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Bai R, Li H, Chen S, Yuan X, Chen Y, Huang Y, Zhou Q, Guan H. Microbiome and response surface methodology analyses reveal Acetobacter pasteurianus as the core bacteria responsible for aerobic spoilage of corn silage ( Zea mays) in hot and humid areas. Front Microbiol 2024; 15:1473238. [PMID: 39323883 PMCID: PMC11422110 DOI: 10.3389/fmicb.2024.1473238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 08/30/2024] [Indexed: 09/27/2024] Open
Abstract
Introduction Weak aerobic stability is a notable challenge for whole-plant corn silage, particularly in hot and humid regions. Acetobacter is commonly regarded as an indicator of aerobic deterioration in silage, yet its precise role in fermentation and during aerobic exposure, as well as the factors that promote its growth, remain insufficiently understood. Methods In this study, whole-plant corn silage was prepared using a bagged method with controlled dry matter (DM) content at 20%, 25%, and 30%, and initial concentrations of A. pasteurianus at 40%, 50%, and 60%. The silage was stored for 60 days under varying temperatures (20°C, 30°C, and 40°C). Following the anaerobic storage phase, the silage was exposed to air at room temperature (20-25°C) for 7 days, both with and without A. pasteurianus inoculation. Results The results demonstrated that A. pasteurianus did not impact the nutritional value of the silage during anaerobic fermentation, maintaining a low pH (< 3.80). However, during aerobic exposure, the presence of A. pasteurianus significantly reduced the aerobic stability of the silage. The microbial community shifted from primarily Klebsiella species initially to Lactobacillus and Acetobacter species post-ensiling. During the aerobic exposure phase, A. pasteurianus and A. fabarum became the dominant species. Response Surface Methodology (RSM) analysis identified optimal conditions for the proliferation of A. pasteurianus during the aerobic phase, which occurred at 28°C, 25% DM, and 52% initial concentration at 3 ml/kg. Discussion These findings confirm that A. pasteurianus plays a critical role in reducing the aerobic stability of whole-plant corn silage. Additionally, the study identifies the optimal conditions that favor the proliferation of A. pasteurianus, offering valuable insights for the development of strategies to prevent and control this bacterium, thereby improving the aerobic stability of silage in hot and humid regions.
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Affiliation(s)
- Rui Bai
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Haiping Li
- School of Mathematics and Statistics, Qinghai Normal University, Xining, China
| | - Shiyong Chen
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Xianjun Yuan
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Youjun Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
- College of Grassland Resources, Southwest Minzu University, Chengdu, China
| | - Yanling Huang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
- College of Grassland Resources, Southwest Minzu University, Chengdu, China
| | - Hao Guan
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
- College of Grassland Resources, Southwest Minzu University, Chengdu, China
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Wang D, Liu N, Qiao M, Xu C. Gallic acid as biofilm inhibitor can improve transformation efficiency of Ruminiclostridium papyrosolvens. Biotechnol Lett 2024:10.1007/s10529-024-03522-y. [PMID: 39162860 DOI: 10.1007/s10529-024-03522-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 08/21/2024]
Abstract
Ruminiclostridium papyrosolvens is an anaerobic, mesophilic, and cellulolytic clostridia, promising consolidated bioprocessing (CBP) candidate for producing renewable green chemicals from cellulose, but its genetic transformation has been severely impeded by extracellular biofilm. Here, we analyzed the effects of five different inhibitors with gradient concentrations on R. papyrosolvens growth and biofilm formation. Gallic acid was proved to be a potent inhibitor of biofilm synthesis of R. papyrosolvens. Furthermore, the transformation efficiency of R. papyrosolvens was significantly increased when the cells were treated by the gallic acid, and the mutant strain was successfully obtained by the improved transformation method. Thus, inhibition of biofilm formation of R. papyrosolvens by using gallic acid will contribute to its genetic transformation and efficient metabolic engineering.
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Affiliation(s)
- Duodong Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China
- College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang Province, China
| | - Na Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Mingqiang Qiao
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Chenggang Xu
- College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, 311300, Zhejiang Province, China.
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Ponsetto P, Sasal EM, Mazzoli R, Valetti F, Gilardi G. The potential of native and engineered Clostridia for biomass biorefining. Front Bioeng Biotechnol 2024; 12:1423935. [PMID: 39219620 PMCID: PMC11365079 DOI: 10.3389/fbioe.2024.1423935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Since their first industrial application in the acetone-butanol-ethanol (ABE) fermentation in the early 1900s, Clostridia have found large application in biomass biorefining. Overall, their fermentation products include organic acids (e.g., acetate, butyrate, lactate), short chain alcohols (e.g., ethanol, n-butanol, isobutanol), diols (e.g., 1,2-propanediol, 1,3-propanediol) and H2 which have several applications such as fuels, building block chemicals, solvents, food and cosmetic additives. Advantageously, several clostridial strains are able to use cheap feedstocks such as lignocellulosic biomass, food waste, glycerol or C1-gases (CO2, CO) which confer them additional potential as key players for the development of processes less dependent from fossil fuels and with reduced greenhouse gas emissions. The present review aims to provide a survey of research progress aimed at developing Clostridium-mediated biomass fermentation processes, especially as regards strain improvement by metabolic engineering.
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Affiliation(s)
| | | | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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Ehsaan M, Yoo M, Kuit W, Foulquier C, Soucaille P, Minton NP. Chromosomal integration of the pSOL1 megaplasmid of Clostridium acetobutylicum for continuous and stable advanced biofuels production. Nat Microbiol 2024; 9:1655-1660. [PMID: 38877224 PMCID: PMC11222136 DOI: 10.1038/s41564-024-01714-w] [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: 05/30/2023] [Accepted: 04/24/2024] [Indexed: 06/16/2024]
Abstract
Biofuel production by Clostridium acetobutylicum is compromised by strain degeneration due to loss of its pSOL1 megaplasmid. Here we used engineering biology to stably integrate pSOL1 into the chromosome together with a synthetic isopropanol pathway. In a membrane bioreactor continuously fed with glucose mineral medium, the final strain produced advanced biofuels, n-butanol and isopropanol, at high yield (0.31 g g-1), titre (15.4 g l-1) and productivity (15.5 g l-1 h-1) without degeneration.
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Affiliation(s)
- Muhammad Ehsaan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Minyeong Yoo
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Wouter Kuit
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Céline Foulquier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Philippe Soucaille
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK.
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
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Branska B, Koppova K, Husakova M, Patakova P. Application of fed-batch strategy to fully eliminate the negative effect of lignocellulose-derived inhibitors in ABE fermentation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:87. [PMID: 38915101 PMCID: PMC11197323 DOI: 10.1186/s13068-024-02520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/16/2024] [Indexed: 06/26/2024]
Abstract
BACKGROUND Inhibitors that are released from lignocellulose biomass during its treatment represent one of the major bottlenecks hindering its massive utilization in the biotechnological production of chemicals. This study demonstrates that negative effect of inhibitors can be mitigated by proper feeding strategy. Both, crude undetoxified lignocellulose hydrolysate and complex medium supplemented with corresponding inhibitors were tested in acetone-butanol-ethanol (ABE) fermentation using Clostridium beijerinckii NRRL B-598 as the producer strain. RESULTS First, it was found that the sensitivity of C. beijerinckii to inhibitors varied with different growth stages, being the most significant during the early acidogenic phase and less pronounced during late acidogenesis and early solventogenesis. Thus, a fed-batch regime with three feeding schemes was tested for toxic hydrolysate (no growth in batch mode was observed). The best results were obtained when the feeding of an otherwise toxic hydrolysate was initiated close to the metabolic switch, resulting in stable and high ABE production. Complete utilization of glucose, and up to 88% of xylose, were obtained. The most abundant inhibitors present in the alkaline wheat straw hydrolysate were ferulic and coumaric acids; both phenolic acids were efficiently detoxified by the intrinsic metabolic activity of clostridia during the early stages of cultivation as well as during the feeding period, thus preventing their accumulation. Finally, the best feeding strategy was verified using a TYA culture medium supplemented with both inhibitors, resulting in 500% increase in butanol titer over control batch cultivation in which inhibitors were added prior to inoculation. CONCLUSION Properly timed sequential feeding effectively prevented acid-crash and enabled utilization of otherwise toxic substrate. This study unequivocally demonstrates that an appropriate biotechnological process control strategy can fully eliminate the negative effects of lignocellulose-derived inhibitors.
