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Gallstone Disease, Obesity and the Firmicutes/Bacteroidetes Ratio as a Possible Biomarker of Gut Dysbiosis. J Pers Med 2020; 11:jpm11010013. [PMID: 33375615 PMCID: PMC7823692 DOI: 10.3390/jpm11010013] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Obesity is a major risk factor for developing gallstone disease (GSD). Previous studies have shown that obesity is associated with an elevated Firmicutes/Bacteroidetes ratio in the gut microbiota. These findings suggest that the development of GSD may be related to gut dysbiosis. This review presents and summarizes the recent findings of studies on the gut microbiota in patients with GSD. Most of the studies on the gut microbiota in patients with GSD have shown a significant increase in the phyla Firmicutes (Lactobacillaceae family, genera Clostridium, Ruminococcus, Veillonella, Blautia, Dorea, Anaerostipes, and Oscillospira), Actinobacteria (Bifidobacterium genus), Proteobacteria, Bacteroidetes (genera Bacteroides, Prevotella, and Fusobacterium) and a significant decrease in the phyla Bacteroidetes (family Muribaculaceae, and genera Bacteroides, Prevotella, Alistipes, Paludibacter, Barnesiella), Firmicutes (genera Faecalibacterium, Eubacterium, Lachnospira, and Roseburia), Actinobacteria (Bifidobacterium genus), and Proteobacteria (Desulfovibrio genus). The influence of GSD on microbial diversity is not clear. Some studies report that GSD reduces microbial diversity in the bile, whereas others suggest the increase in microbial diversity in the bile of patients with GSD. The phyla Proteobacteria (especially family Enterobacteriaceae) and Firmicutes (Enterococcus genus) are most commonly detected in the bile of patients with GSD. On the other hand, the composition of bile microbiota in patients with GSD shows considerable inter-individual variability. The impact of GSD on the Firmicutes/Bacteroidetes ratio is unclear and reports are contradictory. For this reason, it should be stated that the results of reviewed studies do not allow for drawing unequivocal conclusions regarding the relationship between GSD and the Firmicutes/Bacteroidetes ratio in the microbiota.
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Rettenmaier R, Duerr C, Neuhaus K, Liebl W, Zverlov VV. Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermenters. Syst Appl Microbiol 2019; 42:481-487. [DOI: 10.1016/j.syapm.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022]
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Tiwari S, Verma T. Cellulose as a Potential Feedstock for Cellulose Enzyme Production. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Zepeda Mendoza ML, Roggenbuck M, Manzano Vargas K, Hansen LH, Brunak S, Gilbert MTP, Sicheritz-Pontén T. Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. Acta Vet Scand 2018; 60:61. [PMID: 30309375 PMCID: PMC6182802 DOI: 10.1186/s13028-018-0415-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut. Results We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut. Conclusions Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging. Electronic supplementary material The online version of this article (10.1186/s13028-018-0415-3) contains supplementary material, which is available to authorized users.
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Afouda P, Durand GA, Lagier JC, Labas N, Cadoret F, Armstrong N, Raoult D, Dubourg G. Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2 T , the second Intestinimonas species cultured from the human gut. Microbiologyopen 2018; 8:e00621. [PMID: 29654664 PMCID: PMC6341035 DOI: 10.1002/mbo3.621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 01/08/2023] Open
Abstract
Intestinimonas massiliensis sp. nov strain GD2T is a new species of the genus Intestinimonas (the second, following Intestinimonas butyriciproducens gen. nov., sp. nov). First isolated from the gut microbiota of a healthy subject of French origin using a culturomics approach combined with taxono-genomics, it is strictly anaerobic, nonspore-forming, rod-shaped, with catalase- and oxidase-negative reactions. Its growth was observed after preincubation in an anaerobic blood culture enriched with sheep blood (5%) and rumen fluid (5%), incubated at 37°C. Its phenotypic and genotypic descriptions are presented in this paper with a full annotation of its genome sequence. This genome consists of 3,104,261 bp in length and contains 3,074 predicted genes, including 3,012 protein-coding genes and 62 RNA-coding genes. Strain GD2T significantly produces butyrate and is frequently found among available 16S rRNA gene amplicon datasets, which leads consideration of Intestinimonas massiliensis as an important human gut commensal.
