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Liu S, Lu SY, Patel M, Qureshi N, Dunlap C, Hoecker E, Skory CD. Production of a Bacteriocin Like Protein PEG 446 from Clostridium tyrobutyricum NRRL B-67062. Probiotics Antimicrob Proteins 2024:10.1007/s12602-023-10211-1. [PMID: 38252201 DOI: 10.1007/s12602-023-10211-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
Clostridium tyrobutyricum strain NRRL B-67062 was previously isolated from an ethanol production facility and shown to produce high yields of butyric acid. In addition, the cell-free supernatant of the fermentation broth from NRRL B-67062 contained antibacterial activity against certain Gram-positive bacteria. To determine the source of this antibacterial activity, we report the genome and genome mining of this strain. The complete genome of NRRL B-67062 showed one circular chromosome of 3,242,608 nucleotides, 3114 predicted coding sequences, 79 RNA genes, and a G+C content of 31.0%. Analyses of the genome data for genes potentially associated with antimicrobial features were sought after by using BAGEL-4 and anti-SMASH databases. Among the leads, a polypeptide of 66 amino acids (PEG 446) contains the DUF4177 domain, which is an uncharacterized highly conserved domain (pfam13783). The cloning and expression of the peg446 gene in Escherichia coli and Bacillus subtilis confirmed the antibacterial property against Lactococcus lactis LM 0230, Limosilactobacillus fermentum 0315-25, and Listeria innocua NRRL B-33088 by gel overlay and well diffusion assays. Molecular modeling suggested that PEG 446 contains one alpha-helix and three anti-parallel short beta-sheets. These results will aid further functional studies and facilitate simultaneously fermentative production of both butyric acid and a putative bacteriocin from agricultural waste and lignocellulosic biomass materials.
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Affiliation(s)
- Siqing Liu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA.
| | - Shao-Yeh Lu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
| | - Maulik Patel
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, 37830, USA
| | - Nasib Qureshi
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, Peoria, IL, 61604, USA
| | - Christopher Dunlap
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, 61604, USA
| | - Eric Hoecker
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
| | - Christopher D Skory
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, Peoria, IL, 61604, USA
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Liu T, Zhu L, Zhu Z, Jiang L. Genome Sequence Analysis of Clostridium tyrobutyricum, a Promising Microbial Host for Human Health and Industrial Applications. Curr Microbiol 2020; 77:3685-3694. [DOI: 10.1007/s00284-020-02175-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/21/2020] [Indexed: 11/30/2022]
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3
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Song YF, Pei LX, Chen L, Geng H, Yuan MQ, Xu WL, Wu J, Zhou JY, Sun JH. Electroacupuncture Relieves Irritable Bowel Syndrome by Regulating IL-18 and Gut Microbial Dysbiosis in a Trinitrobenzene Sulfonic Acid-Induced Post-Inflammatory Animal Model. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2020; 48:77-90. [PMID: 31918565 DOI: 10.1142/s0192415x20500044] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Post inflammatory irritable bowel syndrome (PI-IBS), a subset of IBS, is characterized by symptoms of visceral pain, bloating, and changed bowel habits that occur post initial episode of intestinal infection. Gut microbial dysbiosis or inflammation plays a key role in the pathogenesis of abdominal hypersensitivity of PI-IBS. Electroacupuncture (EA) stimulation results in an alleviated PI-IBS-associated symptom. This study investigated the effect of EA on IL-18 and gut microbial dysbiosis in one visceral hypersensitive rat models with PI-IBS. A trinitrobenzene sulfonic acid (TNBS)-induced visceral hypersensitivity rat model was developed. EA stimulation was applied to the ST25 and ST36 acupoints. Animals were assessed using abdominal withdrawal reflex (AWR) scores to determine the development of colonic visceral hypersensitivity. The 16S rRNA was used to correlate microbial diversity. IL-18 expression in colon was quantified by quantitative real-time PCR and western blotting. We identified that model rats had an increased visceral hypersensitivity to colorectal distention at different distention pressures compared with the normal group. Sensitivity to colorectal distention decreased after EA stimulation. The composition of the fecal microbiota was different between groups. Specifically, in the model group Empedobacter, Psychrobacter, Enterococcus, Butyricimonas, Vampirovibrio, Kurthia, Intestinimonas, Neisseria, Falsiporphyromonas, Bilophila, Fusobacterium, Alistipes, Veillonella, Flavonifractor, Clostridium XlVa were more abundant affected genera, whereas Lactobacillus was enriched in normal rats. EA stimulation was correlated with significant decrease in the phyla of Fusobacteria. The mRNA and protein levels of IL-18 were higher in the model group. Meanwhile, EA stimulation attenuated this response. In a word, our findings suggest that PI-IBS is associated with significant increase in IL-18 levels as well as an alteration in microbiome diversity. These changes can be reversed with EA treatment. EA stimulation has a positive effect in alleviating symptoms of visceral hypersensitivity and protecting the gastrointestinal tract.