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Affiliation(s)
- Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic.
| | - Kamila Koppova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic
| | - Marketa Husakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic
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Hwang O, Emmett B, Andersen D, Howe A, Ro K, Trabue S. Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120884. [PMID: 38643622 DOI: 10.1016/j.jenvman.2024.120884] [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: 03/09/2023] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/23/2024]
Abstract
Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.
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Affiliation(s)
- Okhwa Hwang
- National Institute of Animal Science, Rural Development Administration, 1500, Kongjwipatjwi-Ro, Iseo-Myeon, Wanju-Gun, Jeollabuk-Do, 55365, Republic of Korea.
| | - Bryan Emmett
- USDA Agricultural Research Service, National Laboratory for Agriculture and the Environment, 1015 N. University Boulevard, Ames, IA, 50011, United States.
| | - Daniel Andersen
- Department of Agricultural and Biosystems Engineering, 3348 Elings Hall, Iowa State University, Ames, IA, 50011, United States.
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, 3348 Elings Hall, Iowa State University, Ames, IA, 50011, United States.
| | - Kyoung Ro
- USDA Agricultural Research Service, Coastal Plains Soil, Water, and Plant Research Center, 2611 West Lucas St., Florence, SC, 29501, United States.
| | - Steven Trabue
- USDA Agricultural Research Service, National Laboratory for Agriculture and the Environment, 1015 N. University Boulevard, Ames, IA, 50011, United States.
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Tang H, Ma JK, Chen L, Jiang LW, Kang LZ, Guo YY, Men GY, Nie DX, Zhong RM. Characterization of key flavor substances and their microbial sources in traditional sour bamboo shoots. Food Chem 2024; 437:137858. [PMID: 37924763 DOI: 10.1016/j.foodchem.2023.137858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
Identifying key flavor compounds and their producing bacteria in sour bamboo shoots is crucial for flavor stabilization and industrial production. This study analyzed 15 traditional sour bamboo shoot samples from northern Guangdong to determine key flavor substances and microbial community. Results showed key flavor substances were acetic acid (RTC ≥ 50% in 10 samples), lactic acid (RTC ≥ 50% in 5 samples), and p-cresol (ROC ≥ 93%). Lactobacillus (ARA: 54.62%) was the dominant genus, significantly correlated with p-cresol (r = 0.80, p ≤ 0.01). Levilactobacillus (ARA: 3.33%) was positively correlated with lactic acid and p-cresol (r = 0.78, p ≤ 0.01; r = 0.66, p ≤ 0.01). Lentilactobacillus (ARA: 4.29%) was positively correlated with acetic acid (r = 0.85, p ≤ 0.01). Levilactobacillus was isolated, screened, identified, and its ability to produce key flavor substances was tested. Four strains of Levilactobacillus spicheri and their mixed strains produced lactic acid (10.12-16.62 g/kg), acetic acid (10.21-21.60 g/kg), and p-cresol (25.67-143.87 mg/kg). This is the first report of Levilactobacillus spicheri producing p-cresol.
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Affiliation(s)
- Hui Tang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan City, Guangdong 512005, China; Henry Fok School of Food Science and Technology, Shaoguan University, Shaoguan City, Guangdong 512005, China
| | - Jin-Kui Ma
- School of Food & Pharmaceutical Engineering, Zhaoqing University, Zhaoqing City, Guangdong 526061, China.
| | - Lin Chen
- Henry Fok School of Food Science and Technology, Shaoguan University, Shaoguan City, Guangdong 512005, China
| | - Li-Wen Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha City, Hunan 410128, China
| | - Lin-Zhi Kang
- Henry Fok School of Food Science and Technology, Shaoguan University, Shaoguan City, Guangdong 512005, China
| | - Ying-Yu Guo
- Henry Fok School of Food Science and Technology, Shaoguan University, Shaoguan City, Guangdong 512005, China
| | - Ge-Yang Men
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan City, Guangdong 512005, China
| | - Dan-Xia Nie
- Henry Fok School of Food Science and Technology, Shaoguan University, Shaoguan City, Guangdong 512005, China
| | - Rui-Min Zhong
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan City, Guangdong 512005, China.
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Barragán-Trinidad M, Buitrón G. Pretreatment of agave bagasse with ruminal fluid to improve methane recovery. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 175:52-61. [PMID: 38159368 DOI: 10.1016/j.wasman.2023.12.041] [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: 09/06/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Agave bagasse, a lignocellulosic waste that results from the milling and juice extraction of Agave tequilana var azul pineapples, is a suitable substrate for the production of methane through anaerobic digestion. However, it is necessary to apply a pretreatment to convert the bagasse into energy. In this context, this paper proposes using ruminal microorganisms to hydrolyze agave bagasse. This study evaluated the effect of the initial agave bagasse to ruminal fluid (S0/X0) ratio (0.33, 0.5, 1, and 2) on the hydrolysis efficiency. Subsequently, the supernatant was used for methane production. The hydrolysis efficiency increased as the S0/X0 ratio decreased. A hydrolysis efficiency of 60 % was achieved using an S0/X0 ratio of 0.33. The S0/X0 ratio of 0.33 optimally improved the specific methane production and energy recovery (155 ± 2 mL CH4/g TS and 6.1 ± 0.1 kJ/g TS) compared to raw biomass. The most abundant hydrolytic bacteria were Prevotella, Ruminococcus and Fibrobacter, and Engyodontium was the most abundant proteolytic fungus.
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Affiliation(s)
- Martín Barragán-Trinidad
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico.
| | - Germán Buitrón
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico.
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Li X, Li M, Shi W, Li X, Xiang Z, Su L. Clostridium lamae sp. nov., a novel bacterium isolated from the fresh feces of alpaca. Antonie Van Leeuwenhoek 2024; 117:36. [PMID: 38367205 DOI: 10.1007/s10482-024-01931-7] [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: 10/28/2023] [Accepted: 01/21/2024] [Indexed: 02/19/2024]
Abstract
A novel Gram-positive, anaerobic, nonspore-forming, rod-shaped bacterium, designated strain NGMCC 1.200840 T, was isolated from the alpacas fresh feces. The taxonomic position of the novel strain was determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed strain NGMCC 1.200840 T was a member of the genus Clostridium and closely related to Clostridium tertium DSM 2485 T (98.16% sequence similarity). Between strains NGMCC 1.200840 T and C. tertium DSM 2485 T, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 79.91% and 23.50%, respectively. Genomic DNA G + C content is 28.44 mol%. The strain can utilise D-glucose, D-mannitol, D-lactose, D-saccharose, D-maltose, D-xylose, L-arabinose, D-cellobiose, D-mannose, D-melezitose, D-raffinose, D-sorbitol, L-rhamnose, D-trehalose, D-galactose and Arbutin to produce acid. The optimal growth pH was 7, the temperature was 37 °C, and the salt concentration was 0-0.5% (w/v). The major cellular fatty acids (> 10%) included iso-C15:0, anteiso-C15:0 and iso-C17:0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two unidentified aminolipids. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, NGMCC 1.200840 T represents a novel species within the genus Clostridium, for which the named Clostridium lamae sp. nov. is proposed. The type strain is NGMCC 1.200840 T (= CGMCC 1.18014 T = JCM 35704 T).
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Affiliation(s)
- Xue Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Ming Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Technology Support Platform, Beijing, 100193, China
| | - Weixiong Shi
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Xia Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Zhiguang Xiang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China.
- Changping National Laboratory (CPNL), Beijing, 102299, China.
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Li S, Kim M, Song YE, Hwan Son S, Kim HI, Jae J, Yan Q, Fei Q, Kim JR. Housing of electrosynthetic biofilms using a roll-up carbon veil electrode increases CO 2 conversion and faradaic efficiency in microbial electrosynthesis cells. BIORESOURCE TECHNOLOGY 2024; 393:130157. [PMID: 38065517 DOI: 10.1016/j.biortech.2023.130157] [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: 09/23/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/18/2024]
Abstract
Electrode-driven microbial electron transfer enables the conversion of CO2 into multi-carbon compounds. The electrosynthetic biofilms grow slowly on the surface and are highly susceptible to operational influences, such as hydrodynamic shear stress. In this study, a cylindrical roll-up carbon felt electrode was developed as a novel strategy to protect biofilms from shear stress within the reactor. The fabricated electrode allowed hydrogen bubble formation inside the structure, which enabled microbes to uptake hydrogen and convert CO2 to multi-carbon organic compounds. The roll-up electrode exhibited faster start-up and biofilm formation than the conventional linear shape carbon felt. The acetate yield and cathodic faradaic efficiency increased by 80% and 34%, respectively, and the bioelectrochemical stability was improved significantly. The roll-up structure increased biofilm development per unit electrode surface by three to five-fold. The roll-up configuration improved biofilm formation on the electrode, which enhanced the performance of microbial electrosynthesis-based CO2 valorization.