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Affiliation(s)
- Pamela Afouda
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Guillaume A Durand
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Noémie Labas
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Fréderic Cadoret
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Nicholas Armstrong
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Grégory Dubourg
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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Zhang KD, Li W, Wang YF, Zheng YL, Tan FC, Ma XQ, Yao LS, Bayer EA, Wang LS, Li FL. Processive Degradation of Crystalline Cellulose by a Multimodular Endoglucanase via a Wirewalking Mode. Biomacromolecules 2018; 19:1686-1696. [DOI: 10.1021/acs.biomac.8b00340] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kun-Di Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
| | - Wen Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
| | - Ye-Fei Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
| | - Yan-Lin Zheng
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, People’s Republic of China
| | - Fang-Cheng Tan
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, People’s Republic of China
| | - Li-Shan Yao
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lu-Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
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Tsavkelova E, Prokudina L, Egorova M, Leontieva M, Malakhova D, Netrusov A. The structure of the anaerobic thermophilic microbial community for the bioconversion of the cellulose-containing substrates into biogas. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Zhang W, Liu W, Hou R, Zhang L, Schmitz-Esser S, Sun H, Xie J, Zhang Y, Wang C, Li L, Yue B, Huang H, Wang H, Shen F, Zhang Z. Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. ISME JOURNAL 2018; 12:1319-1328. [PMID: 29391488 PMCID: PMC5931968 DOI: 10.1038/s41396-018-0051-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/30/2017] [Accepted: 01/10/2018] [Indexed: 01/06/2023]
Abstract
The giant panda feeds almost exclusively on bamboo, a diet highly enriched in lignin and cellulose, but is characterized by a digestive tract similar to carnivores. It is still large unknown if and how the giant panda gut microbiota contributes to lignin and cellulose degradation. Here we show the giant pandas’ gut microbiota does not significantly contribute to cellulose and lignin degradation. We found that no operational taxonomic unit had a nearest neighbor identified as a cellulolytic species or strain with a significant higher abundance in juvenile than cubs, a very low abundance of putative lignin and cellulose genes existed in part of analyzing samples but a significant higher abundance of genes involved in starch and hemicellulose degradation in juveniles than cubs. Moreover, a significant lower abundance of putative cellulolytic genes and a significant higher abundance of putative α-amylase and hemicellulase gene families were present in giant pandas than in omnivores or herbivores.
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Affiliation(s)
- Wenping Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China.
| | - Wenbin Liu
- Novogene Bioinformatics Institute, Beijing, 100083, PR China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | | | - Huaibo Sun
- Novogene Bioinformatics Institute, Beijing, 100083, PR China
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Yunfei Zhang
- Biogas Institute of Ministry of Agriculture, Chengdu, 610064, Sichuan, China
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Lifeng Li
- Novogene Bioinformatics Institute, Beijing, 100083, PR China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, China
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Zhihe Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China.
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Kinet R, Dzaomuho P, Baert J, Taminiau B, Daube G, Nezer C, Brostaux Y, Nguyen F, Dumont G, Thonart P, Delvigne F. Flow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation. BIORESOURCE TECHNOLOGY 2016; 214:450-459. [PMID: 27160955 DOI: 10.1016/j.biortech.2016.04.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses.
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Affiliation(s)
- R Kinet
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - P Dzaomuho
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - J Baert
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - B Taminiau
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Sart-Tilman, B43b, Liège B-4000, Belgium
| | - G Daube
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Sart-Tilman, B43b, Liège B-4000, Belgium
| | - C Nezer
- Quality Partner S.A., Rue Hayeneux, 62, Herstal, B-4040, Belgium
| | - Y Brostaux
- Computer Science and Modeling, Applied Statistics, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, B-5030, Belgium
| | - F Nguyen
- University of Liege, Applied Geophysics, Department ArGEnCo, Engineering Faculty, B52, B-4000 Liege, Belgium
| | - G Dumont
- University of Liege, Applied Geophysics, Department ArGEnCo, Engineering Faculty, B52, B-4000 Liege, Belgium
| | - P Thonart
- Artechno S.A., Rue Herman Méganck, 21, Isnes, B-5032, Belgium
| | - F Delvigne
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium.
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Su L, Yang L, Huang S, Li Y, Su X, Wang F, Bo C, Wang ET, Song A. Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets. Appl Biochem Biotechnol 2016; 181:32-47. [PMID: 27457759 DOI: 10.1007/s12010-016-2197-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/13/2016] [Indexed: 11/29/2022]
Abstract
Termites are well recognized for their thriving on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling microbiota; however, the effects of diet changes on termite gut microbiota are poorly understood, especially for the lower termites. In this study, we employed high-throughput 454 pyrosequencing of 16S V1-V3 amplicons to compare gut microbiotas of Tsaitermes ampliceps fed with lignin-rich and lignin-poor cellulose diets after a 2-week-feeding period. As a result, the majority of bacterial taxa were shared across the treatments with different diets, but their relative abundances were modified. In particular, the relative abundance was reduced for Spirochaetes and it was increased for Proteobacteria and Bacteroides by feeding the lignin-poor diet. The evenness of gut microbiota exhibited a significant difference in response to the diet type (filter paper diets < corn stover diets < wood diets), while their richness was constant, which may be related to the lower recalcitrance of this biomass to degradation. These results have important implications for sampling and analysis strategies to probe the lignocellulose degradation features of termite gut microbiota and suggest that the dietary lignocellulose composition could cause shifting rapidly in the termite gut microbiota.
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Affiliation(s)
- Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Lele Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Shi Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Yan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Xiaoquan Su
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Fengqin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan, 450002, China
| | - Cunpei Bo
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México D.F., Mexico.
| | - Andong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan, 450002, China.
- , No. 93, Nongye Road, Zhengzhou, Henan Province, China.
