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Yang S, Li K, Liu H, Lu J, Yang H, Wu D. Enhancing citric acid tolerance of Acetobacter tropicalis using chemical and physical mutagenesis and adaptive evolution to improve the quality of lemon fruit vinegar. J Food Sci 2024; 89:2581-2596. [PMID: 38551187 DOI: 10.1111/1750-3841.17031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 05/19/2024]
Abstract
The high concentration of citric acid in lemons limits the production of lemon fruit vinegar because it inhibits the metabolism of acetic acid bacteria and reduces the utilization of raw materials. This study aimed to enhance the citric acid tolerance of Acetobacter tropicalis by using complex mutagenesis and adaptive laboratory evolution (ALE) and improving the quality of lemon fruit vinegar. After mutagenesis and ALE, A. tropicalis JY-135 grew well under 40 g/L citric acid, and it showed high physiological activity and excellent fermentation performance under high concentrations of citric acid. The survival rate and ATP content of JY-135 were 15.27 and 9.30 times higher than that of the original strain J-2736. In the fermentation of lemon fruit vinegar, the acid production and the number of aroma-active compounds were 1.61-fold and 2.17-fold than J-2736. In addition, we found that citric acid tolerance of JY-135 is related to the respiratory electron-transport chain and the tricarboxylic acid (TCA) cycle. This work is of great significance for the production of high-quality lemon fruit vinegar and the enrichment of seed resources of acetic acid bacteria.
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Affiliation(s)
- Shaojie Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Kang Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Hua Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Hua Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Dianhui Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
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2
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Román-Camacho JJ, Mauricio JC, Santos-Dueñas IM, García-Martínez T, García-García I. Recent advances in applying omic technologies for studying acetic acid bacteria in industrial vinegar production: A comprehensive review. Biotechnol J 2024; 19:e2300566. [PMID: 38403443 DOI: 10.1002/biot.202300566] [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: 10/20/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Vinegar and related bioproducts containing acetic acid as the main component are among the most appreciated fermented foodstuffs in numerous European and Asian countries because of their exceptional organoleptic and bio-healthy properties. Regarding the acetification process and obtaining of final products, there is still a lack of knowledge on fundamental aspects, especially those related to the study of biodiversity and metabolism of the present microbiota. In this context, omic technologies currently allow for the massive analysis of macromolecules and metabolites for the identification and characterization of these microorganisms working in their natural media without the need for isolation. This review approaches comprehensive research on the application of omic tools for the identification of vinegar microbiota, mainly acetic acid bacteria, with subsequent emphasis on the study of the microbial diversity, behavior, and key molecular strategies used by the predominant groups throughout acetification. The current omics tools are enabling both the finding of new vinegar microbiota members and exploring underlying strategies during the elaboration process. The species Komagataeibacter europaeus may be a model organism for present and future research in this industry; moreover, the development of integrated meta-omic analysis may facilitate the achievement of numerous of the proposed milestones. This work might provide useful guidance for the vinegar industry establishing the first steps towards the improvement of the acetification conditions and the development of new products with sensory and bio-healthy profiles adapted to the agri-food market.
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Affiliation(s)
- Juan J Román-Camacho
- Department of Agricultural Chemistry, Edaphology, and Microbiology (Microbiology area), Severo Ochoa building (C6), Agrifood Campus of International Excellence ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Juan C Mauricio
- Department of Agricultural Chemistry, Edaphology, and Microbiology (Microbiology area), Severo Ochoa building (C6), Agrifood Campus of International Excellence ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Inés María Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering (Chemical Engineering area), Instituto Químico Para la Energía y el Medioambiente (IQUEMA), Marie Curie building (C3), Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), Universidad de Córdoba, Córdoba, Spain
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology, and Microbiology (Microbiology area), Severo Ochoa building (C6), Agrifood Campus of International Excellence ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering (Chemical Engineering area), Instituto Químico Para la Energía y el Medioambiente (IQUEMA), Marie Curie building (C3), Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), Universidad de Córdoba, Córdoba, Spain
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3
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Li T, Wang X, Li C, Fu Q, Shi X, Wang B. Investigation of Acid Tolerance Mechanism of Acetobacter pasteurianus under Different Concentrations of Substrate Acetic Acid Based on 4D Label-Free Proteomic Analysis. Foods 2023; 12:4471. [PMID: 38137274 PMCID: PMC10742644 DOI: 10.3390/foods12244471] [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: 11/23/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Acetobacter pasteurianus is always used to brew vinegar because of its ability of producing and tolerating a high concentration of acetic acid. During vinegar fermentation, initial acetic acid contributes to acetic acid accumulation, which varies with initial concentrations. In this study, to investigate the mechanisms of tolerating and producing acetic acid of Acetobacter pasteurianus under different concentrations of substrate acetic acid, four-dimensional label-free proteomic technology has been used to analyze the protein profiles of Acetobacter pasteurianus at different growth stages (the lag and exponential phases) and different substrate acetic acid concentrations (0%, 3%, and 6%). A total of 2093 proteins were quantified in this study. The differentially expressed proteins were majorly involved in gene ontology terms of metabolic processes, cellular metabolic processes, and substance binding. Under acetic acid stress, strains might attenuate the toxicity of acetic acid by intensifying fatty acid metabolism, weakening the tricarboxylic acid cycle, glycerophospholipid and energy metabolism during the lag phase, while strains might promote the assimilation of acetic acid and inter-conversion of substances during the exponential phase by enhancing the tricarboxylic acid cycle, glycolysis, pyruvate, and energy metabolism to produce and tolerate acid. Besides, cell cycle regulation and protein translation might be potential acid tolerance pathways under high acid stress. The result contributes to the exploration of new potential acid tolerance mechanisms in Acetobacter pasteurianus from four-dimensional label-free relative quantitative proteomics analysis.
