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Chen C, Yang H, Zhang K, Ye G, Luo H, Zou W. Revealing microbiota characteristics and predicting flavor-producing sub-communities in Nongxiangxing baijiu pit mud through metagenomic analysis and metabolic modeling. Food Res Int 2024; 188:114507. [PMID: 38823882 DOI: 10.1016/j.foodres.2024.114507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum, Caproicibacterium, Petrimonas, Lactobacillus, Clostridium, Aminobacterium, Syntrophomonas, Methanobacterium, Methanoculleus, and Methanosarcina. The important enzymes ofPMwere in bothGH and GT familymetabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium, Sphaerochaeta, Muricomes intestini, Methanobacteriaceae, Synergistaceae, and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite-microbiome association and further bioregulation of baijiu.
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Affiliation(s)
- Cong Chen
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Huibo Luo
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, Sichuan 644005, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China; Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, Sichuan 644005, China.
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2
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Atasoy M, Scott WT, Regueira A, Mauricio-Iglesias M, Schaap PJ, Smidt H. Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches. Biotechnol Adv 2024; 73:108363. [PMID: 38657743 DOI: 10.1016/j.biotechadv.2024.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Department of Environmental Technology, Wageningen University & Research, Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
| | - William T Scott
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
| | - Alberte Regueira
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, Belgium.
| | - Miguel Mauricio-Iglesias
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Peter J Schaap
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
| | - Hauke Smidt
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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3
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Zhao H, Du B, Zhao P, Chen X, Zhao J, Wu Q, Zhu L, Ma H, Sun B, Min W, Li X. Analysis of ester-producing performance in high-yield ethyl hexanoate yeast and the effect on metabolites in bio- enhanced Daqu, the starter for Baijiu and other traditional fermented foods. J Appl Microbiol 2024; 135:lxae081. [PMID: 38565314 DOI: 10.1093/jambio/lxae081] [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: 11/10/2023] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/04/2024]
Abstract
AIMS Ethyl hexanoate, one of the key flavor compounds in strong-flavor Baijiu. To improve the content of ethyl hexanoate in strong-flavor Baijiu, a functional strain with high yield of ethyl hexanoate was screened and its ester-producing performance was studied. METHODS AND RESULTS Upon identification, the strain was classified as Candida sp. and designated as ZY002. Under optimal fermentation conditions, the content of ethyl hexanoate synthesized by ZY002 can be as high as 170.56 mg L-1. A fermentation test was carried out using the ZY002 strain bioaugmented Daqu to verify the role of the strain applied to Baijiu brewing. It was found that strain ZY002 could not only improve the moisture and alcohol contents of fermented grains but also diminish the presence of reducing sugar and crude starch. Furthermore, it notably amplified the abundance of flavor compounds. CONCLUSION In this study, Candida sp. ZY002 with a high yield of ethyl hexanoate provided high-quality strain resources for the actual industrial production of Baijiu.
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Affiliation(s)
- He Zhao
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Binghao Du
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Pengju Zhao
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xi Chen
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Jingrong Zhao
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qiuhua Wu
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Lining Zhu
- Hebei Fenglaiyi Distillery Co., Ltd., Xingtai, Hebei 055550, China
| | - Huifeng Ma
- Hebei Fenglaiyi Distillery Co., Ltd., Xingtai, Hebei 055550, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weihong Min
- College of Food and Health, Zhejiang A & F University, Hangzhou 311300, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber Of Commerce, Beijing 100048, China
- China Bio-Specialty Food Enzyme Technology Research Development and Promotion Center, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
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Scott WT, Benito-Vaquerizo S, Zimmermann J, Bajić D, Heinken A, Suarez-Diez M, Schaap PJ. A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. PLoS Comput Biol 2023; 19:e1011363. [PMID: 37578975 PMCID: PMC10449394 DOI: 10.1371/journal.pcbi.1011363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
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Affiliation(s)
- William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
| | - Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany
| | - Djordje Bajić
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Almut Heinken
- Inserm U1256 Laboratoire nGERE, Université de Lorraine, Nancy, France
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
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5
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Huo W, Ye R, Shao Y, Bao M, Stegmann R, Lu W. Enhanced ethanol-driven carboxylate chain elongation by Pt@C in simulated sequencing batch reactors: Process and mechanism. BIORESOURCE TECHNOLOGY 2023:129310. [PMID: 37315622 DOI: 10.1016/j.biortech.2023.129310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
Carboxylate chain elongation can create value-added bioproducts from the organic waste. The effects of Pt@C on chain elongation and associated mechanisms were investigated in simulated sequencing batch reactors. 5.0 g/L of Pt@C greatly increased the synthesis of caproate, with an average yield of 21.5 g COD/L, which was 207.4% higher than the trial without Pt@C. Integrated metagenomic and metaproteomic analyses were used to reveal the mechanism of Pt@C-enhanced chain elongation. Pt@C enriched chain elongators by increasing the relative abundance of dominant species by 115.5%. The expression of functional genes related to chain elongation was promoted in the Pt@C trial. This study also demonstrates that Pt@C may promote overall chain elongation metabolism by enhancing CO2 uptake of Clostridium kluyveri. The study provides insights into the fundamental mechanisms of how chain elongation can perform CO2 metabolism and how it can be enhanced by Pt@C to upgrade bioproducts from organic waste streams.
