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Vaz LP, Sears HB, Miranda EA, Holwerda EK, Lynd LR. Solubilization of sugarcane bagasse by mono and cocultures of thermophilic anaerobes with and without cotreatment. BIORESOURCE TECHNOLOGY 2024; 406:130982. [PMID: 38879055 DOI: 10.1016/j.biortech.2024.130982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Cotreatment, mechanical disruption of lignocellulosic biomass during microbial fermentation, is a potential alternative to thermochemical pretreatment as a means of increasing the accessibility of lignocellulose to biological attack. Successful implementation of cotreatment requires microbes that can withstand milling, while solubilizing and utilizing carbohydrates from lignocellulose. In this context, cotreatment with thermophilic, lignocellulose-fermenting bacteria has been successfully evaluated for a number of lignocellulosic feedstocks. Here, cotreatment was applied to sugarcane bagasse using monocultures of the cellulose-fermenting Clostridium thermocellum and cocultures with the hemicellulose-fermenting Thermoanaerobacterium thermosaccharolyticum. This resulted in 76 % carbohydrate solubilization (a 1.8-fold increase over non-cotreated controls) on 10 g/L solids loading, having greater effect on the hemicellulose fraction. With cotreatment, fermentation by wild-type cultures at low substrate concentrations increased cumulative product formation by 45 % for the monoculture and 32 % for the coculture. These findings highlight the potential of cotreatment for enhancing deconstruction of sugarcane bagasse using thermophilic bacteria.
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Affiliation(s)
- Luisa P Vaz
- Universidade Estadual de Campinas, School of Chemical Engineering, Department of Materials and Bioprocess Engineering, Av. Albert Einstein 500, Campinas, SP 13083-852, Brazil
| | - Helen B Sears
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH 03755, USA
| | - Everson A Miranda
- Universidade Estadual de Campinas, School of Chemical Engineering, Department of Materials and Bioprocess Engineering, Av. Albert Einstein 500, Campinas, SP 13083-852, Brazil
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH 03755, USA.
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH 03755, USA
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2
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Guo H, Chen Y, Dong W, Lu S, Du Y, Duan L. Fecal Coprococcus, hidden behind abdominal symptoms in patients with small intestinal bacterial overgrowth. J Transl Med 2024; 22:496. [PMID: 38796441 PMCID: PMC11128122 DOI: 10.1186/s12967-024-05316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Small intestinal bacterial overgrowth (SIBO) is the presence of an abnormally excessive amount of bacterial colonization in the small bowel. Hydrogen and methane breath test has been widely applied as a non-invasive method for SIBO. However, the positive breath test representative of bacterial overgrowth could also be detected in asymptomatic individuals. METHODS To explore the relationship between clinical symptoms and gut dysbiosis, and find potential fecal biomarkers for SIBO, we compared the microbial profiles between SIBO subjects with positive breath test but without abdominal symptoms (PBT) and healthy controls (HC) using 16S rRNA amplicon sequencing. RESULTS Fecal samples were collected from 63 SIBO who complained of diarrhea, distension, constipation, or abdominal pain, 36 PBT, and 55 HC. For alpha diversity, the Shannon index of community diversity on the genus level showed a tendency for a slight increase in SIBO, while the Shannon index on the predicted function was significantly decreased in SIBO. On the genus level, significantly decreased Bacteroides, increased Coprococcus_2, and unique Butyrivibrio were observed in SIBO. There was a significant positive correlation between saccharolytic Coprococcus_2 and the severity of abdominal symptoms. Differently, the unique Veillonella in the PBT group was related to amino acid fermentation. Interestingly, the co-occurrence network density of PBT was larger than SIBO, which indicates a complicated interaction of genera. Coprococcus_2 showed one of the largest betweenness centrality in both SIBO and PBT microbiota networks. Pathway analysis based on the Kyoto Encyclopedia of Genes and Genome (KEGG) database reflected that one carbon pool by folate and multiple amino acid metabolism were significantly down in SIBO. CONCLUSIONS This study provides valuable insights into the fecal microbiota composition and predicted metabolic functional changes in patients with SIBO. Butyrivibrio and Coprococcus_2, both renowned for their role in carbohydrate fermenters and gas production, contributed significantly to the symptoms of the patients. Coprococcus's abundance hints at its use as a SIBO marker. Asymptomatic PBT individuals show a different microbiome, rich in Veillonella. PBT's complex microbial interactions might stabilize the intestinal ecosystem, but further study is needed due to the core microbiota similarities with SIBO. Predicted folate and amino acid metabolism reductions in SIBO merit additional validation.
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Affiliation(s)
- Huaizhu Guo
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Yuzhu Chen
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Wenxin Dong
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Siqi Lu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Yanlin Du
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Liping Duan
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.
- International Institute of Population Health, Peking University Health Science Center, Beijing, China.
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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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Peng C, Zhang X, Li J, Yang M, Ma S, Fan H, Dai L, Cheng L. Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512751 DOI: 10.1099/ijsem.0.006292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
A microaerophilic, Gram-negative, motile, and spiral-shaped bacterium, designated Y-M2T, was isolated from oil sludge of Shengli oil field. The optimal growth condition of strain Y-M2T was at 25 °C, pH 7.0, and in the absence of NaCl. The major polar lipid was phosphatidylethanolamine. The main cellular fatty acid was iso-C17 : 0 3-OH. It contained Q-9 and Q-10 as the predominant quinones. The DNA G+C content was 68.1 mol%. Strain Y-M2T showed the highest 16S rRNA gene sequence similarity to Telmatospirillum siberiense 26-4bT (91.1 %). Phylogenetic analyses based on 16S rRNA gene and genomes showed that strain Y-M2T formed a distinct cluster in the order Rhodospirillales. Genomic analysis showed that Y-M2T possesses a complete nitrogen-fixation cluster which is phylogenetically close to that of methanogene. The nif cluster, encompassing the nitrogenase genes, was found in every N2-fixing strain within the order Rhodospirillales. Phylogeny, phenotype, chemotaxonomy, and genomic results demonstrated that strain Y-M2T represents a novel species of a novel genus in a novel family Oleispirillaceae fam. nov. in the order Rhodospirillales, for which the name Oleispirillum naphthae gen. nov., sp. nov. was proposed. The type strain is Y-M2T (=CCAM 827T=JCM 34765T).
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Affiliation(s)
- Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu 610213, Sichuan Province, PR China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu 610213, Sichuan Province, PR China
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Yang M, Zhang X, Ma S, Zhang Q, Peng C, Fan H, Dai L, Li J, Cheng L. Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis. Antonie Van Leeuwenhoek 2023; 116:1359-1374. [PMID: 37843737 DOI: 10.1007/s10482-023-01878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/03/2023] [Indexed: 10/17/2023]
Abstract
A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0 µm in length and 0.4-0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).
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Affiliation(s)
- Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China
| | - Qiumei Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China.
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China.
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China.
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Srinivasan S, Austin MN, Fiedler TL, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Beamer MA, Achilles SL, Wiesenfeld HC, Fredricks DN, Hillier SL. Amygdalobacter indicium gen. nov., sp. nov., and Amygdalobacter nucleatus sp. nov., gen. nov.: novel bacteria from the family Oscillospiraceae isolated from the female genital tract. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787404 DOI: 10.1099/ijsem.0.006017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Four obligately anaerobic Gram-positive bacteria representing one novel genus and two novel species were isolated from the female genital tract. Both novel species, designated UPII 610-JT and KA00274T, and an additional isolate of each species were characterized utilizing biochemical, genotypic and phylogenetic analyses. All strains were non-motile and non-spore forming, asaccharolytic, non-cellulolytic and indole-negative coccobacilli. Fatty acid methyl ester analysis for UPII 610-JT and KA00274T and additional isolates revealed C16 : 0, C18 : 0, C18:1ω9c and C18:2ω6,9c to be the major fatty acids for both species. UPII 610-JT had a 16S rRNA gene sequence similarity of 99.4 % to an uncultured clone sequence (AY724740) designated as Bacterial Vaginosis Associated Bacterium 2 (BVAB2). KA00274T had a 16S rRNA gene sequence similarity of 96.5 % to UPII 610-JT. Whole genomic DNA mol% G+C content was 42.2 and 39.3 % for UPII 610-JT and KA00274T, respectively. Phylogenetic analyses indicate these isolates represent a novel genus and two novel species within the Oscillospiraceae family. We propose the names Amygdalobacter indicium gen. nov., sp. nov., for UPII 610-JT representing the type strain of this species (=DSM 112989T, =ATCC TSD-274T) and Amygdalobacter nucleatus gen. nov., sp. nov., for KA00274T representing the type strain of this species (=DSM 112988T, =ATCC TSD-275T).