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Affiliation(s)
| | | | | | | | | | - Bin Wang
- Food College, Shihezi University, Shihezi 832000, China
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4
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Liao C, Na B, Tang X, Zhao M, Zhang C, Chen S, You M, Bai B, Hao L, Tondrob D, Qu G, Yang S, Huang B, Gou W, Xie Y, Bai S, Chen C, Li P. Contribution of the bacterial community of poorly fermented oat silage to biogas emissions on the Qinghai Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165336. [PMID: 37414176 DOI: 10.1016/j.scitotenv.2023.165336] [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: 04/04/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
To better utilize poorly fermented oat silage on the Qinghai Tibetan Plateau, 239 samples of this biomass were collected from the plateau temperate zone (PTZ), plateau subboreal zone (PSBZ), and nonplateau climatic zone (NPCZ) in the region and analyzed for microbial community, chemical composition and in vitro gas production. Climatic factors affect the bacterial α-diversity and β-diversity of poorly fermented oat silage, which led to the NPCZ having the highest relative abundance of Lactiplantibacillus plantarum. Furthermore, the gas production analysis showed that the NPCZ had the highest maximum cumulative gas emissions of methane. Through structural equation modeling analysis, environmental factors (solar radiation) affected methane emissions via the regulation of lactate production by L. plantarum. The enrichment of L. plantarum contributes to lactic acid production and thereby enhances methane emission from poorly fermented oat silage. Notably, there are many lactic acid bacteria detrimental to methane production in the PTZ. This knowledge will be helpful in revealing the mechanisms of environmental factors and microbial relationships influencing the metabolic processes of methane production, thereby providing a reference for the clean utilization of other poorly fermented silage.
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Affiliation(s)
- Chaosheng Liao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Binbin Na
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xiaolong Tang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Man Zhao
- Sichuan Academy of Grassland Sciences, Chengdu 611731, China
| | - Changbing Zhang
- Sichuan Academy of Grassland Sciences, Chengdu 611731, China
| | - Shiyong Chen
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Minghong You
- Sichuan Academy of Grassland Sciences, Chengdu 611731, China
| | - Binqiang Bai
- College of Agricultural Science, Qinghai University, Xining 810016, China
| | - Lizhuang Hao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Dorjeeh Tondrob
- Institute of Pratacultural Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850000, China
| | - Guangpeng Qu
- Institute of Pratacultural Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850000, China
| | - Shuqing Yang
- Tibet Institute of Modern Life and Health, Lhasa 850000, China
| | - Bo Huang
- Tibet Jingliang Agriculture and Animal Husbandry Industry Development Co, Lhasa 850000, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu 611731, China
| | - Yixiao Xie
- College of Animal Science, Guizhou University, Guiyang, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu 611731, China
| | - Chao Chen
- College of Animal Science, Guizhou University, Guiyang, China
| | - Ping Li
- College of Animal Science, Guizhou University, Guiyang, China; Sichuan Academy of Grassland Sciences, Chengdu 611731, China.
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5
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Gao L, Shi W, Xia X. Genomic Plasticity of Acid-Tolerant Phenotypic Evolution in Acetobacter pasteurianus. Appl Biochem Biotechnol 2023; 195:6003-6019. [PMID: 36738389 DOI: 10.1007/s12010-023-04353-9] [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] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Acetic acid bacteria have a remarkable capacity to cope with elevated concentrations of cytotoxic acetic acid in their fermentation environment. In particular, the high-level acetate tolerance of Acetobacter pasteurianus that occurs in vinegar industrial settings must be constantly selected for. However, the improved acetic acid tolerance is rapidly lost without a selection pressure. To understand genetic and molecular biology of this acquired acetic acid tolerance in A. pasteurianus, we evolved three strains A. pasteurianus CICIM B7003, CICIM B7003-02, and ATCC 33,445 over 960 generations (4 months) in two initial acetic acids of 20 g·L-1 and 30 g·L-1, respectively. An acetic acid-adapted strain M20 with significantly improved specific growth rate of 0.159 h-1 and acid productivity of 1.61 g·L-1·h-1 was obtained. Comparative genome analysis of six evolved strains revealed that the genetic variations of adaptation were mainly focused on lactate metabolism, membrane proteins, transcriptional regulators, transposases, replication, and repair system. Among of these, lactate dehydrogenase, acetolactate synthase, glycosyltransferase, ABC transporter ATP-binding protein, two-component regulatory systems, the type II toxin-antitoxin system (RelE/RelB/StbE), exodeoxyribonuclease III, type I restriction endonuclease, tRNA-uridine 2-sulfurtransferase, and transposase might collaboratively contribute to the improved acetic acid tolerance in A. pasteurianus strains. The balance between repair factors and transposition variations might be the basis for genomic plasticity of A. pasteurianus strains, allowing the survival of populations and their offspring in acetic acid stress fluctuations. These observations provide important insights into the nature of acquired acetic acid tolerance phenotype and lay a foundation for future genetic manipulation of these strains.
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Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Wei Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [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: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Heo J, Sombolestani AS, Laureys D, De Clippeleer J, Won M, Vandamme P, Kwon SW. Acetobacter vaccinii sp. nov., a novel acetic acid bacterium isolated from blueberry fruit ( Vaccinium corymbosum L.). Int J Syst Evol Microbiol 2022; 72. [PMID: 36748597 DOI: 10.1099/ijsem.0.005614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Strain C17-3T was isolated from blueberry fruits collected from a farmland located in Damyang-gun, Jeollanam-do, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain C17-3T to the genus Acetobacter, where it occupied a rather isolated line of descent with Acetobacter ghanensis 430AT and Acetobacter lambici LMG 27439T as the nearest neighbours (98.9 % sequence similarity to both species). The highest average nucleotide identity and digital DNA-DNA hybridization values were 76.3 % and 21.7 % with Acetobacter garciniae TBRC 12339T; both values were well below the cutoff values for species delineation. Cells are strictly aerobic, Gram-stain-negative rods, catalase-positive and oxidase-negative. The DNA G+C content calculated from the genome sequence was 59.2 %. Major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C19 : 0cyclo ω8c. The major isoprenoid quinone was ubiquinone 9. On the basis of the results of phylogenetic analyses, phenotypic features and genomic comparisons, it is proposed that strain C17-3T represents a novel species of the genus Acetobacter and the name Acetobacter vaccinii sp. nov. is proposed. The type strain is C17-3T (= KACC 21233T = LMG 31758T).