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Affiliation(s)
- Weizhong Huo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Rong Ye
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuchao Shao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Menggang Bao
- School of Environment, Tsinghua University, Beijing 100084, China
| | | | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China.
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6
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Schroeder WL, Kuil T, van Maris AJA, Olson DG, Lynd LR, Maranas CD. A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis. Metab Eng 2023; 77:306-322. [PMID: 37085141 DOI: 10.1016/j.ymben.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/24/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023]
Abstract
Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PPi) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PPi sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PPi synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PPi-generating cycles. In all cases, the metabolic cost of PPi synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PPi could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PPi sources likely account for most PPi production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PPi levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.
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Affiliation(s)
- Wheaton L Schroeder
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Bioenergy Innovation, Oak Ridge, TN, USA
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Center for Bioenergy Innovation, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- Center for Bioenergy Innovation, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; Center for Bioenergy Innovation, Oak Ridge, TN, USA.
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7
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Feng J, Guo X, Cai F, Fu H, Wang J. Model-based driving mechanism analysis for butyric acid production in Clostridium tyrobutyricum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:71. [PMID: 35752796 PMCID: PMC9233315 DOI: 10.1186/s13068-022-02169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Butyric acid, an essential C4 platform chemical, is widely used in food, pharmaceutical, and animal feed industries. Clostridium tyrobutyricum is the most promising microorganism for industrial bio-butyrate production. However, the metabolic driving mechanism for butyrate synthesis was still not profoundly studied.
Results
This study reports a first-generation genome-scale model (GEM) for C. tyrobutyricum, which provides a comprehensive and systematic analysis for the butyrate synthesis driving mechanisms. Based on the analysis in silico, an energy conversion system, which couples the proton efflux with butyryl-CoA transformation by two redox loops of ferredoxin, could be the main driving force for butyrate synthesis. For verifying the driving mechanism, a hydrogenase (HydA) expression was perturbed by inducible regulation and knockout. The results showed that HydA deficiency significantly improved the intracellular NADH/NAD+ rate, decreased acetate accumulation (63.6% in serum bottle and 58.1% in bioreactor), and improved the yield of butyrate (26.3% in serum bottle and 34.5% in bioreactor). It was in line with the expectation based on the energy conversion coupling driving mechanism.
Conclusions
This work show that the first-generation GEM and coupling metabolic analysis effectively promoted in-depth understanding of the metabolic driving mechanism in C. tyrobutyricum and provided a new insight for tuning metabolic flux direction in Clostridium chassis cells.