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kathy J Agnew
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - May A Beamer
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Sharon L Achilles
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - Harold C Wiesenfeld
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sharon L Hillier
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
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Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023; 11:2412. [PMID: 37894070 PMCID: PMC10608942 DOI: 10.3390/microorganisms11102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.
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Affiliation(s)
- Julia Hassa
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Tom Jonas Tubbesing
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Robert Heyer
- Multidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, Germany
- Multidimensional Omics Data Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Dirk Benndorf
- Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, Germany
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Mathias Effenberger
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, Germany
| | - Christian Henke
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Benedikt Osterholz
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Michael Beckstette
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Alexander Sczyrba
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
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8
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Liu Y, Chen S, Wang J, Shao B, Fang J, Cao J. The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea. Microorganisms 2023; 11:2156. [PMID: 37764000 PMCID: PMC10536192 DOI: 10.3390/microorganisms11092156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel Bacillota bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus Abyssisolibacter within the phylum Bacillota. Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535000, China
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China;
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Baoying Shao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
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9
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Serna-García R, Tsapekos P, Treu L, Bouzas A, Seco A, Campanaro S, Angelidaki I. Unraveling prevalence of homoacetogenesis and methanogenesis pathways due to inhibitors addition. BIORESOURCE TECHNOLOGY 2023; 376:128922. [PMID: 36940878 DOI: 10.1016/j.biortech.2023.128922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
Three inhibitors targeting different microorganisms, both from Archaea and Bacteria domains, were evaluated for their effect on CO2 biomethanation: sodium ionophore III (ETH2120), carbon monoxide (CO), and sodium 2-bromoethanesulfonate (BES). This study examines how these compounds affect the anaerobic digestion microbiome in a biogas upgrading process. While archaea were observed in all experiments, methane was produced only when adding ETH2120 or CO, not when adding BES, suggesting archaea were in an inactivated state. Methane was produced mainly via methylotrophic methanogenesis from methylamines. Acetate was produced at all conditions, but a slight reduction on acetate production (along with an enhancement on CH4 production) was observed when applying 20 kPa of CO. Effects on CO2 biomethanation were difficult to observe since the inoculum used was from a real biogas upgrading reactor, being this a complex environmental sample. Nevertheless, it must be mentioned that all compounds had effects on the microbial community composition.
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Affiliation(s)
- Rebecca Serna-García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain.
| | - Panagiotis Tsapekos
- Department of Chemical Engineering, Søltofts Plads 228A, Technical University of Denmark, DTU, 2800 Lyngby, Denmark
| | - Laura Treu
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35121, Italy
| | - Alberto Bouzas
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Aurora Seco
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35121, Italy
| | - Irini Angelidaki
- Department of Chemical Engineering, Søltofts Plads 228A, Technical University of Denmark, DTU, 2800 Lyngby, Denmark
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10
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Schroeder WL, Kuil T, van Maris AJA, Olson DG, Lynd LR, Maranas CD. A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis. Metab Eng 2023; 77:306-322. [PMID: 37085141 DOI: 10.1016/j.ymben.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/24/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023]
Abstract
Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PPi) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PPi sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PPi synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PPi-generating cycles. In all cases, the metabolic cost of PPi synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PPi could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PPi sources likely account for most PPi production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PPi levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.
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Affiliation(s)
- Wheaton L Schroeder
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Bioenergy Innovation, Oak Ridge, TN, USA
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Center for Bioenergy Innovation, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- Center for Bioenergy Innovation, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Bioenergy Innovation, Oak Ridge, TN, USA.
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11
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Roja B, Saranya S, Chellapandi P. Discovery of novel virulence mechanisms in Clostridium botulinum type A3 using genome-wide analysis. Gene 2023; 869:147402. [PMID: 36972858 DOI: 10.1016/j.gene.2023.147402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
OBJECTIVE Clostridium botulinum type A is a neurotoxin-producing, spore-forming anaerobic bacterium that causes botulism in humans. The evolutionary genomic context of this organism is not yet known to understand its molecular virulence mechanisms in the human intestinal tract. Hence, this study aimed to investigate the mechanisms underlying virulence and pathogenesis by comparing the genomic contexts across species, serotypes, and subtypes. METHODS A comparative genomic approach was used to analyze evolutionary genomic relationships, intergenomic distances, syntenic blocks, replication origins, and gene abundance with phylogenomic neighbors. RESULTS Type A strains have shown genomic proximity to group I strains with distinct accessory genes and vary even within subtypes. Phylogenomic data showed that type C and D strains were distantly related to a group I and group II strains. Synthetic plots indicated that orthologous genes might have evolved from Clostridial ancestry to subtype A3 strains, whereas syntonic out-paralogs might have emerged between subtypes A3 and A1 through α-events. Gene abundance analysis revealed the key roles of genes involved in biofilm formation, cell-cell communication, human diseases, and drug resistance compared to the pathogenic Clostridia. Moreover, we identified 43 unique genes in the type A3 genome, of which 29 were involved in the pathophysiological processes and other genes contributed to amino acid metabolism. The C. botulinum type A3 genome contains 14 new virulence proteins that can provide the ability to confer antibiotic resistance, virulence exertion and adherence to host cells, the host immune system, and mobility of extrachromosomal genetic elements. CONCLUSION The results of our study provide insight into the understanding of new virulence mechanisms to discover new therapeutics for the treatment of human diseases caused by type A3 strains.
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Affiliation(s)
- B Roja
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India
| | - S Saranya
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India
| | - P Chellapandi
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India.
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12
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Hominibacterium faecale gen. nov., sp. nov., an anaerobic l-arginine-degrading bacterium isolated from human feces. Arch Microbiol 2023; 205:33. [DOI: 10.1007/s00203-022-03365-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
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13
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Cazaudehore G, Guyoneaud R, Lallement A, Gassie C, Monlau F. Biochemical methane potential and active microbial communities during anaerobic digestion of biodegradable plastics at different inoculum-substrate ratios. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 324:116369. [PMID: 36202034 DOI: 10.1016/j.jenvman.2022.116369] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The influence of the inoculum-substrate ratio (ISR) on the mesophilic and thermophilic biochemical methane potential test of two biodegradable plastics was evaluated. Poly(lactic acid) (PLA) and polyhydroxybutyrate (PHB) were selected for this study, the first for being recalcitrant to mesophilic anaerobic digestion (AD) and the second, by contrast, for being readily biodegradable. Several ISRs, calculated on the basis of volatile solids (VS), were tested: 1, 2, 2.85, 4, and 10 g(VS of inoculum).g(VS of substrate)-1. A high ISR was associated with an enhanced methane production rate (i.e., biodegradation kinetics). However, the ultimate methane production did not change, except when inhibition was observed. Indeed, applying the lowest ISR to readily biodegradable plastics such as PHB resulted in inhibition of methane production. Based on these experiments, in order to have reproducible degradation kinetics and optimal methane production, an ISR between 2.85 and 4 is recommended for biodegradable plastics. The active microbial communities were analyzed, and the active bacteria differed depending on the plastic digested (PLA versus PHB) and the temperature of the process (mesophilic versus thermophilic). Previously identified PHB degraders (Ilyobacter delafieldii and Enterobacter) were detected in PHB-fed reactors. Thermogutta and Tepidanaerobacter were detected during the thermophilic AD of PLA, and they are probably involved in PLA hydrolysis and lactate conversion, respectively.
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Affiliation(s)
- G Cazaudehore
- APESA, Pôle Valorisation, 64121 Montardon, France; Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France.
| | - R Guyoneaud
- Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France
| | - A Lallement
- APESA, Pôle Valorisation, 64121 Montardon, France
| | - C Gassie
- Université de Pau et des Pays de l'Adour / E2S UPPA / CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000, Pau, France
| | - F Monlau
- APESA, Pôle Valorisation, 64121 Montardon, France
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14
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Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. MICROBIOME 2022; 10:212. [PMID: 36464731 PMCID: PMC9721005 DOI: 10.1186/s40168-022-01410-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both "known" and "unknown" species based on a set of select marker genes. RESULTS We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies. CONCLUSIONS We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs . Video Abstract.