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Affiliation(s)
- Ya-Fang Song
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Li-Xia Pei
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Lu Chen
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Hao Geng
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Meng-Qian Yuan
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Wan-Li Xu
- Department of the First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P. R. China
| | - Jian Wu
- Department of Central Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Jin-Yong Zhou
- Department of Central Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Jian-Hua Sun
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
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Cheng C, Lin M, Jiang W, Zhao J, Li W, Yang ST. Development of an in vivo fluorescence based gene expression reporter system for Clostridium tyrobutyricum. J Biotechnol 2019; 305:18-22. [PMID: 31472166 DOI: 10.1016/j.jbiotec.2019.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/01/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
C. tyrobutyricum, an acidogenic Clostridium, has aroused increasing interest due to its potential to produce biofuel efficiently. However, construction of recombinant C. tyrobutyricum for enhanced biofuel production has been impeded by the limited genetic engineering tools. In this study, a flavin mononucleotide (FMN)-dependent fluorescent protein Bs2-based gene expression reporter system was developed to monitor transformation and explore in vivo strength and regulation of various promoters in C. tyrobutyricum and C. acetobutylicum. Unlike green fluorescent protein (GFP) and its variants, Bs2 can emit green light without oxygen, which makes it extremely suitable for promoter screening and transformation confirmation in organisms grown anaerobically. The expression levels of bs2 under thiolase promoters from C. tyrobutyricum and C. acetobutylicum were measured and compared based on fluorescence intensities. The capacities of the two promoters in driving secondary alcohol dehydrogenase (adh) gene for isopropanol production in C. tyrobutyricum were distinguished, confirming that this reporter system is a convenient, effective and reliable tool for promoter strength assay and real time monitoring in C. tyrobutyricum, while demonstrating the feasibility of producing isopropanol in C. tyrobutyricum for the first time.
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Affiliation(s)
- Chi Cheng
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 Woodruff Ave., Columbus, OH 43210, USA
| | - Meng Lin
- Bioprocessing Innovative Company, 4734 Bridle Path Ct., Dublin, OH 43017, USA
| | - Wenyan Jiang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 Woodruff Ave., Columbus, OH 43210, USA
| | - Jingbo Zhao
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 Woodruff Ave., Columbus, OH 43210, USA
| | - Weiming Li
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 Woodruff Ave., Columbus, OH 43210, USA; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 Woodruff Ave., Columbus, OH 43210, USA.
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Whole-Genome Sequencing and Annotation of Clostridium tyrobutyricum Strain Cirm BIA 2237, Isolated from Silage. Microbiol Resour Announc 2019; 8:8/30/e00492-19. [PMID: 31346011 PMCID: PMC6658681 DOI: 10.1128/mra.00492-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Clostridium tyrobutyricum is the main bacterial species leading to the late blowing defect, a major cause of spoilage in semihard and hard cheeses. This study reports the complete genome sequencing, assembly, and annotation of C. tyrobutyricum strain Cirm BIA 2237, formerly called CNRZ 608, isolated from silage. Clostridium tyrobutyricum is the main bacterial species leading to the late blowing defect, a major cause of spoilage in semihard and hard cheeses. This study reports the complete genome sequencing, assembly, and annotation of C. tyrobutyricum strain Cirm BIA 2237, formerly called CNRZ 608, isolated from silage.