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11
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Yang M, Zhang KD, Zhang PY, Zhou X, Ma XQ, Li FL. Synergistic Cellulose Hydrolysis Dominated by a Multi-Modular Processive Endoglucanase from Clostridium cellulosi. Front Microbiol 2016; 7:932. [PMID: 27379062 PMCID: PMC4908102 DOI: 10.3389/fmicb.2016.00932] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/31/2016] [Indexed: 01/23/2023] Open
Abstract
Recalcitrance of biomass feedstock remains a challenge for microbial conversion of lignocellulose into biofuel and biochemicals. Clostridium cellulosi, one thermophilic bacterial strain dominated in compost, could hydrolyze lignocellulose at elevated temperature by secreting more than 38 glycoside hydrolases belong to 15 different families. Though one multi-modular endoglucanase CcCel9A has been identified from C. cellulosi CS-4-4, mechanism of synergistic degradation of cellulose by various cellulases from strain CS-4-4 remains elusive. In this study, CcCel9A, CcCel9B, and CcCel48A were characterized as processive endoglucanase, non-processive endoglucanase, and exoglucanase, respectively. To understand how they cooperate with each other, we estimated the approximate concentration ratio on the zymogram and optimized it using purified enzymes in vitro. Synergism between individual glycoside hydrolase during cellulose hydrolysis in the mixture was observed. CcCel9A and CcCel48A could degrade cellulose chain from non-reducing ends and reducing ends, respectively, to cello-oligosaccharide. CcCel9B could cut cellulose chain randomly and cello-oligosaccharides with varied length were released. In addition, a β-glucosidase BlgA from Caldicellulosiruptor sp. F32 which could cleave cello-oligosaccharides including G2-G6 to glucose was added to the enzyme mixture to remove the product inhibition of its partners. The combination and ratios of these cellulases were optimized based on the release rate of glucose. Hydrolysis of corn stalk was conducted by a four-component cocktail (CcCel9A:CcCel9B:CcCel48A:BlgA = 25:25:10:18), and only glucose was detected as main production by using high-performance anion-exchange chromatography. Processive endoglucanase CcCel9A, dominated in secretome of C. cellulosi, showed good potential in developing cellulase cocktail due to its exquisite cooperation with various cellulases.
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Affiliation(s)
- Min Yang
- College of Environmental Science and Engineering, Qingdao UniversityQingdao, China; Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Kun-Di Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao, China
| | - Pei-Yu Zhang
- College of Environmental Science and Engineering, Qingdao University Qingdao, China
| | - Xia Zhou
- Exploration & Production Research Institute, China Petroleum & Chemical Corporation Beijing, China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao, China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao, China
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12
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Lal S, Levin DB. Comparative Genomics of Core Metabolism Genes of Cellulolytic and Non-cellulolytic Clostridium Species. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:79-112. [PMID: 26907553 DOI: 10.1007/10_2015_5007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Microbial production of fuels such as ethanol, butanol, hydrogen (H2), and methane (CH4) from waste biomass has the potential to provide sustainable energy systems that can displace fossil fuel consumption. Screening for microbial diversity and genome sequencing of a wide-range of microorganisms can identify organisms with natural abilities to synthesize these alternative fuels and/or other biotechnological applications. Clostridium species are the most widely studied strict anaerobes capable of fermentative synthesis of ethanol, butanol, or hydrogen directly from waste biomass. Clostridium termitidis CT1112 is a mesophilic, cellulolytic species capable of direct cellulose fermentation to ethanol and organic acids, with concomitant synthesis of H2 and CO2. On the basis of 16S ribosomal RNA (rRNA) and chaperonin 60 (cpn60) gene sequence data, phylogenetic analyses revealed a close relationship between C. termitidis and C. cellobioparum. Comparative bioinformatic analyses of the C. termitidis genome with 18 cellulolytic and 10 non-cellulolytic Clostridium species confirmed this relationship, and further revealed that the majority of core metabolic pathway genes in C. termitidis and C. cellobioparum share more than 90% amino acid sequence identity. The gene loci and corresponding amino acid sequences of the encoded enzymes for each pathway were correlated by percentage identity, higher score (better alignment), and lowest e-value (most significant "hit"). In addition, the function of each enzyme was proposed by conserved domain analysis. In this chapter we discuss the comparative analysis of metabolic pathways involved in synthesis of various useful products by cellulolytic and non-cellulolytic biofuel and solvent producing Clostridium species. This study has generated valuable information concerning the core metabolism genes and pathways of C. termitidis CT1112, which is helpful in developing metabolic engineering strategies to enhance its natural capacity for better industrial applications.
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Affiliation(s)
- Sadhana Lal
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6.
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The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations. mBio 2015; 6:e00022-15. [PMID: 25991678 PMCID: PMC4442137 DOI: 10.1128/mbio.00022-15] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The giant panda evolved from omnivorous bears. It lives on a bamboo-dominated diet at present, but it still retains a typical carnivorous digestive system and is genetically deficient in cellulose-digesting enzymes. To find out whether this endangered mammalian species, like other herbivores, has successfully developed a gut microbiota adapted to its fiber-rich diet, we conducted a 16S rRNA gene-based large-scale structural profiling of the giant panda fecal microbiota. Forty-five captive individuals were sampled in spring, summer, and late autumn within 1 year. Significant intraindividual variations in the diversity and structure of gut microbiota across seasons were observed in this population, which were even greater than the variations between individuals. Compared with published data sets involving 124 gut microbiota profiles from 54 mammalian species, these giant pandas, together with 9 captive and 7 wild individuals investigated previously, showed extremely low gut microbiota diversity and an overall structure that diverged from those of nonpanda herbivores but converged with those of carnivorous and omnivorous bears. The giant panda did not harbor putative cellulose-degrading phylotypes such as Ruminococcaceae and Bacteroides bacteria that are typically enriched in other herbivores, but instead, its microbiota was dominated by Escherichia/Shigella and Streptococcus bacteria. Members of the class Clostridia were common and abundant in the giant panda gut microbiota, but most of the members present were absent in other herbivores and were not phylogenetically related with known cellulolytic lineages. Therefore, the giant panda appears not to have evolved a gut microbiota compatible with its newly adopted diet, which may adversely influence the coevolutionary fitness of this herbivore. The giant panda, an endangered mammalian species endemic to western China, is well known for its unique bamboo diet. Unlike other herbivores that have successfully evolved anatomically specialized digestive systems to efficiently deconstruct fibrous plant matter, the giant panda still retains a gastrointestinal tract typical of carnivores. We characterized the fecal bacterial communities from a giant panda population to determine whether this animal relies on its symbiotic gut microbiota to cope with the complex carbohydrates that dominate its diet, as is common in other herbivores. We found that the giant panda gut microbiota is low in diversity and highly variable across seasons. It also shows an overall composition typical of bears and entirely differentiated from other herbivores, with low levels of putative cellulose-digesting bacteria. The gut microbiota of this herbivore, therefore, may not have well adapted to its highly fibrous diet, suggesting a potential link with its poor digestive efficiency.