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Affiliation(s)
- Shuwei Li
- School of Chemical Engineering, Pusan National University, Busan 46241, Republic of Korea; School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China; Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shanxi 710061, China
| | - Minsoo Kim
- School of Chemical Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Young Eun Song
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Sang Hwan Son
- School of Chemical Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Hyoung-Il Kim
- School of Civil & Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungho Jae
- School of Chemical Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Qun Yan
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, Busan 46241, Republic of Korea.
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Bartosiewicz M, Przytulska A, Birkholz A, Zopfi J, Lehmann MF. Controls and significance of priming effects in lake sediments. GLOBAL CHANGE BIOLOGY 2024; 30:e17076. [PMID: 38273585 DOI: 10.1111/gcb.17076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 01/27/2024]
Abstract
Warming and eutrophication influence carbon (C) processing in sediments, with implications for the global greenhouse-gas budget. Temperature effects on sedimentary C loss are well understood, but the mechanism of change in turnover through priming with labile organic matter (OM) is not. Evaluating changes in the magnitude of priming as a function of warming, eutrophication, and OM stoichiometry, we incubated sediments with 13 C-labeled fresh organic matter (FOM, algal/cyanobacterial) and simulated future climate scenarios (+4°C and +8°C). We investigated FOM-induced production of CH4 and microbial community changes. C loss was primed by up to 17% in dominantly allochthonous sediments (ranging from 5% to 17%), compared to up to 6% in autochthonous sediments (-9% to 6%), suggesting that refractory OM is more susceptible to priming. The magnitude of priming was dependent on sediment OM stoichiometry (C/N ratio), the ratio of fresh labile OM to microbial biomass (FOM/MB), and temperature. Priming was strongest at 4°C when FOM/MB was below 50%. Addition of FOM was associated with activation and growth of bacterial decomposers, including for example, Firmicutes, Bacteroidetes, or Fibrobacteres, known for their potential to degrade insoluble and complex structural biopolymers. Using sedimentary C/N > 15 as a threshold, we show that in up to 35% of global lakes, sedimentation is dominated by allochthonous rather than autochthonous material. We then provide first-order estimates showing that, upon increase in phytoplankton biomass in these lakes, priming-enabled degradation of recalcitrant OM will release up to 2.1 Tg C annually, which would otherwise be buried for geological times.
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Affiliation(s)
- Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Institute of Geophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Przytulska
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Axel Birkholz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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12
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Feliu-Paradeda L, Puig S, Bañeras L. Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans. Sci Rep 2023; 13:20073. [PMID: 37973932 PMCID: PMC10654501 DOI: 10.1038/s41598-023-47007-w] [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: 06/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.
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Affiliation(s)
- Laura Feliu-Paradeda
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, Carrer Maria Aurèlia Capmany 40, 17003, Girona, Spain
| | - Sebastià Puig
- LEQUiA, Institute of the Environment, University of Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Lluis Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, Carrer Maria Aurèlia Capmany 40, 17003, Girona, Spain.
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13
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Pascal Andreu V, Augustijn HE, Chen L, Zhernakova A, Fu J, Fischbach MA, Dodd D, Medema MH. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat Biotechnol 2023; 41:1416-1423. [PMID: 36782070 PMCID: PMC10423304 DOI: 10.1038/s41587-023-01675-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2023] [Indexed: 02/15/2023]
Abstract
The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
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Affiliation(s)
| | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lianmin Chen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Changzhou Medical Center, Nanjing Medical University, Changzhou, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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14
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Xu J, Liu X, Geng H, Liu R, Li F, Ma J, Liu M, Liu B, Sun H, Ma S, Wang Z, Zhu X, Li D, Wang C, Shi Y, Cui Y. Alfalfa Silage Diet Improves Meat Quality by Remodeling the Intestinal Microbes of Fattening Pigs. Foods 2023; 12:3209. [PMID: 37685141 PMCID: PMC10486512 DOI: 10.3390/foods12173209] [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: 07/22/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Because the demand for pork is increasing, it is crucial to devise efficient and green methods to improve the quality and quantity of meat. This study investigated the improvement in pork quality after the inclusion of alfalfa meal or alfalfa silage in pig diet. Our results indicated that alfalfa silage improved meat quality more effectively in terms of water-holding capacity, drip loss, and marbling score. Besides, an alfalfa silage diet can affect the level of fatty acids and amino acids in pork. Further, alfalfa silage was found to improve meat quality by remodeling intestinal microbiota and altering the level of SCFAs, providing a viable option for improving meat quality through forage.
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Affiliation(s)
- Junying Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Xiao Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Hongmin Geng
- National Engineering Research Center of Wheat and Corn Further Processing, Henan University of Technology, Zhengzhou 450002, China
| | - Rui Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Fang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Jixiang Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Mengqi Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Boshuai Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Hao Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
| | - Sen Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
| | - Zhichang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
| | - Xiaoyan Zhu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
| | - Defeng Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
| | - Chengzhang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
| | - Yinghua Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
| | - Yalei Cui
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (J.X.)
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Forage Engineering Technology Research Center, Zhengzhou 450002, China
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15
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Zhao B, Chen L, Zhang M, Nie C, Yang Q, Yu K, Xia Y. Electric-Inducive Microbial Interactions in a Thermophilic Anaerobic Digester Revealed by High-Throughput Sequencing of Micron-Scale Single Flocs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4367-4378. [PMID: 36791305 DOI: 10.1021/acs.est.2c08833] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although conductive materials have been shown to improve efficiency in anaerobic digestion (AD) by modifying microbial interactions, the interacting network under thermophilic conditions has not been examined. To identify the true taxon-taxon associations within thermophilic anaerobic digestion (TAD) microbiome and reveal the influence of carbon cloth (CC) addition, we sampled micron-scale single flocs (40-70 μm) randomly isolated from lab-scale thermophilic digesters. Results revealed that CC addition not only significantly boosted methane yield by 25.3% but also increased the spatial heterogeneity of the community in the sludge medium. After CC addition, an evident translocation of Pseudomonas from the medium to the biofilm was observed, showing their remarkable capacity for biofilm formation. Additionally, Clostridium and Thermotogaceae tightly aggregated and steadily co-occurred in the medium and biofilm of the TAD microbiome, which might be associated with their unique extracellular sugar metabolizing style. Finally, CC induced syntrophic interaction between Syntrophomonas and denitrifiers of Rhodocyclaceae. The upregulated respiration-associated electron transferring genes (Cyst-c, complex III) on the cellular membranes of these collaborating partners indicated a potential coupling of the denitrification pathway with syntrophic acetate oxidation via direct interspecies electron transfer (DIET). These findings provide an insight into how conductive materials promote thermophilic digestion performance and open the path for improved community monitoring of biotreatment systems.
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Affiliation(s)
- Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liming Chen
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Cailong Nie
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qing Yang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Kaiqiang Yu
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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16
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Development of an efficient ClosTron system for gene disruption in Ruminiclostridium papyrosolvens. Appl Microbiol Biotechnol 2023; 107:1801-1812. [PMID: 36808278 DOI: 10.1007/s00253-023-12427-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/20/2023]
Abstract
Ruminiclostridium papyrosolvens is an anaerobic, mesophilic, and cellulolytic clostridia, promising consolidated bioprocessing (CBP) candidate for producing renewable green chemicals from cellulose, but its metabolic engineering is limited by lack of genetic tools. Here, we firstly employed the endogenous xylan-inducible promoter to control ClosTron system for gene disruption of R. papyrosolvens. The modified ClosTron can be easily transformed into R. papyrosolvens and specifically disrupt targeting genes. Furthermore, a counter selectable system based on uracil phosphoribosyl-transferase (Upp) was successfully established and introduced into the ClosTron system, which resulted in plasmid curing rapidly. Thus, the combination of xylan-inducible ClosTron and upp-based counter selectable system makes the gene disruption more efficient and convenient for successive gene disruption in R. papyrosolvens. KEY POINTS: • Limiting expression of LtrA enhanced the transformation of ClosTron plasmids in R. papyrosolvens. • DNA targeting specificity can be improved by precise management of the expression of LtrA. • Curing of ClosTron plasmids was achieved by introducing the upp-based counter selectable system.