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Fu X, Liu Z, Zhu C, Mou H, Kong Q. Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria. Crit Rev Food Sci Nutr 2018; 59:S130-S152. [PMID: 30580556 DOI: 10.1080/10408398.2018.1542587] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nondigestible carbohydrates (NDCs) are fermentation substrates in the colon after escaping digestion in the upper gastrointestinal tract. Among NDCs, resistant starch is not hydrolyzed by pancreatic amylases but can be degraded by enzymes produced by large intestinal bacteria, including clostridia, bacteroides, and bifidobacteria. Nonstarch polysaccharides, such as pectin, guar gum, alginate, arabinoxylan, and inulin fructans, and nondigestible oligosaccharides and their derivatives, can also be fermented by beneficial bacteria in the large intestine. Butyrate is one of the most important metabolites produced through gastrointestinal microbial fermentation and functions as a major energy source for colonocytes by directly affecting the growth and differentiation of colonocytes. Moreover, butyrate has various physiological effects, including enhancement of intestinal barrier function and mucosal immunity. In this review, several representative NDCs are introduced, and their chemical components, structures, and physiological functions, including promotion of the proliferation of butyrate-producing bacteria and enhancement of butyrate production, are discussed. We also describe the strategies for achieving directional accumulation of colonic butyrate based on endogenous generation mechanisms.
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Affiliation(s)
- Xiaodan Fu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Zhemin Liu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Changliang Zhu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Haijin Mou
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Qing Kong
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
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Jiang L, Fu H, Yang HK, Xu W, Wang J, Yang ST. Butyric acid: Applications and recent advances in its bioproduction. Biotechnol Adv 2018; 36:2101-2117. [PMID: 30266343 DOI: 10.1016/j.biotechadv.2018.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Abstract
Butyric acid is an important C4 organic acid with broad applications. It is currently produced by chemosynthesis from petroleum-based feedstocks. However, the fermentative production of butyric acid from renewable feedstocks has received growing attention because of consumer demand for green products and natural ingredients in foods, pharmaceuticals, animal feed supplements, and cosmetics. In this review, strategies for improving microbial butyric acid production, including strain engineering and novel fermentation process development are discussed and compared regarding product yield, titer, purity and productivity. Future perspectives on strain and process improvements for butyric acid production are also discussed.
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Affiliation(s)
- Ling Jiang
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China; College of Food Science and Light Industry, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Hongxin Fu
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hopen K Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA; School of Chemical and Biological Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Jufang Wang
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China; Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
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8
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Suo Y, Ren M, Yang X, Liao Z, Fu H, Wang J. Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production with high butyrate/acetate ratio. Appl Microbiol Biotechnol 2018; 102:4511-4522. [DOI: 10.1007/s00253-018-8954-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 11/30/2022]
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9
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Luo H, Yang R, Zhao Y, Wang Z, Liu Z, Huang M, Zeng Q. Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation. BIORESOURCE TECHNOLOGY 2018; 253:343-354. [PMID: 29329775 DOI: 10.1016/j.biortech.2018.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/28/2017] [Accepted: 01/01/2018] [Indexed: 06/07/2023]
Abstract
Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zheng Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Mengyu Huang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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Enhanced butyric acid production in Clostridium tyrobutyricum by overexpression of rate-limiting enzymes in the Embden-Meyerhof-Parnas pathway. J Biotechnol 2018; 272-273:14-21. [PMID: 29501473 DOI: 10.1016/j.jbiotec.2018.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022]
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Wu Q, Zhu L, Xu Q, Huang H, Jiang L, Yang ST. Tailoring the Oxidative Stress Tolerance of Clostridium tyrobutyricum CCTCC W428 by Introducing Trehalose Biosynthetic Capability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8892-8901. [PMID: 28925260 DOI: 10.1021/acs.jafc.7b03172] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fermentations employing anaerobes always suffer from the restriction of stringent anaerobic conditions during the production of bulk and fine chemicals. This work aims to improve the oxidative stress tolerance of C. tyrobutyricum CCTCC W428, an ideal butyric-acid-producing anaerobe, via the introduction of trehalose biosynthesis capability. Compared with the wild type, the engineered strain showed a wider substrate spectrum, an improved metabolic profile, and a significantly increased specific growth rate upon aeration and acid challenge. Molecular simulation experiments indicated that CoA transferase maintained its native folded state when protected by the trehalose system. Furthermore, qRT-PCR was combined assays for acid-related enzyme activities under various conditions to verify the effects of trehalose. These results demonstrate that introducing a trehalose biosynthetic pathway, which is redundant for the metabolism of C. tyrobutyricum, can increase the robustness of the host to achieve a better oxidative resistance.