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A comprehensive study on volatile fatty acids production from rice straw coupled with microbial community analysis. Bioprocess Biosyst Eng 2015; 38:1157-66. [DOI: 10.1007/s00449-015-1357-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/09/2015] [Indexed: 11/25/2022]
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15
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Rozanov AS, Bryanskaya AV, Malup TK, Meshcheryakova IA, Lazareva EV, Taran OP, Ivanisenko TV, Ivanisenko VA, Zhmodik SM, Kolchanov NA, Peltek SE. Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia). BMC Genomics 2014; 15 Suppl 12:S12. [PMID: 25563397 PMCID: PMC4303939 DOI: 10.1186/1471-2164-15-s12-s12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described. Results Pyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions. Conclusions In this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed.
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Zhao B, Li J, Leu SY. An innovative wood-chip-framework soil infiltrator for treating anaerobic digested swine wastewater and analysis of the microbial community. BIORESOURCE TECHNOLOGY 2014; 173:384-391. [PMID: 25444881 DOI: 10.1016/j.biortech.2014.09.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 09/24/2014] [Accepted: 09/28/2014] [Indexed: 06/04/2023]
Abstract
Combined anaerobic-aerobic processes are efficacious and economic approaches in treating swine wastewater. Nitrogen removal efficiency of these processes, however, is usually limited due to the low carbon/nitrogen (C/N) ratio of the wastewater. An innovative wood-chip-framework soil infiltrator (WFSI) was developed and its performance in treating anaerobic digested swine wastewater was investigated. The WFSI showed comparable removal of chemical oxygen demand (COD) and amongst the highest efficiency of nitrogen removal in treating low C/N wastewater. At a COD volume loading rate of 98.6 g/m3 d the WFSI could remove up to 47.7 g/m3 d of COD. Removal rates of NH4+-N and total nitrogen, also reached 69.1 and 30.4 g/m3 d, respectively, when NH4+-N loading rate was 88.4 g/m3 d. Biological analysis indicated that aerobic, anoxic and anaerobic microbiota occurred throughout the WFSI. Abundant cellulose and lignin decomposing bacteria could degrade the wood chips and provided extra carbon source to enhance denitrification.
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Affiliation(s)
- Bowei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Shao-Yuan Leu
- Civil and Environmental Engineering Department, Hong Kong Polytechnic University, Kowloon, Hong Kong, China
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17
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Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant. J Biotechnol 2014; 188:136-7. [DOI: 10.1016/j.jbiotec.2014.08.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/21/2014] [Indexed: 12/26/2022]
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18
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Kallistova AY, Goel G, Nozhevnikova AN. Microbial diversity of methanogenic communities in the systems for anaerobic treatment of organic waste. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714050142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Synergism of glycoside hydrolase secretomes from two thermophilic bacteria cocultivated on lignocellulose. Appl Environ Microbiol 2014; 80:2592-601. [PMID: 24532065 DOI: 10.1128/aem.00295-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two cellulolytic thermophilic bacterial strains, CS-3-2 and CS-4-4, were isolated from decayed cornstalk by the addition of growth-supporting factors to the medium. According to 16S rRNA gene-sequencing results, these strains belonged to the genus Clostridium and showed 98.87% and 98.86% identity with Clostridium stercorarium subsp. leptospartum ATCC 35414(T) and Clostridium cellulosi AS 1.1777(T), respectively. The endoglucanase and exoglucanase activities of strain CS-4-4 were approximately 3 to 5 times those of strain CS-3-2, whereas the β-glucosidase activity of strain CS-3-2 was 18 times higher than that of strain CS-4-4. The xylanase activity of strain CS-3-2 was 9 times that of strain CS-4-4, whereas the β-xylosidase activity of strain CS-4-4 was 27 times that of strain CS-3-2. The enzyme activities in spent cultures following cocultivation of the two strains with cornstalk as the substrate were much greater than those in pure cultures or an artificial mixture of samples, indicating synergism of glycoside hydrolase secretomes between the two strains. Quantitative measurement of the two strains in the cocultivation system indicated that strain CS-3-2 grew robustly during the initial stages, whereas strain CS-4-4 dominated the system in the late-exponential phase. Liquid chromatography-tandem mass spectrometry analysis of protein bands appearing in the native zymograms showed that ORF3880 and ORF3883 from strain CS-4-4 played key roles in the lignocellulose degradation process. Both these open reading frames (ORFs) exhibited endoglucanase and xylanase activities, but ORF3880 showed tighter adhesion to insoluble substrates at 4, 25, and 60°C owing to its five carbohydrate-binding modules (CBMs).