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17
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Benito-Vaquerizo S, Nouse N, Schaap PJ, Hugenholtz J, Brul S, López-Contreras AM, Martins dos Santos VAP, Suarez-Diez M. Model-driven approach for the production of butyrate from CO 2/H 2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Front Microbiol 2022; 13:1064013. [PMID: 36620068 PMCID: PMC9815533 DOI: 10.3389/fmicb.2022.1064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Niels Nouse
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,UNLOCK Large Scale Infrastructure for Microbial Communities, Wageningen University and Research and Delft University of Technology, Wageningen, Netherlands
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Ana M. López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, Netherlands
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Maria Suarez-Diez ✉
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18
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Hu G, Liu L, Miao X, Zhao Y, Peng Y, Li X. Symbiotic bacteria stabilize the intestinal environment by producing phenylpropanoids. Microb Biotechnol 2022; 16:88-98. [PMID: 36448752 PMCID: PMC9803327 DOI: 10.1111/1751-7915.14180] [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: 09/02/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022] Open
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) can colonize in the intestinal tract of chickens and transmit to humans. In order to decrypt the mechanism of avian resistance to S. Enteritidis, we utilized two China local chicken breeds to generate the reciprocal crosses (the Cross and the Reverse-cross). The two lines of hybrids were orally inoculated with S. Enteritidis at 2-day old and sampled at 3 days post-inoculation. Along the analysis direction of multi-omics, differential metabolites, functional pathways and correlated microbes, we found that 12 species of microbes thrived upon S. Enteritidis challenge and probably contributed to the intestinal stability in the Cross by enhancing the production of phenylpropanoids. Our findings can help to understand the symbiotic and resistant mechanisms derived from the intestinal microbiota.
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Affiliation(s)
- Geng Hu
- College of Animal Science and Technology, Key Laboratory of Efficient Utilization of Non‐grain Feed Resources (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai'anChina
| | - Liying Liu
- College of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Xiuxiu Miao
- College of Animal Science and Technology, Key Laboratory of Efficient Utilization of Non‐grain Feed Resources (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai'anChina
| | - Yanan Zhao
- College of Animal Science and Technology, Key Laboratory of Efficient Utilization of Non‐grain Feed Resources (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai'anChina
| | - Yanan Peng
- College of Animal Science and Technology, Key Laboratory of Efficient Utilization of Non‐grain Feed Resources (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai'anChina
| | - Xianyao Li
- College of Animal Science and Technology, Key Laboratory of Efficient Utilization of Non‐grain Feed Resources (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTai'anChina
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19
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Baur T, Wentzel A, Dürre P. Production of propionate using metabolically engineered strains of Clostridium saccharoperbutylacetonicum. Appl Microbiol Biotechnol 2022; 106:7547-7562. [PMID: 36282302 PMCID: PMC9666320 DOI: 10.1007/s00253-022-12210-8] [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: 06/07/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022]
Abstract
Abstract The carboxylic acid propionate is a valuable platform chemical with applications in various fields. The biological production of this acid has become of great interest as it can be considered a sustainable alternative to petrochemical synthesis. In this work, Clostridium saccharoperbutylacetonicum was metabolically engineered to produce propionate via the acrylate pathway. In total, the established synthetic pathway comprised eight genes encoding the enzymes catalyzing the conversion of pyruvate to propionate. These included the propionate CoA-transferase, the lactoyl-CoA dehydratase, and the acryloyl-CoA reductase from Anaerotignum neopropionicum as well as a D-lactate dehydrogenase from Leuconostoc mesenteroides subsp. mesenteroides. Due to difficulties in assembling all genes on one plasmid under the control of standard promoters, the PtcdB-tcdR promoter system from Clostridium difficile was integrated into a two-plasmid system carrying the acrylate pathway genes. Several promoters were analyzed for their activity in C. saccharoperbutylacetonicum using the fluorescence-activating and absorption-shifting tag (FAST) as a fluorescent reporter to identify suitable candidates to drive tcdR expression. After selecting the lactose-inducible PbgaL promoter, engineered C. saccharoperbutylacetonicum strains produced 0.7 mM propionate upon induction of gene expression. The low productivity was suspected to be a consequence of a metabolic imbalance leading to acryloyl-CoA accumulation in the cells. To even out the proposed imbalance, the propionate-synthesis operons were rearranged, thereby increasing the propionate concentration by almost four-fold. This study is the first one to report recombinant propionate production using a clostridial host strain that has opened a new path towards bio-based propionate to be improved further in subsequent work. Key points • Determination of promoter activities in C. saccharoperbutylacetonicum using FAST. • Implementation of propionate production in C. saccharoperbutylacetonicum. • Elevation of propionate production by 375% to a concentration of 3 mM. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12210-8.
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20
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Yang Z, Leero DD, Yin C, Yang L, Zhu L, Zhu Z, Jiang L. Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks. BIORESOURCE TECHNOLOGY 2022; 361:127656. [PMID: 35872277 DOI: 10.1016/j.biortech.2022.127656] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.
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Affiliation(s)
- Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donald Delano Leero
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Chengtai Yin
- College of Overseas Education, Nanjing Tech University, Nanjing 211816, China
| | - Lei Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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21
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Tang H, Li P, Chen L, Ma JK, Guo HH, Huang XC, Zhong RM, Jing SQ, Jiang LW. The formation mechanisms of key flavor substances in stinky tofu brine based on metabolism of aromatic amino acids. Food Chem 2022; 392:133253. [DOI: 10.1016/j.foodchem.2022.133253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 11/04/2022]
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22
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A new method for screening and culture of Clostridium from pit mud under non-anaerobic conditions. J Microbiol Methods 2022; 200:106559. [PMID: 36007702 DOI: 10.1016/j.mimet.2022.106559] [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: 06/22/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 12/27/2022]
Abstract
Strong-flavor Baijiu (SFB) is produced in complex fermentation in pits under ground. Clostridium producing hexanoic acid plays a key role in the flavor formation of SFB. The screening and culture for Clostridium are very difficult because of its strict anaerobic characteristics. In this study, electric field assisted screening (EFAS) was used to screen Clostridium from pit mud, and electric culture (EC) was used to cultivate Clostridium under non-anaerobic conditions. A strain with a high yield of hexanoic acid was screened and named as Clostridium sp. EFAS6. Under non-anaerobic conditions, it grew rapidly only near the cathode end in the EFAS device because of the low oxidation-reduction potential of that electrode. In the experiment of high-density culture in the EC device, the cell concentration reached 106-107. After energy consumption was calculated, the optimal loading voltage was found to be 10 V. In the application, the broth of Clostridium sp. EFAS6 increased the content of ethyl hexanoic in SFB. Under non-anaerobic conditions, the anaerobe was screened by EFAS and cultivated in high density by EC. The EFAS and EC could also be used for the screening and culture of other anaerobes under non-anaerobic conditions.
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Otten JK, Zou Y, Papoutsakis ET. The potential of caproate (hexanoate) production using Clostridium kluyveri syntrophic cocultures with Clostridium acetobutylicum or Clostridium saccharolyticum. Front Bioeng Biotechnol 2022; 10:965614. [PMID: 36072287 PMCID: PMC9441933 DOI: 10.3389/fbioe.2022.965614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 11/18/2022] Open
Abstract
Caproate (hexanoate) and other medium-chain fatty acids are valuable platform chemicals produced by processes utilizing petroleum or plant oil. Clostridium kluyveri, growing on short chain alcohols (notably ethanol) and carboxylic acids (such as acetate) is noted for its ability to perform chain elongation to produce 4- to 8-carbon carboxylates. C. kluyveri has been studied in monoculture and coculture conditions, which lead to relatively modest carboxylate titers after long fermentation times. To assess the biosynthetic potential of C. kluyveri for caproate production from sugars through coculture fermentations, in the absence of monoculture data in the literature suitable for our coculture experiments, we first explored C. kluyveri monocultures. Some monocultures achieved caproate titers of 150 to over 200 mM in 40–50 h with a production rate of 7.9 mM/h. Based on that data, we then explored two novel, syntrophic coculture partners for producing caproate from sugars: Clostridium acetobutylicum and Clostridium saccharolyticum. Neither species has been cocultured with C. kluyveri before, and both demonstrate promising results. Our experiments of C. kluyveri monocultures and C. kluyveri—C. saccharolyticum cocultures demonstrate exceptionally high caproate titers (145–200 mM), fast production rates (3.25–8.1 mM/h), and short fermentation times (18–45 h). These results represent the most caproate produced by a C. kluyveri coculture in the shortest known fermentation time. We also explored the possibility of heterologous cell fusion between the coculture pairs similar to the results seen previously in our group with C. acetobutylicum and Clostridium ljungdahlii. Fusion events were observed only in the C. acetobutylicum—C. kluyveri coculture pair, and we offer an explanation for the lack of fusion between C. saccharolyticum and C. kluyveri. This work supports the promise of coculture biotechnology for sustainable production of caproate and other platform chemicals.