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Affiliation(s)
- Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicolai Karcher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Quentin Clayssen
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Marisa Isabell Keller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel R. Mende
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
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15
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Lu Y, Liu X, Miao Y, Chatzisymeon E, Pang L, Qi L, Yang P, Lu H. Particle size effects in microbial characteristics in thermophilic anaerobic digestion of cattle manure containing copper oxide. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62994-63004. [PMID: 35449326 DOI: 10.1007/s11356-022-20327-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Roles of bulk-, micron-, and nano-copper oxide (CuO) on methane production, microbial diversity, functions during thermophilic anaerobic digestion (AD) were investigated in this study. Results showed that bulk-, micron-, and nano-CuO promoted methane production by 27.8%, 47.6%. and 83.1% compared to the control group, respectively. Microbial community analysis demonstrated that different particle sizes could cause various shifts on bacteria community, while had little effect on archaeal diversity. Thereinto, bacteria belonging to phylum Firmicutes and Coprothermobacterota dominated in enhanced hydrolysis process in groups with nano-CuO and bulk-CuO, respectively, while micron-CuO had stronger promotion on the abundances of hydrolytic and fermentative bacteria belonging to families Peptostreptococcaceae, Caloramatoraceae, Erysipelotrichaceae, and Clostridiaceae, than other two CuO sizes. Metabolic pathways revealed that energy-related metabolism and material transformation in bacteria were only boosted by micron-CuO, and nano-CuO and bulk-CuO were important to methanogenic activity, stimulating energy consumption and methane metabolism, respectively.
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Affiliation(s)
- Yuanyuan Lu
- College of Architecture and Environment, Sichuan University, Chengdu, 610000, People's Republic of China
| | - Xuna Liu
- College of Architecture and Environment, Sichuan University, Chengdu, 610000, People's Republic of China
| | - Yanjun Miao
- China SEDIN Ningbo Engineering Co., Ltd, Ningbo, 315048, People's Republic of China
| | - Efthalia Chatzisymeon
- School of Engineering, Institute for Infrastructure and Environment, The University of Edinburgh, Edinburgh, EH9 3JL, UK
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu, 610000, People's Republic of China.
| | - Luqing Qi
- College of Architecture and Environment, Sichuan University, Chengdu, 610000, People's Republic of China
- Department of Environment Systems, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610000, People's Republic of China
| | - Hongyan Lu
- College of Architecture and Environment, Sichuan University, Chengdu, 610000, People's Republic of China
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16
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Sacco MD, Wang S, Adapa SR, Zhang X, Lewandowski EM, Gongora MV, Keramisanou D, Atlas ZD, Townsend JA, Gatdula JR, Morgan RT, Hammond LR, Marty MT, Wang J, Eswara PJ, Gelis I, Jiang RHY, Sun X, Chen Y. A unique class of Zn 2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. Nat Commun 2022; 13:4370. [PMID: 35902581 PMCID: PMC9334274 DOI: 10.1038/s41467-022-32086-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn2+-binding motif that influences β-lactam binding and protein stability. The Zn2+-binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.
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Affiliation(s)
- Michael D Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Shaohui Wang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy R Adapa
- Department of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL, 33620, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Eric M Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Maura V Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | | | - Zachary D Atlas
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA
| | - Julia A Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jean R Gatdula
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Ryan T Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Lauren R Hammond
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Prahathees J Eswara
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Rays H Y Jiang
- Department of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL, 33620, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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Escuder-Rodríguez JJ, González-Suarez M, deCastro ME, Saavedra-Bouza A, Becerra M, González-Siso MI. Characterization of a novel thermophilic metagenomic GH5 endoglucanase heterologously expressed in Escherichia coli and Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:76. [PMID: 35799200 PMCID: PMC9264688 DOI: 10.1186/s13068-022-02172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/24/2022] [Indexed: 01/05/2023]
Abstract
Background Endoglucanases from thermophilic microorganisms are a valuable resource as they can be used in a wide variety of biotechnological applications including the valorisation of biomass and the production of biofuels. In the present work we analysed the metagenome from the hot spring Muiño da Veiga, located in the northwest of Spain (in the Galicia region), in search for novel thermostable endoglucanases. Results Sequence analysis of the metagenome revealed a promising enzyme (Cel776). Predictions on protein structure and conserved amino acid sequences were conducted, as well as expression in heterologous systems with Escherichia coli and Saccharomyces cerevisiae as the host. Cel776Ec was correctly expressed and purified by taking advantage of the His-Tag system, with a yield of 0.346 U/mL in the eluted fraction. Cel776Sc was expressed extracellulary and was easily recovered from the supernatant without the need of further purification, requiring only a concentration step by ultrafiltration, with a significantly higher yield of 531.95 U/mL, revealing a much more suitable system for production of large amounts of the enzyme. Their biochemical characterization revealed biotechnologically interesting enzymes. Both Cel776Ec and Cel776Sc had an optimal temperature of 80 °C and optimal pH of 5. Cel776Ec exhibited high thermostability maintaining its activity for 24 h at 60 °C and maintained its activity longer than Cel776Sc at increasing incubation temperatures. Moreover, its substrate specificity allowed the degradation of both cellulose and xylan. Whereas Cel776Ec was more active in the presence of calcium and magnesium, manganese was found to increase Cel776Sc activity. A stronger inhibitory effect was found for Cel776Ec than Cel776Sc adding detergent SDS to the reaction mix, whereas EDTA only significantly affected Cel776Sc activity. Conclusions Our study reports the discovery of a new promising biocatalyst for its application in processes, such as the production of biofuel and the saccharification of plant biomass, due to its bifunctional enzymatic activity as an endoglucanase and as a xylanase, as well as highlights the advantages of a yeast expression system over bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02172-4.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María González-Suarez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María-Eugenia deCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Almudena Saavedra-Bouza
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
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18
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Leopold SR, Abdelraouf K, Nicolau DP, Agresta H, Johnson J, Teter K, Dunne WM, Broadwell D, van Belkum A, Schechter LM, Sodergren EJ, Weinstock GM. Murine Model for Measuring Effects of Humanized-Dosing of Antibiotics on the Gut Microbiome. Front Microbiol 2022; 13:813849. [PMID: 35250930 PMCID: PMC8892246 DOI: 10.3389/fmicb.2022.813849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/13/2022] [Indexed: 11/29/2022] Open
Abstract
There is a current need for enhancing our insight in the effects of antimicrobial treatment on the composition of human microbiota. Also, the spontaneous restoration of the microbiota after antimicrobial treatment requires better understanding. This is best addressed in well-defined animal models. We here present a model in which immune-competent or neutropenic mice were administered piperacillin-tazobactam (TZP) according to human treatment schedules. Before, during and after the TZP treatment, fecal specimens were longitudinally collected at established intervals over several weeks. Gut microbial taxonomic distribution and abundance were assessed through culture and molecular means during all periods. Non-targeted metabolomics analyses of stool samples using Quadrupole Time of Flight mass spectrometry (QTOF MS) were also applied to determine if a metabolic fingerprint correlated with antibiotic use, immune status, and microbial abundance. TZP treatment led to a 5–10-fold decrease in bacterial fecal viability counts which were not fully restored during post-antibiotic follow up. Two distinct, relatively uniform and reproducible restoration scenarios of microbiota changes were seen in post TZP-treatment mice. Post-antibiotic flora could consist of predominantly Firmicutes or, alternatively, a more diverse mix of taxa. In general, the pre-treatment microbial communities were not fully restored within the screening periods applied. A new species, closely related to Eubacterium siraeum, Mageeibacillus indolicus, and Saccharofermentans acetigenes, became predominant post-treatment in a significant proportion of mice, identified by 16S rRNA gene sequencing. Principal component analysis of QTOF MS of mouse feces successfully distinguished treated from non-treated mice as well as immunocompetent from neutropenic mice. We observe dynamic but distinct and reproducible responses in the mouse gut microbiota during and after TZP treatment and propose the current murine model as a useful tool for defining the more general post-antibiotic effects in the gastro-intestinal ecosystem where humanized antibiotic dosing may ultimately facilitate extrapolation to humans.