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20
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Ronan P, Yeung CW, Schellenberg J, Sparling R, Wolfaardt GM, Hausner M. A versatile and robust aerotolerant microbial community capable of cellulosic ethanol production. BIORESOURCE TECHNOLOGY 2013; 129:156-163. [PMID: 23238345 DOI: 10.1016/j.biortech.2012.10.164] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 06/01/2023]
Abstract
The use of microbial communities in the conversion of cellulosic materials to bio-ethanol has the potential to improve the economic competitiveness of this biofuel and subsequently lessen our dependency on fossil fuel-based energy sources. Interactions between functionally different microbial groups within a community can expand habitat range, including the creation of anaerobic microenvironments. Currently, research focussing on exploring the nature of the interactions occurring during cellulose degradation and ethanol production within mixed microbial communities has been limited. The aim of this study was to enrich and characterize a cellulolytic bacterial community, and determine if ethanol is a major soluble end-product. Cellulolytic activity by the community was observed in both non-reduced and pre-reduced media, with ethanol and acetate being major fermentation products. Similar results were obtained when sterile wastewater extract was provided as nutrient. Several community members showed high similarity to Clostridium species with overlapping metabolic capabilities, suggesting clostridial functional redundancy.
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Affiliation(s)
- Patrick Ronan
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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21
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Tims S, Derom C, Jonkers DM, Vlietinck R, Saris WH, Kleerebezem M, de Vos WM, Zoetendal EG. Microbiota conservation and BMI signatures in adult monozygotic twins. ISME JOURNAL 2012. [PMID: 23190729 DOI: 10.1038/ismej.2012.146] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human gastrointestinal (GI) tract microbiota acts like a virtual organ and is suggested to be of great importance in human energy balance and weight control. This study included 40 monozygotic (MZ) twin pairs to investigate the influence of the human genotype on GI microbiota structure as well as microbial signatures for differences in body mass index (BMI). Phylogenetic microarraying based on 16S rRNA genes demonstrated that MZ twins have more similar microbiotas compared with unrelated subjects (P<0.001), which allowed the identification of 35 genus-like microbial groups that are more conserved between MZ twins. Half of the twin pairs were selected on discordance in terms of BMI, which revealed an inverse correlation between Clostridium cluster IV diversity and BMI. Furthermore, relatives of Eubacterium ventriosum and Roseburia intestinalis were positively correlated to BMI differences, and relatives of Oscillospira guillermondii were negatively correlated to BMI differences. Lower BMI was associated with a more abundant network of primary fiber degraders, while a network of butyrate producers was more prominent in subjects with higher BMI. Combined with higher butyrate and valerate contents in the fecal matter of higher BMI subjects, the difference in microbial networks suggests a shift in fermentation patterns at the end of the colon, which could affect human energy homeostasis.
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Affiliation(s)
- Sebastian Tims
- Laboratory of Microbiology, Wageningen University and TI Food and Nutrition, Wageningen, The Netherlands
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22
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Carillo P, Carotenuto C, Di Cristofaro F, Kafantaris I, Lubritto C, Minale M, Morrone B, Papa S, Woodrow P. DGGE analysis of buffalo manure eubacteria for hydrogen production: effect of pH, temperature and pretreatments. Mol Biol Rep 2012; 39:10193-200. [PMID: 23014994 DOI: 10.1007/s11033-012-1894-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/18/2012] [Indexed: 01/19/2023]
Abstract
Buffalo dung is a low-cost substrate with plenty of carbohydrates, an optimal carbon/nitrogen ratio, and a rich microbial flora, and could become a valuable source of biogas. Therefore, in the present study we compared the type and amount of specific eubacteria to the different configurations of pH, temperature and thermal pretreatment after fermentation in batch reactors in order to understand the suitability of buffalo manure for hydrogen production. The phylogenetic structure of the microbial community in fermentation samples was studied using denaturing gradient gel electrophoresis to generate fingerprints of 16S rRNA genes. The sequences analysis revealed abundance of the phyla Bacteroidetes and Firmicutes, and in particular of the order Clostridiales. Very active hydrogen producing bacteria belonging to Clostridium cellulosi species were identified demonstrating the suitability of this substrate to produce hydrogen. Moreover, a large fraction of 16S-rDNA amplicons could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms involved in anaerobic fermentation in digesters or bioreactors are still unclassified or unknown.
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Affiliation(s)
- Petronia Carillo
- Department of Life Sciences, Second University of Naples, via Vivaldi 43, 81100 Caserta, Italy.