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Affiliation(s)
- Jonathan K. Otten
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Yin Zou
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Eleftherios T. Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
- *Correspondence: Eleftherios T. Papoutsakis,
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Vamsi Krishna K, Bharathi N, George Shiju S, Alagesan Paari K, Malaviya A. An updated review on advancement in fermentative production strategies for biobutanol using Clostridium spp. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:47988-48019. [PMID: 35562606 DOI: 10.1007/s11356-022-20637-9] [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: 12/12/2021] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
A significant concern of our fuel-dependent era is the unceasing exhaustion of petroleum fuel supplies. In parallel to this, environmental issues such as the greenhouse effect, change in global climate, and increasing global temperature must be addressed on a priority basis. Biobutanol, which has fuel characteristics comparable to gasoline, has attracted global attention as a viable green fuel alternative among the many biofuel alternatives. Renewable biomass could be used for the sustainable production of biobutanol by the acetone-butanol-ethanol (ABE) pathway. Non-extinguishable resources, such as algal and lignocellulosic biomass, and starch are some of the most commonly used feedstock for fermentative production of biobutanol, and each has its particular set of advantages. Clostridium, a gram-positive endospore-forming bacterium that can produce a range of compounds, along with n-butanol is traditionally known for its biobutanol production capabilities. Clostridium fermentation produces biobased n-butanol through ABE fermentation. However, low butanol titer, a lack of suitable feedstock, and product inhibition are the primary difficulties in biobutanol synthesis. Critical issues that are essential for sustainable production of biobutanol include (i) developing high butanol titer producing strains utilizing genetic and metabolic engineering approaches, (ii) renewable biomass that could be used for biobutanol production at a larger scale, and (iii) addressing the limits of traditional batch fermentation by integrated bioprocessing technologies with effective product recovery procedures that have increased the efficiency of biobutanol synthesis. Our paper reviews the current progress in all three aspects of butanol production and presents recent data on current practices in fermentative biobutanol production technology.
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Affiliation(s)
- Kondapalli Vamsi Krishna
- Applied and Industrial Biotechnology Laboratory, CHRIST (Deemed-to-Be University), Hosur road, Bangalore, Karnataka, India
| | - Natarajan Bharathi
- Department of Life Sciences, CHRIST (Deemed to Be University), Bengaluru, India
| | - Shon George Shiju
- Applied and Industrial Biotechnology Laboratory, CHRIST (Deemed-to-Be University), Hosur road, Bangalore, Karnataka, India
| | | | - Alok Malaviya
- Applied and Industrial Biotechnology Laboratory, CHRIST (Deemed-to-Be University), Hosur road, Bangalore, Karnataka, India.
- Department of Life Sciences, CHRIST (Deemed to Be University), Bengaluru, India.
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Onyeaka H, Ekwebelem OC. A review of recent advances in engineering bacteria for enhanced CO 2 capture and utilization. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2022; 20:4635-4648. [PMID: 35755182 PMCID: PMC9207427 DOI: 10.1007/s13762-022-04303-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Carbon dioxide (CO2) is emitted into the atmosphere due to some anthropogenic activities, such as the combustion of fossil fuels and industrial output. As a result, fears about catastrophic global warming and climate change have intensified. In the face of these challenges, conventional CO2 capture technologies are typically ineffective, dangerous, and contribute to secondary pollution in the environment. Biological systems for CO2 conversion, on the other hand, provide a potential path forward owing to its high application selectivity and adaptability. Moreover, many bacteria can use CO2 as their only source of carbon and turn it into value-added products. The purpose of this review is to discuss recent significant breakthroughs in engineering bacteria to utilize CO2 and other one-carbon compounds as substrate. In the same token, the paper also summarizes and presents aspects such as microbial CO2 fixation pathways, engineered bacteria involved in CO2 fixation, up-to-date genetic and metabolic engineering approaches for CO2 fixation, and promising research directions for the production of value-added products from CO2. This review's findings imply that using biological systems like modified bacteria to manage CO2 has the added benefit of generating useful industrial byproducts like biofuels, pharmaceutical compounds, and bioplastics. The major downside, from an economic standpoint, thus far has been related to methods of cultivation. However, thanks to genetic engineering approaches, this can be addressed by large production yields. As a result, this review aids in the knowledge of various biological systems that can be used to construct a long-term CO2 mitigation technology at an industrial scale, in this instance bacteria-based CO2capture/utilization technology.
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Affiliation(s)
- H. Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - O. C. Ekwebelem
- Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001 Nigeria
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Gut microbiome and daytime function in Chinese patients with major depressive disorder. J Psychosom Res 2022; 157:110787. [PMID: 35344817 DOI: 10.1016/j.jpsychores.2022.110787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Major depressive disorder (MDD) is underscored by daytime dysfunction-associated features, including mood disturbances, impaired cognition, fatigue, and daytime sleepiness. Importantly, the gut-brain axis may represent a potential mechanistic link between MDD and daytime dysfunction. Therefore, this study aimed to explore the gut microbiome composition and daytime dysfunction in Chinese patients with MDD. METHODS We enrolled 36 patients with MDD and 45 healthy controls (HCs) matched by age, sex, and body mass index (BMI). Daytime function including emotion, fatigue, and sleepiness were assessed using the Epworth Sleepiness Scale (ESS), Fatigue Severity Scale (FSS), Hamilton Anxiety Scale (HAMA), and Hamilton Depression Scale (HAMD). 16S rRNA sequencing was employed to characterize the gut microbiota in stool samples. RESULTS The operational taxonomic units (OTUs) OTU255, OUT363 were positively correlated with HAMD and HAMA. OTU244, OTU542 and OTU221 were positively correlated with ESS, HAMD and HAMA. OTU725 and OTU80 were positively correlated with FSS, ESS, HAMD and HAMA, while OTU423 and OTU502 were negatively correlated with all above. Flavonifractor positively correlated with fatigue in patients with MDD and all individuals simultaneously. The correlation between gut microbiome and daytime function was different in MDD and HCs. CONCLUSIONS We identified several OTUs associated with the severity of fatigue, depression, daytime sleepiness and anxiety in all individuals. Our results revealed the differences in microbiome found between patients with MDD and HCs. These findings provide insights into the potential microbiota changes that occur in MDD, and will enable the development of specific therapeutic strategies for targeting the various symptoms of depression.
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Lee H, Bae J, Jin S, Kang S, Cho BK. Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization. Front Microbiol 2022; 13:865168. [PMID: 35615514 PMCID: PMC9124964 DOI: 10.3389/fmicb.2022.865168] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood–Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.
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Affiliation(s)
- Hyeonsik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- *Correspondence: Byung-Kwan Cho,
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The Measurement, Application and Effect of Oxygen in Microbial Fermentations: Focusing on Methane and Carboxylate Production. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8040138] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Oxygen is considered detrimental to anaerobic fermentation processes by many practitioners. However, deliberate oxygen sparging has been used successfully for decades to remove H2S in anaerobic digestion (AD) systems. Moreover, microaeration techniques during AD have shown that small doses of oxygen may enhance process performance and promote the in situ degradation of recalcitrant compounds. However, existing oxygen dosing techniques are imprecise, which has led to inconsistent results between studies. At the same time, real-time oxygen fluxes cannot be reliably quantified due to the complexity of most bioreactor systems. Thus, there is a pressing need for robust monitoring and process control in applications where oxygen serves as an operating parameter or an experimental variable. This review summarizes and evaluates the available methodologies for oxygen measurement and dosing as they pertain to anaerobic microbiomes. The historical use of (micro-)aeration in anaerobic digestion and its potential role in other anaerobic fermentation processes are critiqued in detail. This critique also provides insights into the effects of oxygen on these microbiomes. Our assessment suggests that oxygen dosing, when implemented in a controlled and quantifiable manner, could serve as an effective tool for bioprocess engineers to further manipulate anaerobic microbiomes for either bioenergy or biochemical production.