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - David Laureys
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Jessika De Clippeleer
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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8
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Effects of different acetic acid bacteria strains on the bioactive compounds, volatile compounds and antioxidant activity of black tea vinegar. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Anguluri K, La China S, Brugnoli M, Cassanelli S, Gullo M. Better under stress: Improving bacterial cellulose production by Komagataeibacter xylinus K2G30 (UMCC 2756) using adaptive laboratory evolution. Front Microbiol 2022; 13:994097. [PMID: 36312960 PMCID: PMC9605694 DOI: 10.3389/fmicb.2022.994097] [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: 07/14/2022] [Accepted: 09/26/2022] [Indexed: 11/24/2022] Open
Abstract
Among naturally produced polymers, bacterial cellulose is receiving enormous attention due to remarkable properties, making it suitable for a wide range of industrial applications. However, the low yield, the instability of microbial strains and the limited knowledge of the mechanisms regulating the metabolism of producer strains, limit the large-scale production of bacterial cellulose. In this study, Komagataeibacter xylinus K2G30 was adapted in mannitol based medium, a carbon source that is also available in agri-food wastes. K. xylinus K2G30 was continuously cultured by replacing glucose with mannitol (2% w/v) for 210 days. After a starting lag-phase, in which no changes were observed in the utilization of mannitol and in bacterial cellulose production (cycles 1–25), a constant improvement of the phenotypic performances was observed from cycle 26 to cycle 30, accompanied by an increase in mannitol consumption. At cycle 30, the end-point of the experiment, bacterial cellulose yield increased by 38% in comparision compared to cycle 1. Furthermore, considering the mannitol metabolic pathway, D-fructose is an intermediate in the bioconversion of mannitol to glucose. Based on this consideration, K. xylinus K2G30 was tested in fructose-based medium, obtaining the same trend of bacterial cellulose production observed in mannitol medium. The adaptive laboratory evolution approach used in this study was suitable for the phenotypic improvement of K. xylinus K2G30 in bacterial cellulose production. Metabolic versatility of the strain was confirmed by the increase in bacterial cellulose production from D-fructose-based medium. Moreover, the adaptation on mannitol did not occur at the expense of glucose, confirming the versatility of K2G30 in producing bacterial cellulose from different carbon sources. Results of this study contribute to the knowledge for designing new strategies, as an alternative to the genetic engineering approach, for bacterial cellulose production.
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Yang H, He Y, Liao J, Li X, Zhang J, Liebl W, Chen F. RNA-Seq transcriptomic analysis reveals gene expression profiles of acetic acid bacteria under high-acidity submerged industrial fermentation process. Front Microbiol 2022; 13:956729. [PMID: 36246236 PMCID: PMC9557201 DOI: 10.3389/fmicb.2022.956729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Acetic acid bacteria (AAB) are Gram-negative obligate aerobics in Acetobacteraceae family. Producing acetic acid and brewing vinegars are one of the most important industrial applications of AAB, attributed to their outstanding ability to tolerate the corresponding stresses. Several unique acid resistance (AR) mechanisms in AAB have been revealed previously. However, their overall AR strategies are still less-comprehensively clarified. Consequently, omics analysis was widely performed for a better understanding of this field. Among them, transcriptome has recently obtained more and more attention. However, most currently reported transcriptomic studies were conducted under lab conditions and even in low-acidity environment, which may be unable to completely reflect the conditions that AAB confront under industrialized vinegar-brewing processes. In this study, we performed an RNA-Seq transcriptomic analysis concerning AAB’s AR mechanisms during a continuous and periodical industrial submerged vinegar fermentation process, where a single AAB strain performed the fermentation and the acetic acid concentration fluctuated between ~8% and ~12%, the highest acidity as far we know for transcriptomic studies. Samples were directly taken from the initial (CK), mid, and final stages of the same period of the on-going fermentation. 16S rRNA sequence analysis indicated the participation of Komagataeibacter europaeus in the fermentation. Transcriptomic results demonstrated that more genes were downregulated than upregulated at both mid and final stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrich analysis reflected that the upregulated genes mainly carried out tricarboxylic acid cycle and oxidative phosphorylation processes, probably implying a considerable role of acetic acid overoxidation in AR during fermentation. Besides, upregulation of riboflavin biosynthesis pathway and two NAD+-dependent succinate-semialdehyde dehydrogenase-coding genes suggested a critical role of succinate oxidation in AR. Meanwhile, downregulated genes were mainly ribosomal protein-coding ones, reflecting that the adverse impact on ribosomes initiates at the transcription level. However, it is ambiguous whether the downregulation is good for stress responding or it actually reflects the stress. Furthermore, we also assumed that the fermentation stages may have a greater effect on gene expression than acidity. Additionally, it is possible that some physiological alterations would affect the AR to a larger extent than changes in gene expression, which suggests the combination of molecular biology and physiology research will provide deeper insight into the AR mechanisms in AAB.
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Affiliation(s)
- Haoran Yang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Yating He
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Liao
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xin Li
- Jiangsu Hengshun Vinegar Industry Co., Ltd, Zhenjiang, Jiangsu, China
| | - Junhong Zhang
- Jiangsu Hengshun Vinegar Industry Co., Ltd, Zhenjiang, Jiangsu, China
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- *Correspondence: Fusheng Chen,
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11
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Gao L, Wu X, Li C, Xia X. Exploitation of Strong Constitutive and Stress-driven Promoters from Acetobacter pasteurianus for Improving Acetic acid Tolerance. J Biotechnol 2022; 350:24-30. [PMID: 35390361 DOI: 10.1016/j.jbiotec.2022.03.013] [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: 11/13/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
Abstract
Acetobacter pasteurianus is an excellent cell factory for production of highly-strength acetic acid, and attracts an increasing attention in metabolic engineering. However, the available well-characterized constitutive and inducible promoters are rather limited to adjust metabolic fluxes in A. pasteurianus. In this study, we screened a panel of constitutive and acid stress-driven promoters based on time-series of RNA-seq data and characterized in A. pasteurianus and Escherichia coli. Nine constitutive promoters ranged in strength from 1.7-fold to 100-fold that of the well-known strong promoter Padh under non-acetic acid environment. Subsequently, an acetic acid-stable red fluorescent visual reporting system was established and applied to evaluate acid stress-driven promoter in A. pasteurianus during highly-acidic fermentation environment. PgroES was identified as acid stress-driven strong promoters, with expression outputs varied from 100% to 200% when acetic acid treatment. To assess their application potential, ultra-strong constitutive promoter Ptuf and acid stress-driven strong promoter PgroES were selected to overexpress acetyl-CoA synthase and greatly improved acetic acid tolerance. Notably, the acid stress-driven promoter displayed more favorable for regulating strain robustness against acid stress by overexpressing tolerance gene. In summary, this is the first well-characterized constitutive and acid stress-driven promoter library from A. pasteurianus, which could be used as a promising toolbox for metabolic engineering in acetic acid bacteria and other gram-negative bacteria.