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23
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Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2011; 62:716-721. [PMID: 22140171 DOI: 10.1099/ijs.0.038075-0] [Citation(s) in RCA: 4384] [Impact Index Per Article: 337.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
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Affiliation(s)
- Ok-Sun Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yong-Joon Cho
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kihyun Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seok-Hwan Yoon
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mincheol Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Na
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sang-Cheol Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Yoon Seong Jeon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Jae-Hak Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Hana Yi
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sungho Won
- Department of Statistics, Chung-Ang University, Seoul, Republic of Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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24
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Nissilä ME, Tähti HP, Rintala JA, Puhakka JA. Effects of heat treatment on hydrogen production potential and microbial community of thermophilic compost enrichment cultures. BIORESOURCE TECHNOLOGY 2011; 102:4501-4506. [PMID: 21251819 DOI: 10.1016/j.biortech.2010.12.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 05/30/2023]
Abstract
Cellulosic plant and waste materials are potential resources for fermentative hydrogen production. In this study, hydrogen producing, cellulolytic cultures were enriched from compost material at 52, 60 and 70°C. Highest cellulose degradation and highest H(2) yield were 57% and 1.4 mol-H(2) mol-hexose(-1) (2.4 mol-H(2) mol-hexose-degraded(-1)), respectively, obtained at 52°C with the heat-treated (80°C for 20 min) enrichment culture. Heat-treatments as well as the sequential enrichments decreased the diversity of microbial communities. The enrichments contained mainly bacteria from families Thermoanaerobacteriaceae and Clostridiaceae, from which a bacterium closely related to Thermoanaerobium thermosaccharolyticum was mainly responsible for hydrogen production and bacteria closely related to Clostridium cellulosi and Clostridium stercorarium were responsible for cellulose degradation.
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Affiliation(s)
- Marika E Nissilä
- Department of Chemistry and Bioengineering, Tampere University of Technology, Tampere, Finland.
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25
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Zverlov VV, Hiegl W, Köck DE, Kellermann J, Köllmeier T, Schwarz WH. Hydrolytic bacteria in mesophilic and thermophilic degradation of plant biomass. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000059] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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26
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Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Appl Microbiol Biotechnol 2010; 88:389-99. [DOI: 10.1007/s00253-010-2789-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/09/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
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27
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Abstract
Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.
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Affiliation(s)
- Isaac D Wagner
- 212 Biological Sciences Building, 1000 Cedar Street, University of Georgia, Athens, GA 30602-2605, USA
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28
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Doi RH. Cellulases of mesophilic microorganisms: cellulosome and noncellulosome producers. Ann N Y Acad Sci 2007; 1125:267-79. [PMID: 18096849 DOI: 10.1196/annals.1419.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cellulolytic activity of mesophilic bacteria and fungi is described, with special emphasis on the large extracellular enzyme complex called the cellulosome. The cellulosome is composed of a scaffolding protein, which is attached to various cellulolytic and hemicellulolytic enzymes, and this complex allows the organisms to degrade plant cell walls very efficently. The enzymes include a variety of cellulases, hemicellulases, and pectinases that work synergistically to degrade complex cell-wall molecules.
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Affiliation(s)
- Roy H Doi
- Section of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA.
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29
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Yokoyama H, Waki M, Ogino A, Ohmori H, Tanaka Y. Hydrogen fermentation properties of undiluted cow dung. J Biosci Bioeng 2007; 104:82-5. [PMID: 17697988 DOI: 10.1263/jbb.104.82] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 04/07/2007] [Indexed: 11/17/2022]
Abstract
Anaerobic treatment of undiluted cow dung (15% total solids), so-called dry fermentation, produced hydrogen (743 ml-H(2)/kg-cow dung) at an optimum temperature of 60 degrees C, with butyrate and acetate formation. The hydrogen production was inhibited by the addition of NH(4)(+) in a dose-dependent manner. A bacterium with similarity to Clostridium cellulosi was detected in the fermented dung by a 16S rDNA analysis.
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Affiliation(s)
- Hiroshi Yokoyama
- Waste Recycling Research Team, National Institute of Livestock and Grassland Science (NILGS), 2 Ikenodai, Tsukuba, Ibaraki, Japan.
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Uz I, Ogram AV. Cellulolytic and fermentative guilds in eutrophic soils of the Florida Everglades. FEMS Microbiol Ecol 2006; 57:396-408. [PMID: 16907754 DOI: 10.1111/j.1574-6941.2006.00120.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The northern Florida Everglades has been subject to eutrophication in recent years, resulting in well-documented changes in microbial ecology and a shift in the dominant plant species. This study investigated effects of plant quality and eutrophication on activities and composition of cellulolytic and fermentative guilds in soils. Most probable numbers of cellulolytic bacteria in eutrophic (F1) and transition (F4) soils were 10-fold higher than in oligotrophic soils (U3). Higher potential methanogenesis was observed from cellulose in microcosms with soils from F1 and F4, compared to U3 soils. Nutrient status of soil, rather than plant type, was the major factor controlling methanogenesis rates, although numbers of fermentative bacteria were higher in microcosms supplemented with ground cattail (dominant in F1 and F4) than with sawgrass (dominant component of soil in U3), regardless of soil origin. DNA sequence analysis indicated Clostridium assemblage composition correlates with soil nutrient status.