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29
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Mennella JA, Li Y, Bittinger K, Friedman ES, Zhao C, Li H, Wu GD, Trabulsi JC. The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status. Nutrients 2022; 14:nu14061241. [PMID: 35334900 PMCID: PMC8951061 DOI: 10.3390/nu14061241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
This proof-of-principle study analyzed fecal samples from 30 infants who participated in a randomized controlled trial on the effects of the macronutrient composition of infant formula on growth and energy balance. In that study, infants randomized to be fed cow milk formula (CMF) had faster weight-gain velocity during the first 4 months and higher weight-for-length Z scores up to 11.5 months than those randomized to an isocaloric extensive protein hydrolysate formula (EHF). Here we examined associations among infant formula composition, gut microbial composition and maturation, and children’s weight status. Fecal samples collected before and monthly up to 4.5 months after randomization were analyzed by shotgun metagenomic sequencing and targeted metabolomics. The EHF group had faster maturation of gut microbiota than the CMF group, and increased alpha diversity driven by Clostridia taxa. Abundance of Ruminococcus gnavus distinguished the two groups after exclusive feeding of the assigned formula for 3 months. Abundance of Clostridia at 3–4 months negatively correlated with prior weight-gain velocity and body weight phenotypes when they became toddlers. Macronutrient differences between the formulas likely led to the observed divergence in gut microbiota composition that was associated with differences in transient rapid weight gain, a well-established predictor of childhood obesity and other comorbidities.
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Affiliation(s)
| | - Yun Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (Y.L.); (H.L.)
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (K.B.); (C.Z.)
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (E.S.F.); (G.D.W.)
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (K.B.); (C.Z.)
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (Y.L.); (H.L.)
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (E.S.F.); (G.D.W.)
| | - Jillian C. Trabulsi
- Department of Behavioral Health and Nutrition, University of Delaware, Newark, DE 19713, USA
- Correspondence: ; Tel.: +1-302-831-4991
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30
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Huang JR, Chen X, Hu BB, Cheng JR, Zhu MJ. Bioaugmentation combined with biochar to enhance thermophilic hydrogen production from sugarcane bagasse. BIORESOURCE TECHNOLOGY 2022; 348:126790. [PMID: 35104653 DOI: 10.1016/j.biortech.2022.126790] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
In this study, Thermoanaerobacterium thermosaccharolyticum MJ2 and biochar were used to enhance thermophilic hydrogen production from sugarcane bagasse. MJ2 bioaugmentation notably increased the hydrogen production by 95.31%, which was further significantly improved by 158.10% by adding biochar. The addition of biochar promoted the degradation of substrate, improved the activities of hydrogenase and electron transfer system, and stimulated microbial growth and metabolism. Microbial community analysis showed that the relative abundance of Thermoanaerobacterium was significantly increased by bioaugmentation and further enriched by biochar. PICRUSt analysis showed that MJ2 combined with biochar promoted metabolic pathways related to substrate degradation and microbial metabolism. This study provides a novel enhancement method for hydrogen production of the cellulolytic microbial consortium by exogenous hydrogen-producing microorganism combined with biochar and deepens the understanding of its functional mechanism.
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Affiliation(s)
- Jin-Rong Huang
- School of Biology and Biological Engineering, Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou 510006, China
| | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, Hubei, China
| | - Bin-Bin Hu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
| | - Jing-Rong Cheng
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China
| | - Ming-Jun Zhu
- School of Biology and Biological Engineering, Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou 510006, China; Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, Hubei, China; College of Life and Geographic Sciences, The Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis at Colleges & Universities under the Department of Education of Xinjiang Uygur Autonomous Region, Kashi University, Kashi 844000, China.
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Dahle ML, Papoutsakis ET, Antoniewicz MR. 13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions. Metab Eng 2022; 72:161-170. [DOI: 10.1016/j.ymben.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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Oceguera-Contreras E, Aguilar-Juarez O, Oseguera-Galindo D, Macías-Barragán J, Ortiz-Torres G, Luisa Pita-López M, Domínguez J, Titov I, Kamen A. Establishment of the upstream processing for renewable production of hydrogen using vermicomposting-tea and molasses as substrate. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 139:279-289. [PMID: 34995855 DOI: 10.1016/j.wasman.2021.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
This study aimed to establish the optimal operational conditions for hydrogen production using vermicomposting-tea and sugarcane molasses as substrate. The experiments were carried out by triplicate in 110 ml serological bottles, a Box-Behnken design of experiments was performed in anaerobic dark conditions. The maximal hydrogen production (HP), hydrogen production rate (HPR), and hydrogen yield (HY) attained were 1021.0 mlL-1, 5.32 mlL-1h-1, and 60.3 mlLH2-1/gTCC, respectively. The statistical model showed that the optimal operational conditions for pH, molasses concentration, and temperature were 6.5; 30 % (v/v) and 25 °C. The bioreactor run showed 17.202 L of hydrogen, 0.58 Lh-1, and 77.2 mlH2gTCC-1 For HP, HPR, and HY. Chemometric analysis for the volatile fatty acids obtained at the fermentation showed that only two principal components are required to explain 90 % of the variance. The representative pathways for hydrogen production were acetic and butyric acids. This study established the operational conditions for the upstream processing amenable to pilot and industrial-scale operations. Our results add value to molasses within the circular economy for hydrogen production using a novel consortium from vermicompost.
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Affiliation(s)
- Edén Oceguera-Contreras
- Laboratorio de Sistemas Biológicos, Centro Universitario de los Valles, Universidad de Guadalajara. Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México.
| | - Oscar Aguilar-Juarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Avenida de los normalistas No. 800, Colinas de la Normal, C.P. 4470, Guadalajara, Jalisco, México
| | - David Oseguera-Galindo
- Laboratorio de Sistemas Biológicos, Centro Universitario de los Valles, Universidad de Guadalajara. Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México
| | - José Macías-Barragán
- Laboratorio de Sistemas Biológicos, Centro Universitario de los Valles, Universidad de Guadalajara. Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México
| | - Gerardo Ortiz-Torres
- Laboratorio de Mecatrónica, Centro Universitario de los Valles, Universidad de Guadalajara, Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México
| | - María Luisa Pita-López
- Centro de Investigación en Biología Molecular de las Enfermedades Crónicas (CIBIMEC). Centro Universitario del Sur, Universidad de Guadalajara, Av. Enrique Arreola Silva No. 883, C.P. 49000. Zapotlán el Grande, Jalisco, México
| | - Jorge Domínguez
- Departamento de Ecología e Bioloxía Animal (GEA), Universidad de Vigo. As lagoas Marcosende, Vigo E-36310, Vigo, España
| | - Igor Titov
- Technological Institute of Information and Electronic Radio, Vladimir University, 600026, Vladimir st, Gorki d. 87, Vladimir, Russia
| | - Amine Kamen
- Department of Bioengineering, 3480 Rue University, McConnell Engineering Building, McGill University, Montreal, QC H3A OE9, Canada
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Purification and anti-inflammatory effect of selenium-containing protein fraction from selenium-enriched Spirulina platensis. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2021.101469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Hong Y, Zeng AP. Biosynthesis Based on One-Carbon Mixotrophy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:351-371. [DOI: 10.1007/10_2021_198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Zhang J, Zhang Y, Liu R, Cai R, Liu F, Sun C. Iocasia fonsfrigidae NS-1 gen. nov., sp. nov., a Novel Deep-Sea Bacterium Possessing Diverse Carbohydrate Metabolic Pathways. Front Microbiol 2021; 12:725159. [PMID: 34899621 PMCID: PMC8652127 DOI: 10.3389/fmicb.2021.725159] [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: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Resolving metabolisms of deep-sea microorganisms is crucial for understanding ocean energy cycling. Here, a strictly anaerobic, Gram-negative strain NS-1 was isolated from the deep-sea cold seep in the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NS-1 was most closely related to the type strain Halocella cellulosilytica DSM 7362T (with 92.52% similarity). A combination of phylogenetic, genomic, and physiological traits with strain NS-1, was proposed to be representative of a novel genus in the family Halanaerobiaceae, for which Iocasia fonsfrigidae NS-1 was named. It is noteworthy that I. fonsfrigidae NS-1 could metabolize multiple carbohydrates including xylan, alginate, starch, and lignin, and thereby produce diverse fermentation products such as hydrogen, lactate, butyrate, and ethanol. The expressions of the key genes responsible for carbohydrate degradation as well as the production of the above small molecular substrates when strain NS-1 cultured under different conditions, were further analyzed by transcriptomic methods. We thus predicted that part of the ecological role of Iocasia sp. is likely in the fermentation of products from the degradation of diverse carbohydrates to produce hydrogen as well as other small molecules, which are in turn utilized by other members of cold seep microbes.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,School of Life Sciences, Hebei University, Baoding, China
| | - Yuechao Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence. Nat Rev Microbiol 2021; 19:774-785. [PMID: 34183820 PMCID: PMC9191689 DOI: 10.1038/s41579-021-00583-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.