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Affiliation(s)
- Shana R. Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Kamilia Abdelraouf
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, United States
| | - David P. Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, United States
| | - Hanako Agresta
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Jethro Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Kathleen Teter
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | | | - Alex van Belkum
- BioMérieux SA, Clinical Unit, Grenoble, France
- *Correspondence: Alex van Belkum,
| | | | - Erica J. Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
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19
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Qin M, Xu H, Zhao D, Zeng J, Wu QL. Aquaculture drives distinct patterns of planktonic and sedimentary bacterial communities: insights into co-occurrence pattern and assembly processes. Environ Microbiol 2022; 24:4079-4093. [PMID: 35099108 DOI: 10.1111/1462-2920.15922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/13/2021] [Accepted: 01/19/2022] [Indexed: 11/03/2022]
Abstract
Aquaculture would change the environmental condition in the lake ecosystem, affecting the structure and function of the aquatic ecosystem. However, little is known about the underlying mechanisms controlling the distribution patterns of bacterial community respond to aquaculture in water column and sediment. Here, we investigated the composition, co-occurrence patterns, and assembly processes of planktonic and sedimentary bacterial communities (PBC vs. SBC) from an aquaculture-influenced zone of the Eastern Lake Taihu, China. We found that aquaculture activity greatly influenced the diversity and composition of SBC by inducing excess nitrogen into the sediments. Meanwhile, network analysis revealed that aquaculture activity strengthened species interactions within the SBC network but weakened the species interactions within the PBC network. Aquaculture activity also increased the importance of deterministic processes governing the assembly of SBC by heightening the importance of environmental filtering, whereas it decreased the relative importance of deterministic processes within the assembly of PBC. In addition, ecological restoration with macrophytes increased the diversity of PBC and formed a more stable PBC network by increasing the number of network keystones. Overall, our results indicated that aquaculture drove distinct co-occurrence patterns and assembly mechanisms of PBC and SBC. This study has fundamental implications in the lake ecosystem for evaluating the microbially mediated ecological consequences of aquaculture.
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Affiliation(s)
- Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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20
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Xie Z, Cao Q, Chen Y, Luo Y, Liu X, Li D. The biological and abiotic effects of powdered activated carbon on the anaerobic digestion performance of cornstalk. BIORESOURCE TECHNOLOGY 2022; 343:126072. [PMID: 34626759 DOI: 10.1016/j.biortech.2021.126072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
To comprehensively evaluate the biological and abiotic influence of powdered activated carbon (PAC) on the anaerobic digestion of cornstalk, mesophilic and thermophilic digestion were conducted. Adding PAC (10 g/L) under thermophilic system obtained the maximum cellulose degradation rate and methane yield (MY), which were 57.47% and 128.19 L/kg VS. However, adding same dose of PAC at mesophilic system decreased the MY by 8.16% while increased the cellulose degradation rate and methane production rate by 6.48% and 17.92%. Under mesophilic conditions, the enhancement of PAC was owing to the enrichment of cellulolytic microorganisms, improvement of the syntrophic process and direct interspecies electron transfer. The lower methane yield was attributed to the adsorption of carbon source by PAC and CH4 consumption by Norank_c_Bathyarchaeia. The good performance of thermophilic system was owing to the lower adsorption capability of PAC, absence of Norank_c_Bathyarchaeia, and concentrated carbon flow to methane.
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Affiliation(s)
- Zhijie Xie
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qin Cao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yichao Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yiping Luo
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, PR China
| | - Xiaofeng Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Dong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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21
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Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genomics 2021; 113:4196-4205. [PMID: 34780936 DOI: 10.1016/j.ygeno.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspective, we have intensively analyzed its genomic and metabolic characteristics to comprehend the evolutionary conservation of amino acid catabolism by a comparative genomic approach. The whole-genome data indicated that CST has shown a phylogenomic similarity with hyper-ammonia producing, purinolytic, and proteolytic pathogenic Clostridia. CST has shown to common genomic context sharing across the purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genome syntenic analysis described that syntenic orthologs might be originated from the recent ancestor at a slow evolution rate and syntenic-out paralogs evolved from either CDF or CAC via α-event and β-event. Collinearity of either gene orders or gene families was adjusted with syntenic out-paralogs across these genomes. The genome-wide metabolic analysis predicted 11 unique putative metabolic subsystems from the CST genome for amino acid catabolism and hydrogen production. The in silico analysis of our study revealed that a characteristic system for amino acid catabolism-directed biofuel synthesis might have slowly evolved and established as a core genomic content of CST.
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22
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Xie Z, Meng X, Ding H, Cao Q, Chen Y, Liu X, Li D. The synergistic effect of rumen cellulolytic bacteria and activated carbon on thermophilic digestion of cornstalk. BIORESOURCE TECHNOLOGY 2021; 338:125566. [PMID: 34298332 DOI: 10.1016/j.biortech.2021.125566] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
To explore the bioaugmentation of rumen cellulolytic bacteria (RCB) and activated carbon (AC) on thermophilic digestion of cornstalk, biochemical methane potential tests were carried out. Adding RCB or AC can improve methane production, while simultaneous existence of AC (10 g/L) and RCB (5%) obtained the best performance. The maximum cellulose degradation rate, methane production rate and methane yield were 66.92%, 32.2 L/(kgVS·d), and 144.9 L/kgVS, which increased by 30.23%, 51.17%, and 20.35% compared with control group. The cellulolytic and fermentative bacteria (Hydrogenispora), syntrophic acetate-oxidizing bacteria (norank_o_MBA03), and hydrogenotrophic Methanothermobacter were crucial for thermophilic digestion of cornstalk. The enhancement of AC was due to the enrichment of Hydrogenispora and Methanothermobacter, while RCB can increase the abundance of cellulolytic bacteria (Halocella and norank_o_M55-D21) and mixotrophic Methanosarcina. The synergetic effect of AC and RCB owing to the enriched cellulolytic bacteria, the enhanced syntrophic acetate oxidation and the concentrated carbon metabolic flow to methane.
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Affiliation(s)
- Zhijie Xie
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianghui Meng
- College of Engineering, Northeast Agricultural University, No. 600, Changjiang Road, Xiangfang District, Harbin, Heilongjiang, 150030, PR China
| | - Hongxia Ding
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Cao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichao Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiaofeng Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Dong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; College of Engineering, Northeast Agricultural University, No. 600, Changjiang Road, Xiangfang District, Harbin, Heilongjiang, 150030, PR China; University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Hebdon SD, Gerritsen AT, Chen YP, Marcano JG, Chou KJ. Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. Front Microbiol 2021; 12:695517. [PMID: 34566906 PMCID: PMC8457756 DOI: 10.3389/fmicb.2021.695517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.
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Affiliation(s)
- Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Alida T Gerritsen
- Computational Sciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yi-Pei Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Joan G Marcano
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
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Cazaudehore G, Monlau F, Gassie C, Lallement A, Guyoneaud R. Methane production and active microbial communities during anaerobic digestion of three commercial biodegradable coffee capsules under mesophilic and thermophilic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:146972. [PMID: 33892320 DOI: 10.1016/j.scitotenv.2021.146972] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/15/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Biodegradable plastics market is increasing these last decades, including for coffee capsules. Anaerobic digestion, as a potential end-of-life scenario for plastic waste, has to be investigated. For this purpose, mesophilic (38 °C) and thermophilic (58 °C) anaerobic digestion tests on three coffee capsules made up with biodegradable plastic (Beanarella®, Launay® or Tintoretto®) and spent coffee (control) were compared by their methane production and the microbial communities active during the process. Mesophilic biodegradation of the capsules was slow and did not reach completion after 100 days, methane production ranged between 67 and 127 NL (CH4) kg-1 (VS). Thermophilic anaerobic digestion resulted in a better biodegradation and reached completion around 100 days, methane productions were between 257 and 294 NL (CH4) kg-1 (VS). The microbial populations from the reactors fed with plastics versus spent coffee grounds were significantly different, under both the mesophilic and the thermophilic conditions. However, the different biodegradable plastics only had a small impact on the main microbial community composition at a similar operational temperature and sampling time. Interestingly, the genus Tepidimicrobium was identified as a potential key microorganisms involved in the thermophilic conversion of biodegradable plastic in methane.