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Affiliation(s)
- Ilker Uz
- Soil and Water Science Department, University of Florida, Gainesville, FL 32611-0290, USA
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Xing D, Ren N, Li Q, Lin M, Wang A, Zhao L. Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater. Int J Syst Evol Microbiol 2006; 56:755-760. [PMID: 16585689 DOI: 10.1099/ijs.0.63926-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strictly anaerobic bacterial strains (YUAN-3T and X-29) were isolated from anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor. The strains were Gram-positive, non-spore-forming, mesophilic and motile. Cells were regular rods (0·4–0·8×1·5–8·0 μm) and occurred singly, in pairs and sometimes in chains of up to eight. Autoaggregative and autofluorescent growth of strain YUAN-3T and non-aggregative growth of strain X-29 were observed at 20–44 °C and pH 3·5–9·0. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. Fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids iso-C16 : 0 (44·18 %) and iso-C12 : 0 (26·67 %). The DNA G+C contents of strains YUAN-3T and X-29 were 47·8 and 49·0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a novel phyletic sublineage within the Clostridium cellulosi rRNA cluster, with <92 % 16S rRNA gene sequence similarity to currently known species. On the basis of polyphasic evidence from this study, it is proposed that the unknown bacterium should be classified in a new genus as a novel species, Ethanoligenens harbinense gen. nov., sp. nov. The type strain of Ethanoligenens harbinense is YUAN-3T (=JCM 12961T=CGMCC 1.5033T).
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Affiliation(s)
- Defeng Xing
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Nanqi Ren
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Qiubo Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Ming Lin
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Aijie Wang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Lihua Zhao
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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Chen S, Dong X. Acetanaerobacterium elongatum gen. nov., sp. nov., from paper mill waste water. Int J Syst Evol Microbiol 2004; 54:2257-2262. [PMID: 15545467 DOI: 10.1099/ijs.0.63212-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two mesophilic anaerobic bacterial strains (Z7T and Z1) were isolated from waste water sludge of the Xinanzhang paper mill, Beijing, China. The strains were Gram-positive, non-spore-forming and motile. Cells were thin rods (0·2–0·4×4·0–8·0 μm). Growth of the strains was observed at 20–42 °C and pH 5·0–7·5. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. The fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids isoC15 : 0 (42·83 %) and isoC14 : 0 (32·11 %). The DNA G+C contents of strains Z7T and Z1 were 50·4 and 48·6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a new phyletic sublineage within the Clostridium leptum rRNA cluster, with <91 % 16S rRNA gene sequence similarity to currently described species. On the basis of polyphasic evidence from this study, Acetanaerobacterium elongatum gen. nov., sp. nov., a novel genus and species, is proposed, with strain Z7T (=JCM 12359T=AS 1.5012T) as the type strain.
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MESH Headings
- Acetic Acid/metabolism
- Anaerobiosis
- Base Composition
- Carbohydrate Metabolism
- Carbon Dioxide/metabolism
- China
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Esculin/metabolism
- Ethanol/metabolism
- Fatty Acids/chemistry
- Fatty Acids/isolation & purification
- Fermentation
- Gelatin/metabolism
- Genes, rRNA
- Gentian Violet
- Gram-Positive Bacteria/classification
- Gram-Positive Bacteria/cytology
- Gram-Positive Bacteria/isolation & purification
- Gram-Positive Bacteria/physiology
- Hydrogen/metabolism
- Hydrogen-Ion Concentration
- Microscopy, Electron
- Molecular Sequence Data
- Phenazines
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sewage/microbiology
- Spores, Bacterial/cytology
- Temperature
- Water Microbiology
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Affiliation(s)
- Shuangya Chen
- Graduate School of the Chinese Academy of Sciences, Beijing 100080, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
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Holmstrøm K, Collins MD, Møller T, Falsen E, Lawson PA. Subdoligranulum variabile gen. nov., sp. nov. from human feces. Anaerobe 2004; 10:197-203. [PMID: 16701519 DOI: 10.1016/j.anaerobe.2004.01.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Revised: 01/12/2004] [Accepted: 01/29/2004] [Indexed: 11/20/2022]
Abstract
During studies on the microflora of human feces we have isolated a strictly anaerobic, non-spore-forming, Gram-negative staining organism which exhibits a somewhat variable coccus-shaped morphology. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism is phylogenetically a member of the Clostridium leptum supra-generic rRNA cluster and displays a close affinity to some rDNA clones derived from human and pig feces. The nearest named relatives of the unidentified isolate corresponded to Faecalibacterium prausnitzii (formerly Fusobacterium prausnitzii) displaying a 16S rRNA sequence divergence of approximately 9%, with Anaerofilum agile and A. pentosovorans the next closest relatives of the unidentified bacterium (sequence divergence approximately 10%). Based on phenotypic and phylogenetic considerations, it is proposed that the unusual coccoid-shaped organism be classified as a new genus and species, Subdoligranulum variabile. The type strain of S. variabile is BI 114(T) (=CCUG 47106(T)=DSM 15176(T)).
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Affiliation(s)
- Kim Holmstrøm
- Bioneer A/S, Department of Molecular Characterization, Kogle Alle 2, DK-2970 Hørsholm, Denmark.
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Lawson PA, Song Y, Liu C, Molitoris DR, Vaisanen ML, Collins MD, Finegold SM. Anaerotruncus colihominis gen. nov., sp. nov., from human faeces. Int J Syst Evol Microbiol 2004; 54:413-417. [PMID: 15023953 DOI: 10.1099/ijs.0.02653-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic and phylogenetic studies were performed on two isolates of an unidentified Gram-positive, anaerobic, non-spore-forming, rod-shaped bacterium that was isolated from human faeces. The organisms were catalase-negative, produced acetic and butyric acids as end products of metabolism and possessed a DNA G+C content of approximately 54 mol%. Comparative 16S rRNA gene sequencing demonstrated that the two isolates were related closely to each other and formed a hitherto unknown sublineage within the Clostridium leptum rRNA cluster of organisms. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium should be classified in a novel genus as Anaerotruncus colihominis gen. nov., sp. nov. The type strain of Anaerotruncus colihominis is WAL 14565T=CCUG 45055T=CIP 107754T.
