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Kang M, Chhetri G, Kim I, So Y, Seo T. Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov. Sci Rep 2022; 12:21233. [PMID: 36482214 PMCID: PMC9731981 DOI: 10.1038/s41598-022-25718-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, four novel bacterial strains, USB13T, AW1T, GTP1T, and HM2T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13T = KACC 21656T = NBRC 114839T) Ramlibacter aurantiacus sp. nov. (type strain, AW1T = KACC 21544T = NBRC 114862T), Ramlibacter albus sp. nov. (type strain, GTP1T = KACC 21702T = NBRC 114488T), and Ramlibacter pallidus sp. nov. (type strain, HM2T = KCTC 82557T = NBRC 114489T) are proposed.
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Affiliation(s)
- Minchung Kang
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Geeta Chhetri
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Inhyup Kim
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Yoonseop So
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Taegun Seo
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
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Huang Y, Peng Y, Yang Z, Chen S, Liu J, Wang Z, Wang G, Lan S. Effects of Fermented Bamboo Shoot Processing Waste on Growth Performance, Serum Parameters, and Gut Microbiota of Weaned Piglets. Animals (Basel) 2022; 12:ani12202728. [PMID: 36290114 PMCID: PMC9597720 DOI: 10.3390/ani12202728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
Gut microbiota (GM) plays a vital role in the nutrition and metabolism of weaned piglets. Some feed additives can be used to adjust the composition of GM to improve the health of weaned piglets. In this study, we investigated the effects of adding fermented bamboo shoot processing waste (FBSPW) to diet on growth performance, serum parameters, and GM of weaned piglets. Seventy-two piglets were divided into four groups and were fed diets containing 0% (control), 4% (group A), 8% (group B), and 12% (group C) FBSPW for 50 days. We found that the addition of FBSPW significantly decreased the average daily feed intake, serum triglyceride content, and urea nitrogen of weaned piglets compared to the control. The cecum and cecal microbiota of weaned piglets fed the basal diet with 12% FBSPW were significantly different compared to the control. A basal diet with 12% FBSPW significantly reduced the taxon feature number, and the relative abundance of Tenericutes in the cecum and cecal microbiota of weaned piglets compared with the control. The addition of 12% FBSPW to weaned piglet feed could improve their nitrogen and lipid metabolisms and have beneficial effects on GM.
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Affiliation(s)
- Yuanhao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yingjie Peng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zheng Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Siyu Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Jing Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zheng Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Gang Wang
- Hunan Huajun Agricultural Technology Co., Ltd., Taojiang 413000, China
- Correspondence: (G.W.); (S.L.)
| | - Shile Lan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (G.W.); (S.L.)
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New Insights into the Co-Occurrences of Glycoside Hydrolase Genes among Prokaryotic Genomes through Network Analysis. Microorganisms 2021; 9:microorganisms9020427. [PMID: 33669523 PMCID: PMC7922503 DOI: 10.3390/microorganisms9020427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/21/2022] Open
Abstract
Glycoside hydrolase (GH) represents a crucial category of enzymes for carbohydrate utilization in most organisms. A series of glycoside hydrolase families (GHFs) have been classified, with relevant information deposited in the CAZy database. Statistical analysis indicated that most GHFs (134 out of 154) were prone to exist in bacteria rather than archaea, in terms of both occurrence frequencies and average gene numbers. Co-occurrence analysis suggested the existence of strong or moderate-strong correlations among 63 GHFs. A combination of network analysis by Gephi and functional classification among these GHFs demonstrated the presence of 12 functional categories (from group A to L), with which the corresponding microbial collections were subsequently labeled, respectively. Interestingly, a progressive enrichment of particular GHFs was found among several types of microbes, and type-L as well as type-E microbes were deemed as functional intensified species which formed during the microbial evolution process toward efficient decomposition of lignocellulose as well as pectin, respectively. Overall, integrating network analysis and enzymatic functional classification, we were able to provide a new angle of view for GHs from known prokaryotic genomes, and thus this study is likely to guide the selection of GHs and microbes for efficient biomass utilization.