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Affiliation(s)
- G Cazaudehore
- APESA, Pôle Valorisation, Cap Ecologia, 64230 Lescar, France; Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000 Pau, France
| | - F Monlau
- APESA, Pôle Valorisation, Cap Ecologia, 64230 Lescar, France
| | - C Gassie
- Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000 Pau, France
| | - A Lallement
- APESA, Pôle Valorisation, Cap Ecologia, 64230 Lescar, France
| | - R Guyoneaud
- Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, IPREM UMR5254, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Chimie et Microbiologie de l'Environnement, 64000 Pau, France.
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Bao Y, Liu J, Zhang X, Lei P, Qiu J, He J, Li N. Sinanaerobacter chloroacetimidivorans gen. nov., sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge. Antonie van Leeuwenhoek 2021; 114:1609-1617. [PMID: 34410564 DOI: 10.1007/s10482-021-01627-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022]
Abstract
An obligate anaerobic bacterial strain (BAD-6T) capable of degrading acetochlor and butachlor was isolated from an anaerobic acetochlor-degrading reactor. Cells were Gram-stain positive, straight to gently curved rods with flagella. The major fermentation products in peptone-yeast broth were acetate and butyrate. The optimum temperature and pH for growth was 30 °C and 7.2-7.5, respectively. The major cellular fatty acids (> 10%) were C14:0 FAME, C16:0 FAME and cyc-9,10-C19:0 DMA. Genome sequencing revealed a genome size of 4.80 Mb, a G + C content of 43.6 mol% and 4741 protein-coding genes. The most closely related described species on the basis of 16S rRNA gene sequences was Anaerovorax odorimutans NorPutT in the order Clostridiales of the class Clostridia with sequence similarity of 94.9%. The nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) between the genomes of strain BAD-6T and Ana. odorimutans NorPutT were 70.9% and 15.9%, respectively. Based on the distinct differences in phylogenetic and phenotypic characteristics between strain BAD-6T and related species, Sinanaerobacter chloroacetimidivorans gen. nov., sp. nov. is proposed to accommodate the strain. Strain BAD-6T is the type strain (= CCTCC AB 2021092T = KCTC 25290T).
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Affiliation(s)
- Yixuan Bao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Junwei Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Peng Lei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| | - Na Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China. .,College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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Liu J, Bao Y, Zhang X, Zhang K, Chen S, Wu H, He J. Proteiniclasticum sediminis sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge. Antonie van Leeuwenhoek 2021; 114:1541-1549. [PMID: 34401954 DOI: 10.1007/s10482-021-01620-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Abstract
An obligate anaerobic bacterial BAD-10 T was isolated from anaerobic acetochlor-degrading sludge. The strain was Gram-stain negative, curved rod-shaped, non-motile and non-spore-forming. Growth was observed in PYT medium at pH 6.0-9.0 (optimum, pH 7.5), at 25-47 °C (37 °C) and with 0-1.0% NaCl (w/v, 0%). Strain BAD-10 T could degrade acetochlor. The major fermentation products from peptone-yeast (PY) medium were acetate and butyrate. The predominant cellular fatty acids were iso-C15:0 FAME, anteiso-C15:0 FAME and C16:0 FAME. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain BAD-10 T showed closest affiliation to Proteiniclasticum ruminis D3RC-2 T, with a sequence similarity of 97.6%. Genome sequencing revealed a genome size of 2,983,986 bp, a G + C content of 51.4 mol% and protein-coding genes of 3,102. The average nucleotide identity and in silico DNA-DNA hybridization values between strain BAD-10 T and Proteiniclasticum ruminis D3RC-2 T were 71.0% and 20.4%, respectively, which were below the standard thresholds for species differentiation. On the basis of phenotypic, physiological and phylogenetic evidence, strain BAD-10 T represents a novel species in the genus Proteiniclasticum, for which the name Proteiniclasticum sediminis sp. nov. is proposed. Strain BAD-10 T (= CCTCC AB 2021091 T = KCTC 25288 T) is the type strain of the proposed novel species.
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Affiliation(s)
- Junwei Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Yixuan Bao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Kaiyun Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Shuaimin Chen
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, Jilin, 130033, People's Republic of China
| | - Haiyan Wu
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, Jilin, 130033, People's Republic of China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China.
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27
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Biohydrogen-producing from bottom to top? Quali-quantitative characterization of thermophilic fermentative consortia reveals microbial roles in an upflow fixed-film reactor. CHEMICAL ENGINEERING JOURNAL ADVANCES 2021. [DOI: 10.1016/j.ceja.2021.100125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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28
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He J, Liu R, Zheng W, Guo H, Yang Y, Zhao R, Yao W. High ambient temperature exposure during late gestation disrupts glycolipid metabolism and hepatic mitochondrial function tightly related to gut microbial dysbiosis in pregnant mice. Microb Biotechnol 2021; 14:2116-2129. [PMID: 34272826 PMCID: PMC8449678 DOI: 10.1111/1751-7915.13893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/03/2021] [Indexed: 12/11/2022] Open
Abstract
As global warming intensifies, emerging evidence has demonstrated high ambient temperature during pregnancy negatively affects maternal physiology with compromised pregnant outcomes; however, little is known about the roles of gut microbiota and its underlying mechanisms in this process. Here, for the first time, we explored the potential mechanisms of gut microbiota involved in the disrupted glycolipid metabolism via hepatic mitochondrial function. Our results indicate heat stress (HS) reduces fat and protein contents and serum levels of insulin and triglyceride (TG), while increases that of non-esterified fatty acid (NEFA), β-hydroxybutyric acid (B-HBA), creatinine and blood urea nitrogen (BUN) (P < 0.05). Additionally, HS downregulates both mitochondrial genes (mtDNA) and nuclear encoding mitochondrial functional genes with increasing serum levels of malondialdehyde (MDA) and 8-hydroxydeoxyguanosine (8-OHdG) (P < 0.05). Regarding microbial response, HS boosts serum levels of lipopolysaccharide (LPS) (P < 0.05) and alters β-diversity (ANOSIM, P < 0.01), increasing the proportions of Escherichia-Shigella, Acinetobacter and Klebsiella (q < 0.05), while reducing that of Ruminiclostridium, Blautia, Lachnospiraceae_NK4A136_group, Clostridium VadinBB60 and Muribaculaceae (q < 0.05). PICRUSt analysis predicts that HS upregulates 11 KEGG pathways, mainly including bile secretion and bacterial invasion of epithelial cells. The collective results suggest that microbial dysbiosis due to late gestational HS has strong associations with damaged hepatic mitochondrial function and disrupted metabolic profiles.
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Affiliation(s)
- Jianwen He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,Affiliated Hospital of Shaanxi University of Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712000, China
| | - Riliang Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weijiang Zheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huiduo Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunnan Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruqian Zhao
- Key Lab of Animal Physiology and Biochemistry, Nanjing Agricultural University, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Nanjing, 210095, China
| | - Wen Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,Key Lab of Animal Physiology and Biochemistry, Nanjing Agricultural University, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Nanjing, 210095, China
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29
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Gabriel-Barajas JE, Arreola-Vargas J, Toledo-Cervantes A, Méndez-Acosta HO, Rivera-González JC, Snell-Castro R. Prokaryotic population dynamics and interactions in an AnSBBR using tequila vinasses as substrate in co-digestion with acid hydrolysates of Agave tequilana var. azul bagasse for hydrogen production. J Appl Microbiol 2021; 132:413-428. [PMID: 34189819 DOI: 10.1111/jam.15196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
AIMS The purpose of this study was to characterize the prokaryotic community and putative microbial interactions between H2 -producing bacteria (HPB) and non-HPB using two anaerobic sequencing batch biofilm reactors (AnSBBRs) fed with tequila vinasses in co-digestion with acid hydrolysates of Agave tequilana var. azul bagasse (ATAB). METHODS AND RESULTS Two AnSBBRs were operated for H2 production to correlate changes in physicochemical and biological variables by principal component analysis (PCA). Results indicated that H2 yield was supported by Ethanoligenens harbinense and Clostridium tyrobutyricum through the PFOR pathway. However, only E. harbinense was able to compete for sugars against non-HPB. Competitive exclusion associated with competition for sugars, depletion of essential trace elements, bacteriocin production and resistance to inhibitory compounds could be carried out by non-HPB, increasing their relative abundances during the dark fermentation (DF) process. CONCLUSIONS The global scenario obtained by PCA correlated the decrease in H2 production with the lactate:acetate molar ratio in the influent. At the beginning of co-digestion, this ratio had the minimum value considered for a net gain of ATP. This fact could cause the reduction of the relative abundance of C. tyrobutyricum. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study that demonstrated the feasibility of H2 production by Clostridiales from acid hydrolysates of ATAB in co-digestion with tequila vinasses.