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Affiliation(s)
| | - Yuli Song
- Research Service, VA Medical Center West Los Angeles, LA, USA
| | - Chengxu Liu
- Research Service, VA Medical Center West Los Angeles, LA, USA
| | | | | | | | - Sydney M Finegold
- Department of Microbiology, Immunology and Molecular Genetics, UCLA School of Medicine, USA
- Department of Medicine, UCLA School of Medicine, USA
- Infectious Diseases Section, VA Medical Center West Los Angeles, LA, USA
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Ravinder T, Swamy MV, Seenayya G, Reddy G. Clostridium lentocellum SG6--a potential organism for fermentation of cellulose to acetic acid. BIORESOURCE TECHNOLOGY 2001; 80:171-177. [PMID: 11601540 DOI: 10.1016/s0960-8524(01)00094-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A cellulolytic, acetic acid producing anaerobic bacterial isolate, Gram negative, rod-shaped, motile, terminal oval shaped endospore forming bacterium identified as Clostridium lentocellum SG6 based on physiological and biochemical characteristics. It produced acetic acid as a major end product from cellulose fermentation at 37 degrees C and pH 7.2. Acetic acid production was 0.67 g/g cellulose substrate utilized in cellulose mineral salt (CMS) medium. Yeast extract (0.4%) was the best nitrogen source among the various nitrogenous nutrients tested in production medium containing 0.8% cellulose as substrate. No additional vitamins or trace elemental solution were required for acetic acid fermentation. This is the highest acetic acid fermentation yield in monoculture fermentation for direct conversion of cellulose to acetic acid.
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Affiliation(s)
- T Ravinder
- Department of Microbiology, Osmania University, Hyderabad, AP, India
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Bredholt S, Mathrani IM, Ahring BK. Extremely thermophilic cellulolytic anaerobes from Icelandic hot springs. Antonie Van Leeuwenhoek 1995; 68:263-71. [PMID: 8821780 DOI: 10.1007/bf00874135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Anaerobic enrichment cultures with Avicel as substrate and inoculated with biomat samples from Icelandic hot springs were cultured at 70 degrees C or 78 degrees C and examined for the presence of microorganisms that produce extracellular cellulolytic and xylanolytic enzymes. From four enrichments grown at 78 degrees C eighteen strains were isolated. Five of the strains were screened for their substrate utilization, and on the basis of differences in morphology and substrates used, the two most unique strains were selected for further characterization. All cellulolytic cultures were rod-shaped and non-sporeforming. Motility was not observed. Cells stained gram-negative at various stages of the growth phase. During growth on Avicel, most cultures produced acetate as the major fermentation product, with smaller amounts of lactic acid and ethanol. Carbon dioxide and hydrogen were also produced. The phenotypic characteristics of the enrichment cultures and of isolates are described and assessed in relation to temperature and pH in the hot spring environment. A comparison is made between Icelandic strains isolated in our laboratory and strains isolated from hot springs from other parts of the world. The biotechnological potential of this group of bacteria is briefly discussed.
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Affiliation(s)
- S Bredholt
- Institute of Environmental Science and Engineering, Technical University of Denmark, Lyngby
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Rainey FA, Ward NL, Morgan HW, Toalster R, Stackebrandt E. Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. J Bacteriol 1993; 175:4772-9. [PMID: 7687600 PMCID: PMC204929 DOI: 10.1128/jb.175.15.4772-4779.1993] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Small subunit rDNA sequences were determined for 20 species of the genera Acetogenium, Clostridium, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobium, and Thermobacteroides, 3 non-validly described species, and 5 isolates of anaerobic thermophilic bacteria, providing a basis for a phylogenetic analysis of these organisms. Several species contain a version of the molecule significantly longer than that of Escherichia coli because of the presence of inserts. On the basis of normal evolutionary distances, the phylogenetic tree indicates that all bacteria investigated in this study with a maximum growth temperature above 65 degrees C form a supercluster within the subphylum of gram-positive bacteria that also contains Clostridium thermosaccharolyticum and Clostridium thermoaceticum, which have been previously sequenced. This supercluster appears to be equivalent in its phylogenetic depth to the supercluster of mesophilic clostridia and their nonspore-forming relatives. Several phylogenetically and phenotypically coherent clusters that are defined by sets of signature nucleotides emerge within the supercluster of thermophiles. Clostridium thermobutyricum and Clostridium thermopalmarium are members of Clostridium group I. A phylogenetic tree derived from transversion distances demonstrated the artificial clustering of some organisms with high rDNA G+C moles percent, i.e., Clostridium fervidus and the thermophilic, cellulolytic members of the genus Clostridium. The results of this study can be used as an aid for future taxonomic restructuring of anaerobic sporogenous and asporogenous thermophillic, gram-positive bacteria.
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Affiliation(s)
- F A Rainey
- Department of Microbiology, University of Queensland, St. Lucia, Australia
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Hethener P, Brauman A, Garcia JL. Clostridium termitidis sp. nov., a Cellulolytic Bacterium from the Gut of the Wood-feeding Termite, Nasutitermes lujae. Syst Appl Microbiol 1992. [DOI: 10.1016/s0723-2020(11)80138-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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