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Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, PR China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Chenyu Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, PR China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China.
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Santana de Carvalho D, Trovatti Uetanabaro AP, Kato RB, Aburjaile FF, Jaiswal AK, Profeta R, De Oliveira Carvalho RD, Tiwar S, Cybelle Pinto Gomide A, Almeida Costa E, Kukharenko O, Orlovska I, Podolich O, Reva O, Ramos PIP, De Carvalho Azevedo VA, Brenig B, Andrade BS, de Vera JPP, Kozyrovska NO, Barh D, Góes-Neto A. The Space-Exposed Kombucha Microbial Community Member Komagataeibacter oboediens Showed Only Minor Changes in Its Genome After Reactivation on Earth. Front Microbiol 2022; 13:782175. [PMID: 35369445 PMCID: PMC8970348 DOI: 10.3389/fmicb.2022.782175] [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: 09/23/2021] [Accepted: 02/01/2022] [Indexed: 11/23/2022] Open
Abstract
Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (space-exposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications.
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Affiliation(s)
- Daniel Santana de Carvalho
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Paula Trovatti Uetanabaro
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Postgraduate Program in Biology and Biotechnology of Microorganisms, Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Brazil
| | - Rodrigo Bentes Kato
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Profeta
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Dias De Oliveira Carvalho
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwar
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anne Cybelle Pinto Gomide
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eduardo Almeida Costa
- Computational Biology and Biotechnological Information Management Center (NBCGIB), State University of Santa Cruz, Ilhéus, Brazil
| | - Olga Kukharenko
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Orlovska
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Pablo Ivan P. Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Institute Gonçalo Moniz, Oswaldo Cruz Foundation (FIOCRUZ-Bahia), Salvador, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Brazil
| | - Jean-Pierre P. de Vera
- German Aerospace Center (DLR) Berlin, Institute of Planetary Research, Planetary Laboratories, Astrobiological Laboratories, Berlin, Germany
| | | | - Debmalya Barh
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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13
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Song J, Wang J, Wang X, Zhao H, Hu T, Feng Z, Lei Z, Li W, Zheng Y, Wang M. Improving the Acetic Acid Fermentation of Acetobacter pasteurianus by Enhancing the Energy Metabolism. Front Bioeng Biotechnol 2022; 10:815614. [PMID: 35350179 PMCID: PMC8957916 DOI: 10.3389/fbioe.2022.815614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Energy metabolism is important for cell growth and tolerance against environment stress. In acetic acid fermentation by Acetobacter pasteurianus, the correlation coefficients of acid production rate with energy charge and ATP content were 0.9981 and 0.9826, respectively. The main energy metabolism pathway, including glycolysis pathway, TCA cycle, ethanol oxidation, pentose phosphate pathway, and ATP production, was constructed by transcriptome analysis. The effects of fermentation conditions, including dissolved oxygen, initial acetic acid concentration, and total concentration, on acetic acid fermentation and energy metabolism of A. pasteurianus were analyzed by using the RT-PCR method. The results showed the high energy charge inhibited glucose catabolism, and associated with the high ethanol oxidation rate. Consequently, a virtuous circle of increased ethanol oxidation, increased energy generation, and acetic acid tolerance was important for improving acetic acid fermentation.
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Affiliation(s)
- Jia Song
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xinyu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tao Hu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhiwei Feng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhi Lei
- Tian Di No. 1 Beverage Inc., Jiangmen, China
| | - Weizhao Li
- Tian Di No. 1 Beverage Inc., Jiangmen, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Yu Zheng, ; Min Wang,
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Yu Zheng, ; Min Wang,
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14
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Yang H, Chen T, Wang M, Zhou J, Liebl W, Barja F, Chen F. Molecular biology: Fantastic toolkits to improve knowledge and application of acetic acid bacteria. Biotechnol Adv 2022; 58:107911. [PMID: 35033586 DOI: 10.1016/j.biotechadv.2022.107911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 01/09/2022] [Indexed: 12/24/2022]
Abstract
Acetic acid bacteria (AAB) are a group of gram-negative, obligate aerobic bacteria within the Acetobacteraceae family of the alphaproteobacteria class, which are distributed in a wide variety of different natural sources that are rich in sugar and alcohols, as well as in several traditionally fermented foods. Their capabilities are not limited to the production of acetic acid and the brewing of vinegar, as their names suggest. They can also fix nitrogen and produce various kinds of aldehydes, ketones and other organic acids by incomplete oxidation (also referred to as oxidative fermentation) of the corresponding alcohols and/or sugars, as well as pigments and exopolysaccharides (EPS). In order to gain more insight into these organisms, molecular biology techniques have been extensively applied in almost all aspects of AAB research, including their identification and classification, acid resistance mechanisms, oxidative fermentation, EPS production, thermotolerance and so on. In this review, we mainly focus on the application of molecular biological technologies in the advancement of research into AAB while presenting the progress of the latest studies using these techniques.