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Affiliation(s)
| | - Jorge Arreola-Vargas
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
| | - Alma Toledo-Cervantes
- Departamento de Ingeniería química, CUCEI-Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - Hugo Oscar Méndez-Acosta
- Departamento de Ingeniería química, CUCEI-Universidad de Guadalajara, Guadalajara, Jalisco, México
| | | | - Raúl Snell-Castro
- Departamento de Ingeniería química, CUCEI-Universidad de Guadalajara, Guadalajara, Jalisco, México
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30
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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31
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Poudel S, Cope AL, O'Dell KB, Guss AM, Seo H, Trinh CT, Hettich RL. Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:116. [PMID: 33971924 PMCID: PMC8112048 DOI: 10.1186/s13068-021-01964-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/26/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. RESULTS We optimized and employed a pipeline integrating various "guilt-by-association" (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum. Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum. In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. CONCLUSIONS This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Alexander L Cope
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Kaela B O'Dell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Bredesen Center, University of Tennessee, Knoxville, TN, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center, University of Tennessee, Knoxville, TN, USA
| | - Hyeongmin Seo
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Cong T Trinh
- The Center for Bioenergy Innovation at Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
- The Bredesen Center, University of Tennessee, Knoxville, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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32
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De Anda V, Chen LX, Dombrowski N, Hua ZS, Jiang HC, Banfield JF, Li WJ, Baker BJ. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404. [PMID: 33893309 PMCID: PMC8065059 DOI: 10.1038/s41467-021-22736-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.
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Affiliation(s)
- Valerie De Anda
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Den Burg, Netherlands
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.
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33
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The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil. AGRONOMY-BASEL 2021. [DOI: 10.3390/agronomy11040772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.
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34
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Rettenmaier R, Kowollik ML, Klingl A, Liebl W, Zverlov V. Ruminiclostridium herbifermentans sp. nov., a mesophilic and moderately thermophilic cellulolytic and xylanolytic bacterium isolated from a lab-scale biogas fermenter fed with maize silage. Int J Syst Evol Microbiol 2021; 71. [PMID: 33555241 DOI: 10.1099/ijsem.0.004692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic bacterial strain, designated MA18T, was isolated from a laboratory-scale biogas fermenter fed with maize silage. Cells stained Gram-negative and performed Gram-negative in the KOH test. The peptidoglycan type was found to be A1y-meso-Dpm direct. The major cellular fatty acids were C14 : 0 iso, C15 : 0 iso, anteiso and iso DMA as well as a C16 unidentified fatty acid. Oxidase and catalase activities were absent. Cells were slightly curved rods, motile, formed spores and measured approximately 0.35 µm in diameter and 3.0-5.0 µm in length. When cultivated on GS2 agar with cellobiose, round, arched, shiny and slightly yellow-pigmented colonies were formed. The isolate was mesophilic to moderately thermophilic with a growth optimum between 40 and 48 °C. Furthermore, neutral pH values were preferred and up to 1.2 % (w/v) NaCl supplemented to the GS2 medium was tolerated. Producing mainly acetate and ethanol, MA18T fermented arabinose, cellobiose, crystalline and amorphous cellulose, ribose, and xylan. The genome of MA18T consists of 4 817 678 bp with a G+C content of 33.16 mol%. In the annotated protein sequences, cellulosomal components were detected. Phylogenetically, MA18T is most closely related to Ruminiclostridium sufflavum DSM 19573T (76.88 % average nucleotide identity of the whole genome sequence; 97.23 % 16S rRNA gene sequence similarity) and can be clustered into one clade with other species of the genus Ruminiclostridium, family Oscillospiraceae, class Clostridia. Based on morphological, physiological and genetic characteristics, this strain represents a novel species in the genus Ruminiclostridium. Therefore, the name Ruminiclostridium herbifermentans sp. nov. is proposed. The type strain is MA18T (=DSM 109966T=JCM 39124T).
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Affiliation(s)
- Regina Rettenmaier
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Marie-Louise Kowollik
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Andreas Klingl
- LMU Munich, Plant Development & Electron Microscopy, Biocenter LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Wolfgang Liebl
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir Zverlov
- Institute of Molecular Genetics of National Research Centre «Kurchatov Institute», Kurchatov Sq. 2, 123182 Moscow, Russia.,Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
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35
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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36
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Froese AG, Sparling R. Cross-feeding and wheat straw extractives enhance growth of Clostridium thermocellum-containing co-cultures for consolidated bioprocessing. Bioprocess Biosyst Eng 2021; 44:819-830. [PMID: 33392746 DOI: 10.1007/s00449-020-02490-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/24/2020] [Indexed: 01/19/2023]
Abstract
Co-cultures consisting of three thermophilic and lignocellulolytic bacteria, namely Clostridium thermocellum, C. stercorarium, and Thermoanaerobacter thermohydrosulfuricus, degrade lignocellulosic material in a synergistic manner. When cultured in a defined minimal medium two of the members appeared to be auxotrophic and unable to grow, but the growth of all species was observed in all co-culture combinations, indicating cross-feeding of unidentified growth factors between the members. Growth factors also appeared to be present in water-soluble extractives obtained from wheat straw, allowing for the growth of the auxotrophic monocultures in the defined minimal medium. Cell enumeration during growth on wheat straw in this medium revealed different growth profiles of the members that varied between the co-cultures. End-product profiles also varied substantially between the cultures, with significantly higher ethanol production in all co-cultures compared to the mono-cultures. Understanding interactions between co-culture members, and the additional nutrients provided by lignocellulosic substrates, will aid us in consolidated bioprocessing design.
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Affiliation(s)
- Alan G Froese
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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37
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Hildebrand F, Pallen MJ, Bork P. Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology. Gut 2020; 69:1358-1359. [PMID: 31203204 PMCID: PMC7306977 DOI: 10.1136/gutjnl-2019-319045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/30/2019] [Indexed: 12/08/2022]
Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mark J Pallen
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
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38
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Rettenmaier R, Schneider M, Munk B, Lebuhn M, Jünemann S, Sczyrba A, Maus I, Zverlov V, Liebl W. Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum. Microorganisms 2020; 8:E915. [PMID: 32560349 PMCID: PMC7355431 DOI: 10.3390/microorganisms8060915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 01/02/2023] Open
Abstract
Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, Hungateiclostridium thermocellum was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of H. thermocellum and the saccharolytic bacterium Defluviitalea raffinosedens from a laboratory-scale biogas fermenter. The characterization focused on cellulose breakdown by applying the measurement of cellulose hydrolysis, production of metabolites, and the activity of secreted enzymes. Substrate degradation and the production of volatile metabolites was considerably enhanced when both organisms acted synergistically. The metabolic properties of H. thermocellum have been studied well in the past. To predict the role of D. raffinosedens in this bacterial duet, the genome of D. raffinosedens was sequenced for the first time. Concomitantly, to deduce the prevalence of D. raffinosedens in anaerobic digestion, taxonomic composition and transcriptional activity of different biogas microbiomes were analyzed in detail. Defluviitalea was abundant and metabolically active in reactor operating at highly efficient process conditions, supporting the importance of this organism for the hydrolysis of the raw substrate.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Martina Schneider
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Bernhard Munk
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
- Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
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Lv XM, Yang M, Dai LR, Tu B, Chang C, Huang Y, Deng Y, Lawson PA, Zhang H, Cheng L, Tang YQ. Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes. Int J Syst Evol Microbiol 2020; 70:3361-3373. [DOI: 10.1099/ijsem.0.004178] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and
Methanothermobacter thermautotrophicus
ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of
Desulfitibacter alkalitolerans
,
Calderihabitans maritimus
and members of the genus
Moorella
. Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family
Peptococcaceae
were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.