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Affiliation(s)
| | | | | | | | | | - Shang-Tian Yang
- Department of Chemical Engineering, The Ohio State University , Columbus, Ohio 43210, United States
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Fermentative hydrogen production from Jerusalem artichoke by Clostridium tyrobutyricum expressing exo-inulinase gene. Sci Rep 2017; 7:7940. [PMID: 28801602 PMCID: PMC5554141 DOI: 10.1038/s41598-017-07207-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/23/2017] [Indexed: 12/01/2022] Open
Abstract
Clostridium tyrobutyricum ATCC25755 has been reported as being able to produce significant quantities of hydrogen. In this study, the exo-inulinase encoding gene cloned from Paenibacillus polymyxa SC-2 was into the expression plasmid pSY6 and expressed in the cells of C. tyrobutyricum. The engineered C. tyrobutyricum strain efficiently fermented the inulin-type carbohydrates from Jerusalem artichoke, without any pretreatment being necessary for the production of hydrogen. A comparatively high hydrogen yield (3.7 mol/mol inulin-type sugar) was achieved after 96 h in a batch process with simultaneous saccharification and fermentation (SSF), with an overall volumetric productivity rate of 620 ± 60 mL/h/L when the initial total sugar concentration of the inulin extract was increased to 100 g/L. Synthesis of inulinase in the batch SSF culture was closely associated with strain growth until the end of the exponential phase, reaching a maximum activity of 28.4 ± 0.26 U/mL. The overall results show that the highly productive and abundant biomass crop Jerusalem artichoke can be a good substrate for hydrogen production, and that the application of batch SSF for its conversion has the potential to become a cost-effective process in the near future.
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Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production from glucose and xylose. Metab Eng 2017; 40:50-58. [DOI: 10.1016/j.ymben.2016.12.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/25/2016] [Accepted: 12/26/2016] [Indexed: 12/28/2022]
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Metabolic engineering of Clostridium tyrobutyricum for n-butanol production from sugarcane juice. Appl Microbiol Biotechnol 2017; 101:4327-4337. [DOI: 10.1007/s00253-017-8200-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/12/2017] [Accepted: 02/14/2017] [Indexed: 12/25/2022]
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15
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Storari M, Kulli S, Wüthrich D, Bruggmann R, Berthoud H, Arias-Roth E. Genomic approach to studying nutritional requirements of Clostridium tyrobutyricum and other Clostridia causing late blowing defects. Food Microbiol 2016; 59:213-23. [PMID: 27375262 DOI: 10.1016/j.fm.2016.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 11/16/2022]
Abstract
Clostridium tyrobutyricum is the main microorganism responsible for the late blowing defect in hard and semi-hard cheeses, causing considerable economic losses to the cheese industry. Deeper knowledge of the metabolic requirements of this microorganism can lead to the development of more effective control approaches. In this work, the amino acids and B vitamins essential for sustaining the growth of C. tyrobutyricum were investigated using a genomic approach. As the first step, the genomes of four C. tyrobutyricum strains were analyzed for the presence of genes putatively involved in the biosynthesis of amino acids and B vitamins. Metabolic pathways could be reconstructed for all amino acids and B vitamins with the exception of biotin (vitamin B7) and folate (vitamin B9). The biotin pathway was missing the enzyme amino-7-oxononanoate synthase that catalyzes the condensation of pimeloyl-ACP and l-alanine to 8-amino-7-oxononanoate. In the folate pathway, the missing genes were those coding for para-aminobenzoate synthase and aminodeoxychorismate lyase enzymes. These enzymes are responsible for the conversion of chorismate into para-aminobenzoate (PABA). Two C. tyrobutyircum strains whose genome was analyzed in silico as well as other 10 strains isolated from cheese were tested in liquid media to confirm these observations. 11 strains showed growth in a defined liquid medium containing biotin and PABA after 6-8 days of incubation. No strain showed growth when only one or none of these compounds were added, confirming the observations obtained in silico. Furthermore, the genome analysis was extended to genomes of single strains of other Clostridium species potentially causing late blowing, namely Clostridium beijerinckii, Clostridium sporogenes and Clostridium butyricum. Only the biotin biosynthesis pathway was incomplete for C. butyricum and C. beijerincki. In contrast, C. sporogenes showed missing enzymes in biosynthesis pathways of several amino acids as well as biotin, folate, and cobalamin (vitamin B12). These observations agree with the results of growth experiments of these species in liquid media reported in the literature. The results of this study suggest that biotin and folate are potential targets for reducing late blowing in cheese and highlight the usefulness of genomic analysis for identifying essential nutrients in bacteria.