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Liu G, Li P, Hou L, Niu Q, Pu G, Wang B, Du T, Kim SW, Niu P, Li Q, Huang R. Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs. Front Microbiol 2021; 12:746717. [PMID: 34867862 PMCID: PMC8637618 DOI: 10.3389/fmicb.2021.746717] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022] Open
Abstract
Making full use of high fiber and low-cost crop coproducts is helpful to alleviate the situation of people and livestock competing for crops. Digestion of dietary fibers in pigs is mainly through microbial fermentation in the large intestine. To reveal microbiota related to fiber digestion in pigs, fecal samples have been collected from 274 healthy female Suhuai pigs at 160 days of age under the same feeding conditions and have measured apparent neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility. Samples from Suhuai pigs with extreme high and low apparent NDF digestibility and extreme high and low apparent ADF digestibility were subjected to shotgun metagenomic sequencing. At the species level, 62 microbial species in H_NDF group and 54 microbial species in H_ADF group were related to high fiber digestibility. Among them, Lachnospiraceae bacterium 3-1 and Alistipes sp. CAG:514 may be new types of microorganisms associated with fiber digestion. In addition, we found that more abundant GH5 and GH48 family (contribute to cellulose degradation) genes, GH39 and GH53 family (contribute to hemicellulose degradation) genes in microorganisms may contribute to the higher apparent NDF digestibility of pigs, and more abundant GH3 and GH9 family (contribute to cellulose degradation) genes in microorganisms may contribute to the higher apparent ADF digestibility of pigs. The abundance of AA4 family (helps in lignin degradation) genes in H_NDF and H_ADF groups was significantly higher than that in L_NDF and L_ADF groups, respectively (P < 0.05). Three pathways in H_NDF group and four pathways in H_ADF group are important pathways associated with degradation of non-starch polysaccharides, and their relative abundance is significantly higher than that in L_NDF and L_ADF groups, respectively. Gut microbiota of Suhuai pigs with high apparent fiber digestibility had higher abundance of genes and microbiota related to fiber digestion and may have stronger fiber digestion potential compared with low apparent fiber digestibility group. This study revealed that the characteristics of gut microbiota and microbial gene functions of pigs with high fiber apparent digestibility, which provided a theoretical basis and reference for further understanding the impact of gut microbiota on fiber digestibility of pigs.
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Affiliation(s)
- Gensheng Liu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Liming Hou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Qing Niu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guang Pu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Binbin Wang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Taoran Du
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
| | - Peipei Niu
- Huaian Academy of Nanjing Agricultural University, Huaian, China
| | - Qiang Li
- Huaiyin Xinhuai Pig Breeding Farm, Huaian, China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy of Nanjing Agricultural University, Huaian, China
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38
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Schneider M, Bäumler M, Lee NM, Weuster-Botz D, Ehrenreich A, Liebl W. Monitoring co-cultures of Clostridium carboxidivorans and Clostridium kluyveri by fluorescence in situ hybridization with specific 23S rRNA oligonucleotide probes. Syst Appl Microbiol 2021; 44:126271. [PMID: 34735802 DOI: 10.1016/j.syapm.2021.126271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
The development of co-cultures of clostridial strains which combine different physiological traits represents a promising strategy to achieve the environmentally friendly production of biofuels and chemicals. For the optimization of such co-cultures it is essential to monitor their composition and stability throughout fermentation. FISH is a quick and sensitive method for the specific labeling and quantification of cells within microbial communities. This technique is neither limited by the anaerobic fermenter environment nor by the need of prior genetic modification of strains. In this study, two specific 23S rRNA oligonucleotide probes, ClosKluy and ClosCarb, were designed for the monitoring of C. kluyveri and C. carboxidivorans, respectively. After the optimization of hybridization conditions for both probes, which was achieved at 30% (v/v) formamide, a high specificity was observed with epifluorescence microscopy using cells from different pure reference strains. The discriminating properties of the ClosKluy and ClosCarb probes was verified with samples from heterotrophic co-cultures in anaerobic flasks as well as autotrophic stirred-tank bioreactor co-cultures of C. kluyveri and C. carboxidivorans. Besides being suited to monitor defined co-cultures of these two species, the new specific FISH oligonucleotide probes for C. kluyveri and C. carboxidivorans additionally have potential to be applied in environmental studies.
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Affiliation(s)
- Martina Schneider
- Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany
| | - Miriam Bäumler
- Department of Mechanical Engineering, Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Natuschka M Lee
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Research Infrastructure Fluorescence in Situ Hybridization (FISH), Chemical Biological Centre, Umeå University, Umeå, Sweden
| | - Dirk Weuster-Botz
- Department of Mechanical Engineering, Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Armin Ehrenreich
- Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany.
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Freising, Germany
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39
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Ma S, Yang D, Xu K, Li K, Ren H. Bacterial survival strategies in sludge alkaline fermentation for volatile fatty acids production: Study on the physiological properties, temporal evolution and spatial distribution of bacterial community. BIORESOURCE TECHNOLOGY 2021; 340:125701. [PMID: 34352644 DOI: 10.1016/j.biortech.2021.125701] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the dynamics of ATP synthase activity, phospholipid fatty acid (PLFA) profile, and temporal evolution and spatial distribution of bacterial community to analyze bacterial survival strategies in sludge alkaline fermentation (SAF) for volatile fatty acids (VFAs) production. The results revealed a significant increase in ATP synthase activity at pH 9 and 10 (p < 0.05), which could contribute to proton entry into cells and benefit bacterial survival. PLFA analysis indicated that the unsaturated fatty acids content increased with the increase of pH. Firmicutes were the dominant microorganisms in the running stage of the pH 10 reactor (35.81-62.34%) and might have been the key microbes that influenced VFAs production. Further analysis of the spatial distribution of microbial community suggested that Firmicutes mainly lived inside flocs during SAF. These findings provide an understanding for bacterial survival strategies in SAF, which could help to develop methods to further improve VFAs yield.
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Affiliation(s)
- Sijia Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Dongli Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China.
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40
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Miguel MA, Kim SH, Lee SS, Cho YI. Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses. Animals (Basel) 2021; 11:2937. [PMID: 34679958 PMCID: PMC8532636 DOI: 10.3390/ani11102937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.
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Affiliation(s)
| | | | | | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.A.M.); (S.-H.K.); (S.-S.L.)
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41
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Meng Q, Li P, Qu J, Liu Y, Wang Y, Chen Z, Zhang Y. Study on the community structure and function of anaerobic granular sludge under trichloroethylene stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1408-1418. [PMID: 33471269 DOI: 10.1007/s10646-020-02343-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Trichloroethylene (TCE) is one of the most common groundwater pollutants. It is carcinogenic, teratogenic, mutagenic and poses a serious threat to human health and the environment. Therefore, reducing the environmental toxicity of TCE is of great significance. Anaerobic sludge was cultured and acclimated in an upflow anaerobic sludge blanket (UASB) reactor in this study. The Chemical Oxygen Demand (COD) concentration of the influent was approximately 2500 mg L-1, and the TCE concentration of the influent ranged from 1.46 mg L-1 to 73 mg L-1. After biodegradation of the anaerobic microflora, the COD removal rate was approximately 85%, and the TCE removal rate was over 85%. The microbial community of anaerobic sludge was analysed by 16 S rDNA clone libray and 454 high-throughput sequencing. Through analysis of the sequencing results, we found that there were a variety of acid-forming bacteria, anaerobic dechlorinating bacteria, and methanogenic bacteria. Based on the analysis of microflora function, it was speculated that the TCE metabolic pathway took place in UASB reactors. Desulfovibrio and Syntrophobacter provided an anaerobic environment, and acid-forming bacteria metabolise organic compounds into hydrogen. With Dehalobacter and Geobacter, TCE as an electron acceptor is dechlorinated and reduced under the anaerobic environment, in which hydrogen acts as an electron donor. By this, we clarified the metabolic pathway for improving TCE bioremediation.
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Affiliation(s)
- Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Jianhua Qu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yifan Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, 116600, China
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
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42
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Montaño López J, Duran L, Avalos JL. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol 2021; 20:35-48. [PMID: 34341566 DOI: 10.1038/s41579-021-00600-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.