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Miao Z, Hao H, Yan R, Wang X, Wang B, Sun J, Li Z, Zhang Y, Sun B. Individualization of Chinese alcoholic beverages: Feasibility towards a regulation of organic acids. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Liu C, Du Y, Zheng J, Qiao Z, Luo H, Zou W. Production of caproic acid by Rummeliibacillus suwonensis 3B-1 isolated from the pit mud of strong-flavor baijiu. J Biotechnol 2022; 358:33-40. [PMID: 36049550 DOI: 10.1016/j.jbiotec.2022.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022]
Abstract
Caproic acid is the precursor of ethyl caproate, the main representative flavor substance of strong-flavor baijiu (SFB). Caproic acid-producing bacteria are considered to be the most important type of acid-producing microorganisms in the pit mud of the SFB ecosystem. In this study, the Rummeliibacillus suwonensis 3B-1 with a high yield of caproic acid (4.064g/L) was screened from SFB pit mud. The genome of the R. suwonensis 3B-1 was sequenced, the total size was found to be 4,117,671bp and a calculated GC content of 35.86%. The caproic acid biosynthesis pathway was identified and analyzed, and it showed that 3B-1 could not only use ethanol, but it could also use glucose and other carbon sources as substrates to produce caproic acid. According to the genome analysis and with an optimized medium, the optimal conditions for caproic acid production were yeast powder at 3g/L, sodium acetate at 15g/L, and 1% biotin at 8mL/100mL. The yield of caproic acid reached 4.627g/L, an increase of 13.9%, which was higher than that of general caproic acid bacteria. This is the first report of the synthesis of caproic acid by R. suwonensis. This strain could be used to produce caproic acid, an artificial pit mud preparation, and/or an enhanced inoculum in the production of SFB.
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Affiliation(s)
- Chaojie Liu
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Yuanfen Du
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Jia Zheng
- Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Wuliangye Group, Yibin, Sichuan 644007, China
| | - Zongwei Qiao
- Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Wuliangye Group, Yibin, Sichuan 644007, China
| | - Huibo Luo
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China.
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10
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Kim H, Kang S, Sang BI. Metabolic cascade of complex organic wastes to medium-chain carboxylic acids: A review on the state-of-the-art multi-omics analysis for anaerobic chain elongation pathways. BIORESOURCE TECHNOLOGY 2022; 344:126211. [PMID: 34710599 DOI: 10.1016/j.biortech.2021.126211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Medium-chain carboxylic acid (MCCA) production from organic wastes has attracted much attention because of their higher energy contents and diverse applications. Anaerobic reactor microbiomes are stable and resilient and have resulted in efficient performance during many years of operation for thousands of full-scale anaerobic digesters worldwide. The method underlying how the relevant microbial pathways contribute to elongate carbon chains in reactor microbiomes is important. In particular, the reverse β-oxidation pathway genes are critical to upgrading short-chain fermentation products to MCCAs via a chain elongation (CE) process. Diverse genomics and metagenomics studies have been conducted in various fields, ranging from intracellular metabolic pathways to metabolic cascades between different strains. This review covers taxonomic approach to culture processes depending on types of organic wastes and the deeper understanding of genome and metagenome-scale CE pathway construction, and the co-culture and multi-omics technology that should be addressed in future research.
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Affiliation(s)
- Hyunjin Kim
- Department of Chemical Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Seongcheol Kang
- Department of Chemical Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea.
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Qian W, Lu ZM, Chai LJ, Zhang XJ, Li Q, Wang ST, Shen CH, Shi JS, Xu ZH. Cooperation within the microbial consortia of fermented grains and pit mud drives organic acid synthesis in strong-flavor Baijiu production. Food Res Int 2021; 147:110449. [PMID: 34399451 DOI: 10.1016/j.foodres.2021.110449] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 10/21/2022]
Abstract
Mud cellars have long been used as anaerobic bioreactors for the fermentation of Chinese strong-flavor Baijiu, where starchy raw materials (mainly sorghum) are metabolized to ethanol and various flavor compounds by multi-species microorganisms. Jiupei (fermented grains) and pit mud are two spatially linked microbial habitats in the mud cellar, yet their metabolic division of labor remains unclear. Here, we investigated the changes in environmental variables (e.g., temperature, oxygen, pH), key metabolites (e.g., ethanol, organic acids) and microbial communities in jiupei and pit mud during fermentation. Jiupei (low pH, high ethanol) and pit mud (neutral pH) provided two habitats with distinctly different environmental conditions for microbial growth. Lactic acid accumulated in jiupei, while butyric and hexanoic acids were mainly produced by microbes inhabiting the pit mud. Biomass analysis using quantitative real-time PCR showed that bacteria dominated the microbial consortia during fermentation, moreover cluster and principal coordinate analysis (PCoA) analysis showed that the bacterial communities of jiupei and pit mud were significantly divergent. The bacterial community diversity of jiupei