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Affiliation(s)
- Haoran Yang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tao Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | | | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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15
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Almeida OGG, Gimenez MP, De Martinis ECP. Comparative pangenomic analyses and biotechnological potential of cocoa-related Acetobacter senegalensis strains. Antonie van Leeuwenhoek 2021; 115:111-123. [PMID: 34817761 DOI: 10.1007/s10482-021-01684-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/06/2021] [Indexed: 10/19/2022]
Abstract
Acetobacter senegalensis belongs to the group of acetic acid bacteria (AAB) that present potential biotechnological applications, for production of D-gluconate, cellulose and acetic acid. AAB can overcome heat and acid stresses by using strategies involving the overexpression of heat-shock proteins and enzymes from the complex pyrroquinoline-ADH, besides alcohol dehydrogenases (ADH). Nonetheless, the isolation of A. senegalensis and other AAB from food may be challenging due to presence of viable but non-culturable (VBNC) cells and due to uncertainties about nutritional requirements. To contribute for a better understanding of the ecology of AAB, this paper reports on the pangenome analysis of five strains of A. senegalensis recently isolated from a Brazilian spontaneous cocoa fermentation. The results showed biosynthetic clusters exclusively found in some cocoa-related AAB, such as those related to terpene pathways, which are important for flavour development. Genes related to oxidative stress were conserved in all the genomes, with multiple clusters. Moreover, there were genes coding for ADH and putative ABC transporters distributed in core, shell and cloud genomes, while chaperonin-encoding genes were present only in the core and soft-core genomes. Regarding quorum sensing, a response regulator gene was in the shell genome, and the gene encoding for acyl-homoserine lactone efflux protein was in the soft-core genome. There were quorum quenching-related genes, mainly encoding for lactonases, but also for acylases. Moreover, A. senegalensis did not have determinants of virulence or antibiotic resistance, which are good traits for strains intended to be applied in food fermentation.
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Affiliation(s)
- O G G Almeida
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - M P Gimenez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - E C P De Martinis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Avenida do Café s/n, Ribeirão Preto, São Paulo, 14040-903, Brazil.
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16
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Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation. Appl Environ Microbiol 2021; 87:e0058421. [PMID: 34105982 DOI: 10.1128/aem.00584-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, in silico approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, Yamadazyma tenuis (n = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum (n = 5), Liquorilactobacillus cacaonum (n = 1), Liquorilactobacillus nagelli (n = 1), Leuconostoc pseudomesenteroides (n = 1), and Lactiplantibacillus plantarum subsp. plantarum (n = 1); (iii) acetic acid bacteria, Acetobacter senegalensis (n = 2) and Kozakia baliensis (n = 1); and (iv) Bacillus subtilis (n = 1), Brevundimonas sp. (n = 2), and Pseudomonas sp. (n = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. IMPORTANCE The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.
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Wu Y, Xia M, Zhao N, Tu L, Xue D, Zhang X, Zhao C, Cheng Y, Zheng Y, Wang M. Metabolic profile of main organic acids and its regulatory mechanism in solid-state fermentation of Chinese cereal vinegar. Food Res Int 2021; 145:110400. [PMID: 34112403 DOI: 10.1016/j.foodres.2021.110400] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/16/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Shanxi aged vinegar (SAV), a traditional Chinese cereal vinegar, is produced using solid-state fermentation (SSF) technology. Organic acids are the key flavor compounds of vinegar. However, the metabolic mechanism of organic acids during SSF process is still unclear. In this study, metatranscriptomics was used to explore the metabolic profile of main organic acids in SSF. The results show that carbon metabolism is the dominant pathway during fermentation, among which pyruvate metabolism, glycolysis and starch and sucrose metabolism associated with organic acids were the most abundant. The metabolic pathways of acetic acid and lactic acid shift from acetyl-P and pyruvate pathways at early and middle-early stages of fermentation to acetaldehyde and L-lactaldehyde pathways at later stages, respectively, and Lactobacillus and Acetobacter are the predominant microorganisms contributed to them. Temperature and acetic acid are proven to be the environmental factors that regulate the metabolic activity during SSF. This study sheds new lights on metabolism of flavor substances in the spontaneous ecosystems of traditional fermented food.
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Affiliation(s)
- Yanfang Wu
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Menglei Xia
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Nan Zhao
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Linna Tu
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Danni Xue
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Xianglong Zhang
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Cuimei Zhao
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yang Cheng
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China.
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China.
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18
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Abstract
Acetic acid bacteria are involved in many food and beverage fermentation processes. They play an important role in cocoa bean fermentation through their acetic acid production. They initiate the development of some of the flavor precursors that are necessary for the organoleptic quality of cocoa, and for the beans’ color. The development of starter cultures with local strains would enable the preservation of the microbial biodiversity of each country in cocoa-producing areas, and would also control the fermentation. This approach could avoid the standardization of cocoa bean fermentation in the producing countries. One hundred and thirty acetic acid bacteria were isolated from three different cocoa-producing countries, and were identified based on their 16S rRNA gene sequence. The predominate strains were grown in a cocoa pulp simulation medium (CPSM-AAB) in order to compare their physiological traits regarding their specific growth rate, ethanol and lactic acid consumption, acetic acid production, and relative preferences of carbon sources. Finally, the intraspecific diversity of the strains was then assessed through the analysis of their genomic polymorphism by (GTG)5-PCR fingerprinting. Our results showed that Acetobacter pasteurianus was the most recovered species in all of the origins, with 86 isolates out of 130 cultures. A great similarity was observed between the strains according to their physiological characterization and genomic polymorphisms. However, the multi-parametric clustering results in the different groups highlighted some differences in their basic metabolism, such as their efficiency in converting carbon substrates to acetate, and their relative affinity to lactic acid and ethanol. The A. pasteurianus strains showed different behaviors regarding their ability to oxidize ethanol and lactic acid into acetic acid, and in their relative preference for each substrate. The impact of these behaviors on the cocoa quality should be investigated, and should be considered as a criterion for the selection of acetic acid bacteria starters.
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Qiu X, Zhang Y, Hong H. Classification of acetic acid bacteria and their acid resistant mechanism. AMB Express 2021; 11:29. [PMID: 33595734 PMCID: PMC7889782 DOI: 10.1186/s13568-021-01189-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Acetic acid bacteria (AAB) are obligate aerobic Gram-negative bacteria that are commonly used in vinegar fermentation because of their strong capacity for ethanol oxidation and acetic acid synthesis as well as their acid resistance. However, low biomass and low production rate due to acid stress are still major challenges that must be overcome in industrial processes. Although acid resistance in AAB is important to the production of high acidity vinegar, the acid resistance mechanisms of AAB have yet to be fully elucidated. In this study, we discuss the classification of AAB species and their metabolic processes and review potential acid resistance factors and acid resistance mechanisms in various strains. In addition, we analyze the quorum sensing systems of Komagataeibacter and Gluconacetobacter to provide new ideas for investigation of acid resistance mechanisms in AAB in the form of signaling pathways. The results presented herein will serve as an important reference for selective breeding of high acid resistance AAB and optimization of acetic acid fermentation processes.