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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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Bhati N, Shreya, Sharma AK. Cost‐effective cellulase production, improvement strategies, and future challenges. J FOOD PROCESS ENG 2020. [DOI: 10.1111/jfpe.13623] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikita Bhati
- Department of Bioscience and Biotechnology Banasthali Vidyapith Vanasthali India
| | - Shreya
- Department of Bioscience and Biotechnology Banasthali Vidyapith Vanasthali India
| | - Arun Kumar Sharma
- Department of Bioscience and Biotechnology Banasthali Vidyapith Vanasthali India
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Wang F, Wang M, Zhao Q, Niu K, Liu S, He D, Liu Y, Xu S, Fang X. Exploring the Relationship Between Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17. Front Microbiol 2019; 10:2035. [PMID: 31551972 PMCID: PMC6746925 DOI: 10.3389/fmicb.2019.02035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Characterizing and engineering microbial communities for lignocellulosic biofuel production has received widespread attention. Previous research has established that Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17 coculture significantly improves overall cellulosic biofuel production efficiency. Here, we investigated this interaction and revealed the mechanism underlying the improved efficiency observed. In contrast to the previously reported mutualistic relationship, a harmful effect toward C. thermocellum JN4 was observed in these microbial consortia. Although T. thermosaccharolyticum GD17 relieves the carbon catabolite repression of C. thermocellum JN4 regarding obtaining more cellobiose or glucose released from lignocellulose, T. thermosaccharolyticum GD17 significantly hampers the growth of C. thermocellum JN4 in coculture. The increased formation of end products is due to the strong competitive metabolic advantage of T. thermosaccharolyticum GD17 over C. thermocellum JN4 in the conversion of glucose or cellobiose into final products. The possibility of controlling and rebalancing these microbial consortia to modulate cellulose degradation was achieved by adding T. thermosaccharolyticum GD17 stimulants into the system. As cellulolytic bacteria are usually at a metabolic disadvantage, these discoveries may apply to a large proportion of cellulosic biofuel-producing microbial consortia. These findings provide a reference for engineering efficient and modular microbial consortia for modulating cellulosic conversion.
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Affiliation(s)
- Fangzhong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shasha Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Didi He
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yan Liu
- College of Life Science, Qufu Normal University, Qufu, China
| | - Shiping Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Understanding aerobic/anaerobic metabolism in Caldibacillus debilis through a comparison with model organisms. Syst Appl Microbiol 2017; 40:245-253. [PMID: 28527624 DOI: 10.1016/j.syapm.2017.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 11/20/2022]
Abstract
Caldibacillus debilis GB1 is a facultative anaerobe isolated from a thermophilic aero-tolerant cellulolytic enrichment culture. There is a lack of representative proteomes of facultative anaerobic thermophilic Bacillaceae, exploring aerobic/anaerobic expression. The C. debilis GB1 genome was sequenced and annotated, and the proteome characterized under aerobic and anaerobic conditions while grown on cellobiose. The draft sequence of C. debilis GB1 contains a 3,340,752 bp chromosome and a 5,386 bp plasmid distributed over 49 contigs. Two-dimensional liquid chromatography mass spectrometry/mass spectrometry was used with Isobaric Tags for Relative and Absolute Quantification (iTRAQ) to compare protein expression profiles, focusing on energy production and conversion pathways. Under aerobic conditions, proteins in glycolysis and pyruvate fermentation pathways were down-regulated. Simultaneously, proteins within the tricarboxylic acid cycle, pyruvate dehydrogenase, the electron transport chain, and oxygen scavenging pathways showed increased amounts. Under anaerobic conditions, protein levels in fermentation pathways were consistent with the generated end-products: formate, acetate, ethanol, lactate, and CO2. Under aerobic conditions CO2 and acetate production was consistent with incomplete respiration. Through a direct comparison with gene expression profiles from Escherichia coli, we show that global regulation of core metabolism pathways is similar in thermophilic and mesophilic facultative anaerobes of the Phylum Proteobacteria and Firmicutes.
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Behera SS, Ray RC. Solid state fermentation for production of microbial cellulases: Recent advances and improvement strategies. Int J Biol Macromol 2016; 86:656-69. [DOI: 10.1016/j.ijbiomac.2015.10.090] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/23/2022]
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Akinosho H, Yee K, Close D, Ragauskas A. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2014; 2:66. [PMID: 25207268 PMCID: PMC4143619 DOI: 10.3389/fchem.2014.00066] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/28/2014] [Indexed: 01/25/2023] Open
Abstract
First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
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Affiliation(s)
- Hannah Akinosho
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology Atlanta, GA, USA ; Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA
| | - Kelsey Yee
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, TN, USA
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