decreased significantly during the fermentation process, and was relatively stable in pit mud. Lactobacillus dominated the jiupei bacterial community, and its relative abundance reached 98.0% at the end of fermentation. Clostridia (relative abundance: 42.9-85.5%) was the most abundant bacteria in pit mud, mainly distributed in the genus Hydrogenispora (5.3-68.4%). Fungal communities of jiupei and pit mud showed a similar succession pattern, and Kazachstania, Aspergillus and Thermoascus were the predominant genera. PICRUSt analysis demonstrated that enzymes participating in the biosynthesis of acetic and lactic acid were mainly enriched in jiupei samples, while the bacterial community in the pit mud displayed greater potential for butyric and hexanoic acid synthesis. Assays from an in vitro simulated fermentation further validated the roles of jiupei microbiota in acetic and lactic acid production, and these acids were subsequently metabolized to butyric and hexanoic acid by the pit mud microbiota. This work has demonstrated the synergistic cooperation between the microbial communities of jiupei and pit mud for the representative flavor formation of strong-flavor Baijiu.
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Affiliation(s)
- Wei Qian
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Li-Juan Chai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xiao-Juan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Song-Tao Wang
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Cai-Hong Shen
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Jin-Song Shi
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China.
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12
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Dahal S, Zhao J, Yang L. Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0061-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Du Y, Zou W, Zhang K, Ye G, Yang J. Advances and Applications of Clostridium Co-culture Systems in Biotechnology. Front Microbiol 2020; 11:560223. [PMID: 33312166 PMCID: PMC7701477 DOI: 10.3389/fmicb.2020.560223] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/20/2020] [Indexed: 01/09/2023] Open
Abstract
Clostridium spp. are important microorganisms that can degrade complex biomasses such as lignocellulose, which is a widespread and renewable natural resource. Co-culturing Clostridium spp. and other microorganisms is considered to be a promising strategy for utilizing renewable feed stocks and has been widely used in biotechnology to produce bio-fuels and bio-solvents. In this review, we summarize recent progress on the Clostridium co-culture system, including system unique advantages, composition, products, and interaction mechanisms. In addition, biochemical regulation and genetic modifications used to improve the Clostridium co-culture system are also summarized. Finally, future prospects for Clostridium co-culture systems are discussed in light of recent progress, challenges, and trends.
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Affiliation(s)
- Yuanfen Du
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China.,Research Laboratory of Baijiu Resource Microorgannisms and Big Data, Sichuan University of Science and Engineering, Yibin, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China.,Research Laboratory of Baijiu Resource Microorgannisms and Big Data, Sichuan University of Science and Engineering, Yibin, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China
| | - Jiangang Yang
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China
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14
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Benito-Vaquerizo S, Diender M, Parera Olm I, Martins Dos Santos VAP, Schaap PJ, Sousa DZ, Suarez-Diez M. Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids. Comput Struct Biotechnol J 2020; 18:3255-3266. [PMID: 33240469 PMCID: PMC7658664 DOI: 10.1016/j.csbj.2020.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
We model a co-culture of C. autoethanogenum and C. kluyveri for syngas fermentation. Biomass species ratio affects ethanol and acetate profiles in the co-culture. The model predicts that addition of succinate increases caproate production. Genetic interventions in C. autoethanogenum could increase caproate production.
Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use of Clostridium species for the production of small organic molecules such as ethanol and acetate. The co-cultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri on syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that one strategy to optimize the production of medium-chain fatty-acids from syngas would be the addition of succinate. According to the prediction, addition of succinate would increase the pool of crotonyl-CoA and the ethanol/acetate uptake ratio in C. kluyveri, resulting in a flux of up to 60% of electrons into hexanoate. Another potential way to further optimize butyrate and hexanoate production would be an increase of C. autoethanogenum ethanol production. Blocking either acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) activity or formate transport, in the C. autoethanogenum metabolic model could potentially lead to an up to 150% increase in ethanol production.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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15
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Vees CA, Neuendorf CS, Pflügl S. Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives. J Ind Microbiol Biotechnol 2020; 47:753-787. [PMID: 32894379 PMCID: PMC7658081 DOI: 10.1007/s10295-020-02296-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
Abstract
The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.