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Affiliation(s)
- Xiaoman Qiu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
- National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Yao Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
- National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Housheng Hong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China.
- National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China.
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20
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Gao L, Wu X, Xia X, Jin Z. Fine-tuning ethanol oxidation pathway enzymes and cofactor PQQ coordinates the conflict between fitness and acetic acid production by Acetobacter pasteurianus. Microb Biotechnol 2020; 14:643-655. [PMID: 33174682 PMCID: PMC7936290 DOI: 10.1111/1751-7915.13703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/23/2020] [Accepted: 10/22/2020] [Indexed: 12/28/2022] Open
Abstract
The very high concentrations required for industrial production of free acetic acid create toxicity and low pH values, which usually conflict with the host cell growth, leading to a poor productivity. Achieving a balance between cell fitness and product synthesis is the key challenge to improving acetic acid production efficiency in metabolic engineering. Here, we show that the synergistic regulation of alcohol/aldehyde dehydrogenase expression and cofactor PQQ level could not only efficiently relieve conflict between increased acetic acid production and compromised cell fitness, but also greatly enhance acetic acid tolerance of Acetobacter pasteurianus to a high initial concentration (3% v/v) of acetic acid. Combinatorial expression of adhA and pqqABCDE greatly shortens the duration of starting‐up process from 116 to 99 h, leading to a yield of 69 g l‐1 acetic acid in semi‐continuous fermentation. As a final result, average acetic acid productivity has been raised to 0.99 g l‐1 h‐1, which was 32% higher than the parental A. pasteurianus. This study is of great significance for decreasing cost of semi‐continuous fermentation for producing high‐strength acetic acid industrially. We envisioned that this strategy will be useful for production of many other desired organic acids, especially those involving cofactor reactions.
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Affiliation(s)
- Ling Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.,State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaole Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
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21
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Xia K, Han C, Xu J, Liang X. Transcriptome response of Acetobacter pasteurianus Ab3 to high acetic acid stress during vinegar production. Appl Microbiol Biotechnol 2020; 104:10585-10599. [PMID: 33156446 DOI: 10.1007/s00253-020-10995-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Acetic acid accumulation is a universal limiting factor to the vinegar manufacture because of the toxic effect of acetic acid on the acid producing strain, such as Acetobacter pasteurianus. In this study, we aimed to investigate the genome-wide transcriptional response of A. pasteurianus Ab3 to high acid stress during vinegar production. By comparing the transcriptional landscape of cells harvested from a long-term cultivation with high acidity (70 ± 3 g/L) to that of low acidity (10 ± 2 g/L), we demonstrated that 1005 genes were differentially expressed. By functional enrichment analysis, we found that the expression of genes related to the two-component systems (TCS) and toxin-antitoxin systems (TAS) was significantly regulated under high acid stress. Cells increased the genome stability to withstand the intracellular toxicity caused by the acetic acid accumulation by repressing the expression of transposases and integrases. Moreover, high acid stress induced the expression of genes involved in the pathways of peptidoglycan, ceramide, and phosphatidylcholine biosynthesis as well as the Tol-Pal and TonB-ExbB systems. In addition, we observed that cells increased and diversified the ATP production to resist high acid stress. Transcriptional upregulation in the pathways of pyrroloquinoline quinone (PQQ) synthesis and thiamine metabolism suggested that cells may increase the production of prosthetic groups to ensure the enzyme activity upon high acid stress. Collectively, the results of this study increase our current understanding of the acetic acid resistance (AAR) mechanisms in A. pasteurianus and provide opportunities for strain improvement and scaled-up vinegar production.Key Points• TCS and TAS are responsive to the acid stress and constitute the regulating networks.• Adaptive expression changes of cell envelope elements help cell resist acid stress.• Cells promote genome stability and diversify ATP production to withstand acid stress.
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Affiliation(s)
- Kai Xia
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Chengcheng Han
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
- Institute of Food Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Jun Xu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
- Institute of Food Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
- Institute of Food Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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22
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Han C, Xia K, Yang J, Zhang H, DeLisa MP, Liang X. Investigation of lipid profile in Acetobacter pasteurianus Ab3 against acetic acid stress during vinegar production. Extremophiles 2020; 24:909-922. [PMID: 33026498 DOI: 10.1007/s00792-020-01204-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Elucidation of the acetic acid resistance (AAR) mechanisms of Acetobacter pasteurianus is significant for vinegar production. In this study, cell membrane lipid profile of A. pasteurianus Ab3 was investigated by gas chromatography-mass spectrometer (GC-MS) and high performance liquid chromatography-electrospray ionization (HPLC-ESI) combined with high resolution accurate mass/mass spectrometry (HRAM/MS). We observed that cell remodeled the membrane physical state by decreasing the ratio of saturated fatty acids (SFAs)/unsaturated fatty acids (UFAs), and increasing the chain length of fatty acids (FAs) and the content of cyclopropane FAs in response to extreme acid stress. Noticeably, the content of octadecadienoic acid (C18:2) elevated remarkably. Moreover, a continuous reduction in cell membrane fluidity and a "V-type" variance in permeability were discovered. The content of glycerophospholipid and ceramide increased significantly in cells harvested from culture with acidity of 75 g/L and 95 g/L compared to that with acidity of 30 g/L. Among the identified lipid species, the content of phosphatidylcholine (e.g. PC 19:0/18:2 and 19:1/18:0), ceramide (e.g. Cer d18:0/16:1 and d18:0/16:1 + O), and dimethylphosphatidylethanolamine (e.g. dMePE 19:1/16:1) increased notably with increasing acidity. Collectively, these findings refresh our current understanding of the AAR mechanisms in A. pasteurianus Ab3, and should direct future strain breeding and vinegar fermentation.