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Affiliation(s)
| | - Sandra Kulli
- Institute for Food Sciences, Agroscope, Bern, Switzerland
| | - Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
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Zhou XY, Li M, Li X, Long X, Zuo XL, Hou XH, Cong YZ, Li YQ. Visceral hypersensitive rats share common dysbiosis features with irritable bowel syndrome patients. World J Gastroenterol 2016; 22:5211-5227. [PMID: 27298564 PMCID: PMC4893468 DOI: 10.3748/wjg.v22.i22.5211] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/01/2016] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate gut microbial dysbiosis in two visceral hypersensitive models in comparison with irritable bowel syndrome (IBS) patients and to explore the extent to which these models capture the dysbiosis of IBS patients.
METHODS: Visceral hypersensitivity was developed using the maternal separation (MS) rat model and post-inflammatory rat model. The visceral sensitivity of the model groups and control group was evaluated using the abdominal withdraw reflex score and electromyography in response to graded colorectal distention. The 16S ribosomal RNA gene from fecal samples was pyrosequenced and analyzed. The correlation between dysbiosis in the microbiota and visceral hypersensitivity was calculated. Positive findings were compared to sequencing data from a published human IBS cohort.
RESULTS: Dysbiosis triggered by neonatal maternal separation was lasting but not static. Both MS and post-inflammatory rat fecal microbiota deviated from that of the control rats to an extent that was larger than the co-housing effect. Two short chain fatty acid producing genera, Fusobacterium and Clostridium XI, were shared by the human IBS cohort and by the maternal separation rats and post-inflammatory rats, respectively, to different extents. Fusobacterium was significantly increased in the MS group, and its abundance positively correlated with the degree of visceral hypersensitivity. Porphyromonadaceae was a protective biomarker for both the rat control group and healthy human controls.
CONCLUSION: The dysbiosis MS rat model and the post-inflammatory rat model captured some of the dysbiosis features of IBS patients. Fusobacterium, Clostridium XI and Porphyromonadaceae were identified as targets for future mechanistic research.
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Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses. mBio 2016; 7:mBio.00743-16. [PMID: 27302759 PMCID: PMC4916380 DOI: 10.1128/mbio.00743-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces butyric acid and is considered a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the genetic and metabolic characteristics of this strain, however, little progress has been made in metabolic engineering of this strain. Here we report the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a 3.07-Mbp chromosome and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces butyrate from butyryl-coenzyme A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from Clostridium acetobutylicum, which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse transcription-PCR (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and fed-batch fermentation. In addition, the changes in protein expression levels during the course of batch fermentations on glucose were examined by shotgun proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic and fermentative pathways in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy conservation mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in C. acetobutylicum, were identified. Such features explain why this organism can produce butyric acid to a much higher titer and better tolerate toxic metabolites. This study presenting the complete genome sequence, global protein expression profiles, and genome-based metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable in designing strategies for metabolic engineering of this strain. IMPORTANCE Bio-based production of chemicals from renewable biomass has become increasingly important due to our concerns on climate change and other environmental problems. C. tyrobutyricum has been used for efficient butyric acid production. In order to further increase the performance and expand the capabilities of this strain toward production of other chemicals, metabolic engineering needs to be performed. For this, better understanding on the metabolic and physiological characteristics of this bacterium at the genome level is needed. This work reporting the results of complete genomic and proteomic analyses together with new insights on butyric acid biosynthetic pathway and energy conservation will allow development of strategies for metabolic engineering of C. tyrobutyricum for the bio-based production of various chemicals in addition to butyric acid.
