomology; Purdue University; West Lafayette IN 47907-2089 USA
| | | | - Michael E. Scharf
- Department of Entomology; Purdue University; West Lafayette IN 47907-2089 USA
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Thong-On A, Suzuki K, Noda S, Inoue JI, Kajiwara S, Ohkuma M. Isolation and characterization of anaerobic bacteria for symbiotic recycling of uric acid nitrogen in the gut of various termites. Microbes Environ 2012; 27:186-92. [PMID: 22791052 PMCID: PMC4036019 DOI: 10.1264/jsme2.me11325] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recycling of the nitrogenous waste uric acid (UA) of wood-feeding termites by their gut bacteria is one of the significant aspects of symbiosis for the conservation of nitrogen sources. Diverse anaerobic UA-degrading bacteria comprising 16 species were isolated from the gut of eight termite species, and were assigned to Clostridia, Enterobacteriaceae, and low G+C Gram-positive cocci. UA-degrading Clostridia had never been isolated from termite guts. UA-degrading ability was sporadically distributed among phylogenetically various culturable anaerobic bacteria from termite guts. A strain of Clostridium sp., which was commonly isolated from three termite species and represented a probable new species in cluster XIVa of clostridia, utilized UA as a nitrogen source but not as a sole carbon and energy source. This feature is in clear contrast to that of well-studied purinolytic clostridia or previously isolated UA degraders from termite guts, which also utilize UA as a sole carbon and energy source. Ammonia is the major nitrogenous product of UA degradation. Various purines stimulated the growth of this strain when added to an otherwise growth-limiting, nitrogen poor medium. The bacterial species involved the recycling of UA nitrogen in the gut microbial community of termites are more diverse in terms of both taxonomy and nutritional physiology than previously recognized.
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Affiliation(s)
- Arunee Thong-On
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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Abstract
The main challenge in second generation bioethanol production is the efficient breakdown of cellulose to sugar monomers (hydrolysis). Due to the recalcitrant character of cellulose, feedstock pretreatment and adapted hydrolysis steps are needed to obtain fermentable sugar monomers. The conventional industrial production process of second-generation bioethanol from biomass comprises several steps: thermochemical pretreatment, enzymatic hydrolysis and sugar fermentation. This process is undergoing continuous optimization in order to increase the bioethanol yield and reduce the economic cost. Therefore, the discovery of new enzymes with high lignocellulytic activity or new strategies is extremely important. In nature, wood-feeding termites have developed a sophisticated and efficient cellulose degrading system in terms of the rate and extent of cellulose hydrolysis and exploitation. This system, which represents a model for digestive symbiosis has attracted the attention of biofuel researchers. This review describes the termite digestive system, gut symbionts, termite enzyme resources, in vitro studies of isolated enzymes and lignin degradation in termites.
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Bacterial chitin utilisation at extremely haloalkaline conditions. Extremophiles 2012; 16:883-94. [PMID: 23007247 DOI: 10.1007/s00792-012-0484-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/09/2012] [Indexed: 10/27/2022]
Abstract
Chitin is produced in large amounts in hypersaline habitats with neutral pH due to the high biomass production of brine shrimp Artemia. Recently, a high abundance of Artemia was also noticed in hypersaline soda lakes in the Kulunda Steppe (Altai, Russia), which prompted us to survey the possibility of microbial chitin utilization at extremely haloalkaline conditions in soda brines. Most active chitin utilisation-supporting microbial growth was found at anaerobic conditions at pH 10 and up to 3.5 M total Na(+). At aerobic conditions, the degradation of chitin was slower, mostly incomplete and active at <2 M total Na(+), although very slow partial degradation was possible up to 4 M Na(+). Anaerobic enrichments at pH 10 yielded two different groups of obligately haloalkaliphilic fermentative anaerobes, exclusively specialized to utilise insoluble chitin as the only growth substrate. One group was represented by a single strain growing at moderate salinity, and another comprised multiple isolates growing up to 3.5 M Na(+). These groups represent two novel bacterial phyla not closely related to any other cultured bacteria. Aerobic enrichments from the lake sediments were dominated by several obligately haloalkaliphilic members of the genus Marinimicrobium in the Gammaproteobacteria. They were less specialised than the anaerobes and grew with chitin and its monomer and oligomers at a pH of 10 up to 2.5 M Na(+). Furthermore, several strains of haloalkaliphilic Gram-positive chitinolytics belonging to bacilli and actinobacteria were isolated from soda lake sediments and surrounding soda soils. In general, the results indicate the presence of an active and diverse haloalkaliphilic chitinolytic microbial community in hypersaline soda habitats.
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Colman DR, Toolson EC, Takacs-Vesbach CD. Do diet and taxonomy influence insect gut bacterial communities? Mol Ecol 2012; 21:5124-37. [PMID: 22978555 DOI: 10.1111/j.1365-294x.2012.05752.x] [Citation(s) in RCA: 334] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 07/11/2012] [Indexed: 12/28/2022]
Abstract
Many insects contain diverse gut microbial communities. While several studies have focused on a single or small group of species, comparative studies of phylogenetically diverse hosts can illuminate general patterns of host-microbiota associations. In this study, we tested the hypotheses that (i) host diet and (ii) host taxonomy structure intestinal bacterial community composition among insects. We used published 16S rRNA gene sequence data for 58 insect species in addition to four beetle species sampled from the Sevilleta National Wildlife Refuge to test these hypotheses. Overall, gut bacterial species richness in these insects was low. Decaying wood xylophagous insects harboured the richest bacterial gut flora (102.8 species level operational taxonomic units (OTUs)/sample ± 71.7, 11.8 ± 5.9 phylogenetic diversity (PD)/sample), while bees and wasps harboured the least rich bacterial communities (11.0 species level OTUs/sample ± 5.4, 2.6 ± 0.8 PD/sample). We found evidence to support our hypotheses that host diet and taxonomy structure insect gut bacterial communities (P < 0.001 for both). However, while host taxonomy was important in hymenopteran and termite gut community structure, diet was an important community structuring factor particularly for insect hosts that ingest lignocellulose-derived substances. Our analysis provides a baseline comparison of insect gut bacterial communities from which to test further hypotheses concerning proximate and ultimate causes of these associations.
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Affiliation(s)
- D R Colman
- Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
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Köhler T, Dietrich C, Scheffrahn RH, Brune A. High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl Environ Microbiol 2012; 78:4691-701. [PMID: 22544239 PMCID: PMC3370480 DOI: 10.1128/aem.00683-12] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 04/13/2012] [Indexed: 11/20/2022] Open
Abstract
Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H(2), O(2), pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H(2) to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.
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Affiliation(s)
- Tim Köhler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | - Andreas Brune
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Suzuki K, Asano S, Iijima K, Kitamoto K. Sake and Beer Spoilage Lactic Acid Bacteria - A Review. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2008.tb00331.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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