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Affiliation(s)
- Xiao-meng Lv
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Li-rong Dai
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Chen Chang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yan Huang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
| | - Yue-qin Tang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
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40
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Cruz R, Palmeira JD, Martins ZE, Faria MA, Ferreira H, Marques A, Casal S, Cunha SC. Multidisciplinary approach to determine the effect of polybrominated diphenyl ethers on gut microbiota. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:113920. [PMID: 31991346 DOI: 10.1016/j.envpol.2020.113920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/02/2020] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
Environmental health is increasingly compromised by persistent toxic substances, which may have serious implications in food safety and, thus, in human health. Polybrominated diphenyl ethers (PBDEs) are anthropogenic contaminants with endocrine disruption abilities and are commonly found in seafood, the main route of human exposure. Growing evidence points out that the human gut microbiota interacts with xenobiotics, which may lead to impairment of host homeostasis if functions of microbiota become compromised. The aim of this study was to ascertain if the physiological balance of human gut microbiome is affected by the presence and degree of exposure to PBDEs. Fermentation was performed in a batch closed-system using an inoculum made from fresh human stool. The volatolomic profile was analysed by solid-phase microextraction coupled to gas chromatography-mass spectrometry. Mesophilic, Gram-negative bacteria and coliforms were quantified by classic plating methods. Changes in the gut microbiome were evaluated after DNA extraction followed by deep sequencing of the 16S rDNA region. The exposure to PBDEs resulted in an imbalance in sulfur, short-chain fatty acids and aromatic organic compounds, changing the microbial volatolome in a dose- and time-dependent manner. Slight deviations in the microbial structure of human gut occurred in the presence of PBDEs, especially for high doses of exposure. For the first time, the impact of PBDEs on the microbial homeostasis of human gut microbiota was taken into consideration, revealing noteworthy modifications with serious health implications even at oral exposure doses considered as safe by worldwide regulatory entities.
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Affiliation(s)
- Rebeca Cruz
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313, Porto, Portugal
| | - Josman D Palmeira
- UCIBIO, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Zita E Martins
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel A Faria
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313, Porto, Portugal
| | - Helena Ferreira
- UCIBIO, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - António Marques
- IPMA, Divisão de Aquacultura e Valorização, Instituto Português do Mar e da Atmosfera, I.P., Avenida Doutor Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal; CIIMAR, Universidade do Porto, Rua dos Bragas 289, 4050-123, Porto, Portugal
| | - Susana Casal
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas 135, 4050-600, Porto, Portugal
| | - Sara C Cunha
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313, Porto, Portugal.
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41
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Ueki A, Takehara T, Ishioka G, Kaku N, Ueki K. β-1,3-Glucanase production as an anti-fungal enzyme by phylogenetically different strains of the genus Clostridium isolated from anoxic soil that underwent biological disinfestation. Appl Microbiol Biotechnol 2020; 104:5563-5578. [PMID: 32328681 PMCID: PMC7275012 DOI: 10.1007/s00253-020-10626-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/01/2020] [Accepted: 04/14/2020] [Indexed: 01/10/2023]
Abstract
Biological (or reductive) soil disinfestation (BSD or RSD) is a bioremediation process to control soil-borne plant pathogens using activities of indigenous bacteria in the soil. Three obligate anaerobic bacterial strains (TW1, TW10, and TB10), which were isolated from anoxic soil subjected to BSD treatments, were examined for their abilities to produce anti-fungal enzymes. All strains were affiliated with the different lineages of the genus Clostridium. The three strains decomposed β-1,3-glucans (curdlan and laminarin), and β-1,3-glucanase activities were detected from their culture supernatants with these glucans. The three strains also produced the enzyme with wheat bran as a growth substrate and killed the Fusarium pathogen (Fusarium oxysporum f. sp. spinaciae) in the anaerobic co-incubation conditions. Observation by fluorescence microscopy of the pathogen cells showed that the three strains had degraded the fungal cells in different manners upon co-incubation with wheat bran. When the three strains were cultivated with the dead cells or the cell wall samples prepared from the Fusarium pathogen, strain TW1 utilized these materials as easily decomposable substrates by releasing β-1,3-glucanase. When observed by fluorescence microscopy, it appeared that strain TW1 degraded the mycelial cell wall nearly thoroughly, with the septa remaining as undecomposed luminous rings. In contrast, the other two strains decomposed neither the dead cells nor the cell wall samples directly. The results indicate that the various anaerobic bacteria proliferated in the soil under the BSD treatments should play key roles as an organized bacterial community to eliminate fungal pathogens, namely by release of anti-fungal enzymes with different properties.Key points •Three clostridial strains isolated from BSD-treated soils produced β-1,3-glucanase. •All strains killed the Fusarium pathogen in the anaerobic co-incubation conditions. •One of the strains produced β-1,3-glucanase with the fungal cell wall as a substrate. •The strain degraded the cell wall almost completely, except for the mycelial septa. |
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Affiliation(s)
- Atsuko Ueki
- Faculty of Agriculture, Yamagata University, 1-23, Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan.
| | - Toshiaki Takehara
- NARO Western Region Agricultural Research Center, Hiroshima, 721-8514, Japan.,NARO Technical Support Center of Central Region, Ibaraki, 305-8517, Japan
| | - Gen Ishioka
- NARO Western Region Agricultural Research Center, Hiroshima, 721-8514, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, 1-23, Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan
| | - Katsuji Ueki
- Faculty of Agriculture, Yamagata University, 1-23, Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan
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42
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Chaplin AV, Sokolova SR, Shcherbakova VA, Suzina NE, Kochetkova TO, Goltsov AY, Trofimov DY, Efimov BA. Hydrogeniiclostidium mannosilyticum gen. nov., sp. nov. isolated from human faeces. Int J Syst Evol Microbiol 2020; 70:1210-1216. [PMID: 32122456 DOI: 10.1099/ijsem.0.003900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A strain of obligately anaerobic, spore-forming, Gram-positive rods was isolated from child faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole genome sequencing revealed the strain to represent a member of the family Ruminococcaceae distant from described species and genera. The strain was moderately saccharolytic with mannose as the preferred substrate and produced lactic acid, acetic acid and H2 as the end products. The major cellular long-chain fatty acids were C16 : 0 and C16 : 0 aldehyde. The genomic DNA G+C content was 52.3 mol%. On the basis of chemotaxonomic and genomic properties it was concluded that the strain represents a novel species in a new genus within the family Ruminococcaceae, for which the name Hydrogeniiclostidium mannosilyticum gen. nov., sp. nov. is proposed. The type strain of Hydrogeniiclostidium mannosilyticum is ASD2818T (=VKM B-3268T=JCM 33295T).
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Affiliation(s)
- Andrei V Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Sofia R Sokolova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research, Russian Academy of Sciences", Prospect Nauki 5, Pushchino, Moscow region 142290, Russia
| | - Natalia E Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research, Russian Academy of Sciences", Prospect Nauki 5, Pushchino, Moscow region 142290, Russia
| | - Taisiya O Kochetkova
- Laboratory of Molecular Genetic Methods, Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Andrey Y Goltsov
- Laboratory of Molecular Genetic Methods, Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Dmitriy Y Trofimov
- Laboratory of Molecular Genetic Methods, Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Boris A Efimov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
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43
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Lackner N, Wagner AO, Markt R, Illmer P. pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion. Microorganisms 2020; 8:E286. [PMID: 32093251 PMCID: PMC7074938 DOI: 10.3390/microorganisms8020286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/11/2023] Open
Abstract
pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0-8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.
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Affiliation(s)
- Nina Lackner
- Department of Microbiology, Universität Innsbruck, 6020 Innsbruck, Austria; (A.O.W.); (R.M.); (P.I.)