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Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923). GENOME ANNOUNCEMENTS 2016; 4:4/2/e00048-16. [PMID: 26941139 PMCID: PMC4777750 DOI: 10.1128/genomea.00048-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Clostridium tyrobutyricum CIP I-776 (IFP923), an efficient producer of butyric acid. The genome consists of a single chromosome of 3.19 Mb and provides useful data concerning the metabolic capacities of the strain.
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Bassi D, Puglisi E, Cocconcelli PS. Understanding the bacterial communities of hard cheese with blowing defect. Food Microbiol 2015; 52:106-18. [DOI: 10.1016/j.fm.2015.07.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/19/2015] [Accepted: 07/03/2015] [Indexed: 11/17/2022]
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Yu L, Zhao J, Xu M, Dong J, Varghese S, Yu M, Tang IC, Yang ST. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production: effects of CoA transferase. Appl Microbiol Biotechnol 2015; 99:4917-30. [DOI: 10.1007/s00253-015-6566-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/31/2023]
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Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00078-15. [PMID: 25767226 PMCID: PMC4357748 DOI: 10.1128/genomea.00078-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively.
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Ma C, Kojima K, Xu N, Mobley J, Zhou L, Yang ST, Liu X(M. Comparative proteomics analysis of high n-butanol producing metabolically engineered Clostridium tyrobutyricum. J Biotechnol 2015; 193:108-19. [DOI: 10.1016/j.jbiotec.2014.10.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 12/20/2022]
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Nishihara M, Takahashi H, Sudo T, Kyoi D, Kawahara T, Ikeuchi Y, Fujita T, Kuda T, Kimura B, Yanahira S. Multilocus variable-number of tandem repeat analysis (MLVA) for Clostridium tyrobutyricum strains isolated from cheese production environment. Int J Food Microbiol 2014; 190:61-5. [PMID: 25190602 DOI: 10.1016/j.ijfoodmicro.2014.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 08/09/2014] [Accepted: 08/15/2014] [Indexed: 11/16/2022]
Abstract
Clostridium tyrobutyricum is a gram-positive spore-forming anaerobe that is considered as the main causative agent for late blowing in cheese due to butyric acid fermentation. In this study, multilocus variable-number of tandem repeat (VNTR) analysis (MLVA) for C. tyrobutyricum was developed to identify the source of contamination by C. tyrobutyricum spores in the cheese production environment. For each contig constructed from the results of a whole genome draft sequence of C. tyrobutyricum JCM11008(T) based on next-generation sequencing, VNTR loci that were effective for typing were searched using the Tandem Repeat Finder program. Five VNTR loci were amplified by polymerase chain reaction (PCR) to determine their number of repeats by sequencing, and MLVA was conducted. 25 strains of C. tyrobutyricum isolated from the environment, raw milk, and silage were classified into 18 MLVA types (DI=0.963). Of the C. tyrobutyricum strains isolated from raw milk, natural cheese, and blown processed cheese, strains with identical MLVA type were detected, which suggested that these strains might have shifted from natural cheese to blown processed cheese. MLVA could be an effective tool for monitoring contamination of natural cheese with C. tyrobutyricum in the processed cheese production environment because of its high discriminability, thereby allowing the analyst to trace the source of contamination.
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Affiliation(s)
- Masaharu Nishihara
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Hajime Takahashi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan.
| | - Tomoko Sudo
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Daisuke Kyoi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Toshio Kawahara
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Yoshihiro Ikeuchi
- Central Food Analysis Laboratory, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Takashi Fujita
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Takashi Kuda
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Bon Kimura
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Shuichi Yanahira
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
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