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Affiliation(s)
- Chengcheng Han
- Department of Biochemical Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Kai Xia
- Department of Biochemical Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Jieqiong Yang
- Department of Biochemical Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Hong Zhang
- Department of Biochemical Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Xinle Liang
- Department of Biochemical Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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23
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Jeon EJ, Cho YS, Kim AH, Shim JM, Kim YS, Piao Z, Shin YC, Kwon J. Enhanced alcohol degradation and hepatic protective effects of an Acetobacter Pasteurianus-derived product, CureZyme-ACE, in an acute intoxication rat model. Lab Anim Res 2020; 36:15. [PMID: 32518763 PMCID: PMC7275519 DOI: 10.1186/s42826-020-00050-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/27/2020] [Indexed: 02/24/2023] Open
Abstract
Excessive alcohol consumption induces acute intoxication and various hepatic diseases. In this study, we investigated the effect of the CureZyme-ACE (CA), Acetobacter Pasteurianus (AP)-derived product, in acute intoxication rats. The ethanol and acetaldehyde levels of serum were lower in rats treated with CA than those who only treated ethanol. The activities of alcohol dehydrogenase and acetaldehyde dehydrogenase also recovered faster in the CA group than only-ethanol group. The transaminase levels (AST, ALT) in the CA group were significantly lower than only-ethanol group. In addition, Hepatic histological analyses and stomach wall were demonstrated that the CA-treated group recovered faster than only-ethanol group. With regard to most characteristics, we found that CA had dose-dependent effects. At high concentrations of CA, there were no differences in the tested parameters compared to those of normal rats. These findings indicate that CA reduces the serum alcohol concentration and some of the hepatic damage caused by alcohol intoxication.
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Affiliation(s)
- Eun-Jong Jeon
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk National UniversityJeonbuk, 54596 Iksan, Republic of Korea
| | - Yun-Sang Cho
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk National UniversityJeonbuk, 54596 Iksan, Republic of Korea
| | - Ae-Hyang Kim
- Amicogen, Inc., Jinsung, Jinju, Republic of Korea
| | - Jae-Min Shim
- Amicogen, Inc., Jinsung, Jinju, Republic of Korea
| | - Yi-Soo Kim
- Amicogen, Inc., Jinsung, Jinju, Republic of Korea
| | - Zhe Piao
- Amicogen, Inc., Jinsung, Jinju, Republic of Korea
| | | | - Jungkee Kwon
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk National UniversityJeonbuk, 54596 Iksan, Republic of Korea
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24
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Baek JH, Kim KH, Moon JY, Yeo SH, Jeon CO. Acetobacter oryzoeni sp. nov., isolated from Korean rice wine vinegar. Int J Syst Evol Microbiol 2020; 70:2026-2033. [PMID: 31995463 DOI: 10.1099/ijsem.0.004008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A Gram-stain-negative, obligately aerobic bacterium, designated strain B6T, was isolated from rice wine vinegar in the Republic of Korea. Cells were non-motile and oval short rods showing catalase-positive and oxidase-negative activities. Growth was observed at 15-45 °C (optimum, 30 °C) and pH 3.5-8.0 (optimum, pH 5.5-6.5). Strain B6T contained summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1 ω6c), and C16 : 0 as major fatty acids and ubiquinone-9 was identified as the sole isoprenoid quinone. The G+C content of the genomic DNA calculated from the whole genome was 53.1 mol%. Strain B6T was most closely related to Acetobacter pasteurianus LMG 1262T with very high 16S rRNA gene sequence similarity (100 %) and the strains formed a very close phylogenetic lineage together in phylogenetic trees based on 16S rRNA gene sequences. However, relatedness analyses based on concatenated amino acid sequences of 354 core genes and whole-cell MALDI-TOF profiles showed that strain B6T may form a distinct phyletic lineage from Acetobacter species. In addition, average nucleotide identity and in silico DNA-DNA hybridization values between strain B6T and the type strains of Acetobacter species were less than 93.3 and 51.4 %, respectively. The genomic features of strain B6T were also differentiated from those of closely related Acetobacter type strains. Based on the phenotypic, chemotaxonomic and genomic features, strain B6T clearly represents a novel species of the genus Acetobacter, for which the name Acetobacter oryzoeni sp. nov. is proposed. The type strain is B6T (=KACC 21201T=JCM 33371T).
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Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ji Young Moon
- Department of Agrofood Resources, National Institute of Agricultural Sciences, RDA, Wanju-gun 55365, Republic of Korea
| | - Soo-Hwan Yeo
- Department of Agrofood Resources, National Institute of Agricultural Sciences, RDA, Wanju-gun 55365, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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25
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Laureys D, Britton SJ, De Clippeleer J. Kombucha Tea Fermentation: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1734150] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- David Laureys
- Innovation centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Scott J. Britton
- Department of Research & Development, Brewery Duvel Moortgat, Puurs-Sint-Amands, Belgium
- International Centre for Brewing and Distilling, Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Jessika De Clippeleer
- Innovation centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Innovation centre for Brewing & Fermentation, School of Bioscience and Industrial Technology, HOGENT University of Applied Sciences and Arts, Ghent, Belgium
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26
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Gao L, Wu X, Zhu C, Jin Z, Wang W, Xia X. Metabolic engineering to improve the biomanufacturing efficiency of acetic acid bacteria: advances and prospects. Crit Rev Biotechnol 2020; 40:522-538. [DOI: 10.1080/07388551.2020.1743231] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ling Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology Shandong Academy of Sciences, Jinan, PR China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Cailin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Wu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
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27
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Yang H, Yu Y, Fu C, Chen F. Bacterial Acid Resistance Toward Organic Weak Acid Revealed by RNA-Seq Transcriptomic Analysis in Acetobacter pasteurianus. Front Microbiol 2019; 10:1616. [PMID: 31447789 PMCID: PMC6691051 DOI: 10.3389/fmicb.2019.01616] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/28/2019] [Indexed: 11/29/2022] Open
Abstract
Under extreme acidic environments, bacteria exploit several acid resistance (AR) mechanisms for enhancing their survival, which is concerned with several aspects, such as issues in human health and fermentation for acidic products. Currently, knowledge of bacterial AR mainly comes from the strong acid (such as hydrochloric acid) stresses, whereas AR mechanisms against organic weak acids (such as acetic acid), which are indeed encountered by bacteria, are less understood. Acetic acid bacteria (AAB), with the ability to produce acetic acid up to 20 g/100 mL, possess outstanding acetic acid tolerance, which is conferred by their unique AR mechanisms, including pyrroloquinoline quinine-dependent alcohol dehydrogenase, acetic acid assimilation and molecular chaperons. The distinguished AR of AAB toward acetic acid may provide a paradigm for research in bacterial AR against weak organic acids. In order to understand AAB’s AR mechanism more holistically, omics approaches have been employed in the corresponding field. However, the currently reported transcriptomic study was processed under a low-acidity (1 g/100 mL) environment, which could not reflect the general conditions that AAB are usually faced with. This study performed RNA-Seq transcriptomic analysis investigating AR mechanisms in Acetobacter pasteurianus CGMCC 1.41, a widely used vinegar-brewing AAB strain, at different stages of fermentation, namely, under different acetic acid concentrations (from 0.6 to 6.03 g/100 mL). The results demonstrated the even and clustered genomic distribution of up- and down-regulated genes, respectively. Difference in AR between AAB and other microorganisms was supported by the down-regulation of urea degradation and trehalose synthesis-related genes in response to acetic acid. Detailed analysis reflected the role of ethanol respiration as the main energy source and the limited effect of acetic acid assimilation on AR during fermentation as well as the competition between ethanol respiratory chain and NADH, succinate dehydrogenase-based common respiratory chain. Molecular chaperons contribute to AR, too, but their regulatory mechanisms require further investigation. Moreover, pathways of glucose catabolism and fatty acid biosynthesis are also related to AR. Finally, 2-methylcitrate cycle was proposed as an AR mechanism in AAB for the first time. This study provides new insight into AR mechanisms of AAB, and it also indicates the existence of numerous undiscovered AR mechanisms.