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44
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Koendjbiharie JG, Hon S, Pabst M, Hooftman R, Stevenson DM, Cui J, Amador-Noguez D, Lynd LR, Olson DG, van Kranenburg R. The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase. J Biol Chem 2020; 295:1867-1878. [PMID: 31871051 PMCID: PMC7029132 DOI: 10.1074/jbc.ra119.011239] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Indexed: 01/24/2023] Open
Abstract
The genomes of most cellulolytic clostridia do not contain genes annotated as transaldolase. Therefore, for assimilating pentose sugars or for generating C5 precursors (such as ribose) during growth on other (non-C5) substrates, they must possess a pathway that connects pentose metabolism with the rest of metabolism. Here we provide evidence that for this connection cellulolytic clostridia rely on the sedoheptulose 1,7-bisphosphate (SBP) pathway, using pyrophosphate-dependent phosphofructokinase (PPi-PFK) instead of transaldolase. In this reversible pathway, PFK converts sedoheptulose 7-phosphate (S7P) to SBP, after which fructose-bisphosphate aldolase cleaves SBP into dihydroxyacetone phosphate and erythrose 4-phosphate. We show that PPi-PFKs of Clostridium thermosuccinogenes and Clostridium thermocellum indeed can convert S7P to SBP, and have similar affinities for S7P and the canonical substrate fructose 6-phosphate (F6P). By contrast, (ATP-dependent) PfkA of Escherichia coli, which does rely on transaldolase, had a very poor affinity for S7P. This indicates that the PPi-PFK of cellulolytic clostridia has evolved the use of S7P. We further show that C. thermosuccinogenes contains a significant SBP pool, an unusual metabolite that is elevated during growth on xylose, demonstrating its relevance for pentose assimilation. Last, we demonstrate that a second PFK of C. thermosuccinogenes that operates with ATP and GTP exhibits unusual kinetics toward F6P, as it appears to have an extremely high degree of cooperative binding, resulting in a virtual on/off switch for substrate concentrations near its K½ value. In summary, our results confirm the existence of an SBP pathway for pentose assimilation in cellulolytic clostridia.
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Affiliation(s)
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830
| | - Martin Pabst
- Cell Systems Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Robert Hooftman
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jingxuan Cui
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755
| | - Daniel Amador-Noguez
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830
| | - Richard van Kranenburg
- Corbion, 4206 AC Gorinchem, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
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45
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Tindall BJ. The names Hungateiclostridium Zhang et al. 2018, Hungateiclostridium thermocellum (Viljoen et al. 1926) Zhang et al. 2018, Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 contravene Rule 51b of the International Code of Nomenclature of Prokaryotes and require replacement names in the genus Acetivibrio Patel et al. 1980. Int J Syst Evol Microbiol 2019; 69:3927-3932. [PMID: 31526446 DOI: 10.1099/ijsem.0.003685] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A recent publication has created the genus name HungateiclostridiumZhang et al. 2018 and the new combinations Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990.) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 for names at the rank of species that were previously either included in the genus ClostridiumPrazmowski 1880, Acetivibrio Patel et al. 1980 or HerbivoraxKoeck et al. 2016. Rules 23a, 38, 39b, 41a, 42 and 44 have not been followed and an illegitimate name at the rank of genus or illegitimate combinations at the rank of species as defined in Rule 51b(1) and (2) have been created. Another aspect is recognising the fact that an instance of heterotypic synonym has been created between Acetivibrio Patel et al. 1980, HerbivoraxKoeck et al. 2016 and HungateiclostridiumZhang et al. 2018, where the earliest validly published genus name is Acetivibrio Patel et al. 1980, of which the nomenclatural type is Acetivibrio cellulolyticus Patel et al. 1980. It follows from Rules 23a, 38, 39a, 39b, 41a, 42 and 44 that the genus name to be used is Acetivibrio Patel et al. 1980, with new combinations in that genus replacing those published in the genus HungateiclostridiumZhang et al. 2018, which together with the genus name are illegitimate according to Rule 51b of the International Code of Nomenclature of Prokaryotes. Additional issues are also addressed with regards to the names Pseudoclostridium thermosuccinogenes (Drent et al. 1995) Zhang et al. 2018, PseudoclostridiumZhang et al. 2018 OscillospiraceaePeshkoff 1940 (Approved Lists 1980), RuminococcaceaeRainey 2010, Eubacteriales Buchanan 1917 (Approved Lists 1980) and ClostridialesPrévot 1953 (Approved Lists 1980).
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Affiliation(s)
- B J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B 38124, Braunschweig, Germany
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46
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Tindall B. Replacement of the illegitimate genus name Hungateiclostridium Zhang et al. 2018 in Hungateiclostridium mesophilum Rettenmaier et al. 2019 by Acetivibrio Patel et al. 1980, creating Acetivibrio mesophilus (Rettenmaier et al. 2019). Int J Syst Evol Microbiol 2019; 69:3967-3968. [DOI: 10.1099/ijsem.0.003810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- B.J. Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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47
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Wu K, Dai L, Tu B, Zhang X, Zhang H, Deng Y, Lawson PA, Cheng L. Gudongella oleilytica gen. nov., sp. nov., an aerotorelant bacterium isolated from Shengli oilfield and validation of family Tissierellaceae. Int J Syst Evol Microbiol 2019; 70:951-957. [PMID: 31751197 DOI: 10.1099/ijsem.0.003854] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, rod shaped and anaerobic bacterium, designated as W6T, was isolated from Shengli oilfield in China. Strain W6T was observed to grow from 20 to 45 °C with pH 6.5-9.0 (optimally at 40 °C and pH of 7.5) and without addition of NaCl. The major cellular fatty acids were iso-C15 : 0 (29.1%), C14 : 0 (27.0%) and C16 : 0 (12.2%), and the main polar lipids were lipids (L) and aminolipids (AL). The DNA G+C content is 42.9 mol%. Based on 16S rRNA gene sequence analysis, strain W6T showed highest similarities to Tissierella creatinini DSM 9508T (94.9%) and Soehngenia saccharolytica DSM 12858T (94.1%). The morphological, physiological, biochemical, phylogenetic and phylogenomic analyses demonstrated strain W6T (CCAM 534T=DSM 28124T=CGMCC 1.5291T) represents a novel species in a new genus, for which the name Gudongella oleilytica gen. nov. sp. nov. is proposed. The family Tissierellaceae is proposed as a new family containing the genera Anaerosalibacter, Gudongella, Keratinibaculum, Soehngenia, Sporanaerobacter, Tepidimicrobium, Tissierella, Urmitella and species Clostridium ultunense based on the phylogenetic and phylogenomic analyses.
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Affiliation(s)
- Kejia Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Yu Deng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
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Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium. Sci Rep 2019; 9:15924. [PMID: 31685873 PMCID: PMC6828813 DOI: 10.1038/s41598-019-52251-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/23/2019] [Indexed: 01/19/2023] Open
Abstract
Carbohydrate active enzymes are classified in databases based on sequence and structural similarity. However, their function can vary considerably within a similarity-based enzyme family, which makes biochemical characterisation indispensable to unravel their physiological role and to arrive at a meaningful annotation of the corresponding genes. In this study, we biochemically characterised the four related enzymes Tm_Ram106B, Tn_Ram106B, Cb_Ram106B and Ts_Ram106B from the thermophilic bacteria Thermotoga maritima MSB8, Thermotoga neapolitana Z2706-MC24, Caldicellulosiruptor bescii DSM 6725 and Thermoclostridium stercorarium DSM 8532, respectively, as α-l-rhamnosidases. Cobalt, nickel, manganese and magnesium ions stimulated while EDTA and EGTA inhibited all four enzymes. The kinetic parameters such as Km, Vmax and kcat were about average compared to other rhamnosidases. The enzymes were inhibited by rhamnose, with half-maximal inhibitory concentrations (IC50) between 5 mM and 8 mM. The α-l-rhamnosidases removed the terminal rhamnose moiety from the rutinoside in naringin, a natural flavonone glycoside. The Thermotoga sp. enzymes displayed the highest optimum temperatures and thermostabilities of all rhamnosidases reported to date. The four thermophilic and divalent ion-dependent rhamnosidases are the first biochemically characterised orthologous enzymes recently assigned to glycoside hydrolase family 106.
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Hungateiclostridium mesophilum sp. nov., a mesophilic, cellulolytic and spore-forming bacterium isolated from a biogas fermenter fed with maize silage. Int J Syst Evol Microbiol 2019; 69:3567-3573. [DOI: 10.1099/ijsem.0.003663] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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