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Affiliation(s)
- Charlotte Anne Vees
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Christian Simon Neuendorf
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
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16
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Li X, Henson MA. Metabolic modeling of bacterial co-culture systems predicts enhanced carbon monoxide-to-butyrate conversion compared to monoculture systems. Biochem Eng J 2019; 151. [PMID: 32863734 DOI: 10.1016/j.bej.2019.107338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We used metabolic modeling to computationally investigate the potential of bacterial coculture system designs for CO conversion to the platform chemical butyrate. By taking advantage of the native capabilities of wild-type strains, we developed two anaerobic coculture designs by combining Clostridium autoethanogenum for CO-to-acetate conversion with bacterial strains that offer high acetate-to-butyrate conversion capabilities: the environmental bacterium the human gut bacteriumEubacterium rectale. When grown in continuous stirred tank reactor on a 70/0/30 CO/H2/N2 gas mixture, the C. autoethanogenum-C Kluyveri co-culture was predicted to offer no mprovement in butyrate volumetric productivity compared to an engineered C. autoethanogenum monoculture despite utilizing vinyl acetate as a secondary carbon source for C. kluyveri growth enhancement. A coculture consisting of C. autoethanogenum and C. kluyveri engineered in silico to eliminate hexanoate synthesis was predicted to enhance both butyrate productivity and titer. The C. autoethanogenum-E. rectale coculture offered similar improvements in butyrate productivity without the need for metabolic engineering when glucose was provided as a secondary carbon source to enhance E. rectale growth. A bubble column model developed to assess the potential for large-scale butyrate production of the C. autoethanogenum-E. rectale design predicted that a 40/30/30 CO/H2/N2 gas mixture and a 5 m column length would be preferred to enhance C. autoethanogenum growth and counteract CO inhibitory effects on E. rectale.
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Affiliation(s)
- Xiangan Li
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, 01003, USA
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17
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San-Valero P, Fernández-Naveira Á, Veiga MC, Kennes C. Influence of electron acceptors on hexanoic acid production by Clostridium kluyveri. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 242:515-521. [PMID: 31075646 DOI: 10.1016/j.jenvman.2019.04.093] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/12/2019] [Accepted: 04/22/2019] [Indexed: 05/12/2023]
Abstract
Clostridium kluyveri was used for chain elongation of C2C4 fatty acids in stirred tank bioreactors. The influence of different electron acceptors (acetic acid, butyric acid and the mixture of both) on C6 fatty acid production was evaluated in presence of ethanol using similar molar alcohol/acid ratios around 3.5. Bottle batch assays without pH regulation and with only acetic acid as electron acceptor yielded a final C6 fatty acid concentration of 6.8 ± 0.6 g L-1. Then, pH-regulated bioreactors were operated at constant pH of 6.8. Under such conditions, the maximum growth rate was 0.039 h-1 obtained using acetic acid and butyric acid as electron acceptors, whereas the lowest growth rate was 0.010 h-1 with only butyric acid as electron acceptor. The maximum growth rate with acetic acid only, was similar, though slightly lower, as with the mixture of C2C4 fatty acids. Besides, the maximum productions of hexanoic acid were 11.8 g L-1, 13.1 g L-1 and 21.2 g L-1 using, respectively, acetic acid, butyric acid and the mixture of both acids as electron acceptors. Thus, the use of a mixture of acetic acid and butyric acid in presence of ethanol for chain elongation, at constant pH, proved to be efficient for hexanoic acid production.
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Affiliation(s)
- P San-Valero
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of La Coruña (UDC), Rúa da Fraga 10, E-15008, La Coruña, Spain
| | - Á Fernández-Naveira
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of La Coruña (UDC), Rúa da Fraga 10, E-15008, La Coruña, Spain
| | - M C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of La Coruña (UDC), Rúa da Fraga 10, E-15008, La Coruña, Spain
| | - C Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of La Coruña (UDC), Rúa da Fraga 10, E-15008, La Coruña, Spain.
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