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Affiliation(s)
- José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA. .,Princeton Environmental Institute, Princeton University, Princeton, NJ, USA.
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43
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Morvan C, Folgosa F, Kint N, Teixeira M, Martin-Verstraete I. Responses of Clostridia to oxygen: from detoxification to adaptive strategies. Environ Microbiol 2021; 23:4112-4125. [PMID: 34245087 DOI: 10.1111/1462-2920.15665] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022]
Abstract
Clostridia comprise bacteria of environmental, biotechnological and medical interest and many commensals of the gut microbiota. Because of their strictly anaerobic lifestyle, oxygen is a major stress for Clostridia. However, recent data showed that these bacteria can cope with O2 better than expected for obligate anaerobes through their ability to scavenge, detoxify and consume O2 . Upon O2 exposure, Clostridia redirect their central metabolism onto pathways less O2 -sensitive and induce the expression of genes encoding enzymes involved in O2 -reduction and in the repair of oxidized damaged molecules. While Faecalibacterium prausnitzii efficiently consumes O2 through a specific extracellular electron shuttling system requiring riboflavin, enzymes such as rubrerythrins and flavodiiron proteins with NAD(P)H-dependent O2 - and/or H2 O2 -reductase activities are usually encoded in other Clostridia. These two classes of enzymes play indeed a pivotal role in O2 tolerance in Clostridioides difficile and Clostridium acetobutylicum. Two main signalling pathways triggering O2 -induced responses have been described so far in Clostridia. PerR acts as a key regulator of the O2 - and/or reactive oxygen species-defence machinery while in C. difficile, σB , the sigma factor of the general stress response also plays a crucial role in O2 tolerance by controlling the expression of genes involved in O2 scavenging and repair systems.
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Affiliation(s)
- Claire Morvan
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Nicolas Kint
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, F-75015, France
- Institut Universitaire de France, Paris, France
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44
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Ibrahim M, Raajaraam L, Raman K. Modelling microbial communities: Harnessing consortia for biotechnological applications. Comput Struct Biotechnol J 2021; 19:3892-3907. [PMID: 34584635 PMCID: PMC8441623 DOI: 10.1016/j.csbj.2021.06.048] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Microbes propagate and thrive in complex communities, and there are many benefits to studying and engineering microbial communities instead of single strains. Microbial communities are being increasingly leveraged in biotechnological applications, as they present significant advantages such as the division of labour and improved substrate utilisation. Nevertheless, they also present some interesting challenges to surmount for the design of efficient biotechnological processes. In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that enable us to characterise and understand the metabolic capabilities of microbial communities. Complementary approaches to model microbial communities, such as those based on graph theory, are also briefly discussed. Taken together, these methods provide rich insights into the interactions between microbes and how they influence microbial community productivity. We finally overview approaches that allow us to generate and test numerous synthetic community compositions, followed by tools and methodologies that can predict effective genetic interventions to further improve the productivity of communities. With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological processes.
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Affiliation(s)
- Maziya Ibrahim
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Lavanya Raajaraam
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
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45
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Wang Q, Al Makishah NH, Li Q, Li Y, Liu W, Sun X, Wen Z, Yang S. Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production. Front Bioeng Biotechnol 2021; 9:661694. [PMID: 34164382 PMCID: PMC8215697 DOI: 10.3389/fbioe.2021.661694] [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: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Naief H Al Makishah
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wenzheng Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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46
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Diallo M, Kengen SWM, López-Contreras AM. Sporulation in solventogenic and acetogenic clostridia. Appl Microbiol Biotechnol 2021; 105:3533-3557. [PMID: 33900426 PMCID: PMC8102284 DOI: 10.1007/s00253-021-11289-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.
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Affiliation(s)
- Mamou Diallo
- Wageningen Food and Biobased Research, Wageningen, The Netherlands.
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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47
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Fackler N, Heijstra BD, Rasor BJ, Brown H, Martin J, Ni Z, Shebek KM, Rosin RR, Simpson SD, Tyo KE, Giannone RJ, Hettich RL, Tschaplinski TJ, Leang C, Brown SD, Jewett MC, Köpke M. Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation. Annu Rev Chem Biomol Eng 2021; 12:439-470. [PMID: 33872517 DOI: 10.1146/annurev-chembioeng-120120-021122] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.
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Affiliation(s)
- Nick Fackler
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | | | - Blake J Rasor
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Hunter Brown
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Jacob Martin
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Zhuofu Ni
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Kevin M Shebek
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Rick R Rosin
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Séan D Simpson
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Keith E Tyo
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | | | - Ching Leang
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Steven D Brown
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , , .,Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, USA
| | - Michael Köpke
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
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48
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Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture. mSystems 2021; 6:6/1/e01325-20. [PMID: 33622858 PMCID: PMC8573953 DOI: 10.1128/msystems.01325-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum-evolved H2 and through acquisition of C. acetobutylicum-native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community.IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum/C. ljungdahlii culture is a novel observation that has not been explored in silico The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.
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Shi XC, Tremblay PL, Wan L, Zhang T. Improved robustness of microbial electrosynthesis by adaptation of a strict anaerobic microbial catalyst to molecular oxygen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142440. [PMID: 33254866 DOI: 10.1016/j.scitotenv.2020.142440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
Microbial electrosynthesis (MES) and other bioprocesses such as syngas fermentation developed for energy storage and the conversion of carbon dioxide into valuable chemicals often employs acetogens as microbial catalysts. Acetogens are sensitive to molecular oxygen, which means that bioproduction reactors must be maintained under strict anaerobic conditions. This requirement increases cost and does not eliminate the possibility of O2 leakage. For MES, the risk is even greater since the system generates O2 when water splitting is the anodic reaction. Here, we show that O2 from the anode of a MES reactor diffuses into the cathode chamber where strict anaerobes reduce CO2. To overcome this drawback, a stepwise adaptive laboratory evolution (ALE) strategy is used to develop the O2 tolerance of the acetogen Sporomusa ovata. Two heavily-mutated S. ovata strains growing well autotrophically in the presence of 0.5 to 5% O2 were obtained. The adapted strains were more performant in the MES system than the wild type converting electrical energy and CO2 into acetate 1.5 fold faster. This study shows that the O2 tolerance of acetogens can be increased, which leads to improvement of the performance and robustness of energy-storage bioprocesses such as MES where O2 is an inhibitor.
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Affiliation(s)
- Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Lulu Wan
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China.
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Branska B, Vasylkivska M, Raschmanova H, Jureckova K, Sedlar K, Provaznik I, Patakova P. Changes in efflux pump activity of Clostridium beijerinckii throughout ABE fermentation. Appl Microbiol Biotechnol 2021; 105:877-889. [PMID: 33409609 DOI: 10.1007/s00253-020-11072-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 12/05/2020] [Accepted: 12/17/2020] [Indexed: 01/08/2023]
Abstract
Pumping toxic substances through a cytoplasmic membrane by protein transporters known as efflux pumps represents one bacterial mechanism involved in the stress response to the presence of toxic compounds. The active efflux might also take part in exporting low-molecular-weight alcohols produced by intrinsic cell metabolism; in the case of solventogenic clostridia, predominantly acetone, butanol and ethanol (ABE). However, little is known about this active efflux, even though some evidence exists that membrane pumps might be involved in solvent tolerance. In this study, we investigated changes in overall active efflux during ABE fermentation, employing a flow cytometric protocol adjusted for Clostridia and using ethidium bromide (EB) as a fluorescence marker for quantification of direct efflux. A fluctuation in efflux during the course of standard ABE fermentation was observed, with a maximum reached during late acidogenesis, a high efflux rate during early and mid-solventogenesis and an apparent decrease in EB efflux rate in late solventogenesis. The fluctuation in efflux activity was in accordance with transcriptomic data obtained for various membrane exporters in a former study. Surprisingly, under altered cultivation conditions, when solvent production was attenuated, and extended acidogenesis was promoted, stable low efflux activity was reached after an initial peak that appeared in the stage comparable to standard ABE fermentation. This study confirmed that efflux pump activity is not constant during ABE fermentation and suggests that undisturbed solvent production might be a trigger for activation of pumps involved in solvent efflux. KEY POINTS: • Flow cytometric assay for efflux quantification in Clostridia was established. • Efflux rate peaked in late acidogenesis and in early solventogenesis. • Impaired solventogenesis led to an overall decrease in efflux.
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Affiliation(s)
- Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic.
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Hana Raschmanova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00, Brno, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00, Brno, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
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