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Affiliation(s)
- Haoran Yang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongjian Yu
- Jiangsu Hengshun Vinegar Industry Co., Ltd., Zhenjiang, China
| | - Caixia Fu
- Hubei Tulaohan Flavouring and Food Co., Ltd., Yichang, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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28
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Characterization and comparative analysis of toxin-antitoxin systems in Acetobacter pasteurianus. J Ind Microbiol Biotechnol 2019; 46:869-882. [PMID: 30805740 DOI: 10.1007/s10295-019-02144-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022]
Abstract
Bacterial toxin-antitoxin (TA) systems play important roles in diverse cellular regulatory processes. Here, we characterize three putative type II TA candidates from Acetobacter pasteurianus and investigate the profile of type II TA systems in the genus Acetobacter. Based on the gene structure and activity detection, two-pairs loci were identified as the canonical hicAB and higAB TA systems, respectively, and DB34_01190-DB34_01195 as a putative new one without a canonical TA architecture. Physiologically, the expression of the three pairs conferred E. coli with additional plasmid maintenance and survival when under acetic acid stress. Chromosomal TA systems can be horizontally transferred within an ecological vinegar microbiota by co-option, and there was a tendency for toxin module loss. The antitoxin retention in the genome is suggested to have a broad role in bacterial physiology. Furthermore, A. pasteurianus strains, universally domesticated and used for industrial vinegar fermentation, showed a higher number of type II TA loci compared to the host-associated ones. The amount of TA loci per genome showed little positive relationship to insertion sequences, although its prevalence was species-associated, to the extent of even being strain-associated. The TA system is a candidate of studying the resistant mechanistic network, the TAs-dependent translatome affords a real-time profile to explore stress adaptation of A. pasteurianus, promoting industrial development.
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29
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Ryngajłło M, Kubiak K, Jędrzejczak-Krzepkowska M, Jacek P, Bielecki S. Comparative genomics of the Komagataeibacter strains-Efficient bionanocellulose producers. Microbiologyopen 2018; 8:e00731. [PMID: 30365246 PMCID: PMC6528568 DOI: 10.1002/mbo3.731] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/13/2018] [Accepted: 08/21/2018] [Indexed: 12/21/2022] Open
Abstract
Komagataeibacter species are well-recognized bionanocellulose (BNC) producers. This bacterial genus, formerly assigned to Gluconacetobacter, is known for its phenotypic diversity manifested by strain-dependent carbon source preference, BNC production rate, pellicle structure, and strain stability. Here, we performed a comparative study of nineteen Komagataeibacter genomes, three of which were newly contributed in this work. We defined the core genome of the genus, clarified phylogenetic relationships among strains, and provided genetic evidence for the distinction between the two major clades, the K. xylinus and the K. hansenii. We found genomic traits, which likely contribute to the phenotypic diversity between the Komagataeibacter strains. These features include genome flexibility, carbohydrate uptake and regulation of its metabolism, exopolysaccharides synthesis, and the c-di-GMP signaling network. In addition, this work provides a comprehensive functional annotation of carbohydrate metabolism pathways, such as those related to glucose, glycerol, acetan, levan, and cellulose. Findings of this multi-genomic study expand understanding of the genetic variation within the Komagataeibacter genus and facilitate exploiting of its full potential for bionanocellulose production at the industrial scale.
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Affiliation(s)
- Małgorzata Ryngajłło
- Institute of Technical Biochemistry, Lodz University of Technology, Lodz, Poland
| | - Katarzyna Kubiak
- Institute of Technical Biochemistry, Lodz University of Technology, Lodz, Poland
| | | | - Paulina Jacek
- Institute of Technical Biochemistry, Lodz University of Technology, Lodz, Poland
| | - Stanisław Bielecki
- Institute of Technical Biochemistry, Lodz University of Technology, Lodz, Poland
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30
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Zheng Y, Chang Y, Zhang R, Song J, Xu Y, Liu J, Wang M. Two-stage oxygen supply strategy based on energy metabolism analysis for improving acetic acid production by Acetobacter pasteurianus. J Ind Microbiol Biotechnol 2018; 45:781-788. [PMID: 30008048 DOI: 10.1007/s10295-018-2060-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/02/2018] [Indexed: 11/24/2022]
Abstract
Oxygen acts as the electron acceptor to oxidize ethanol by acetic acid bacteria during acetic acid fermentation. In this study, the energy release rate from ethanol and glucose under different aerate rate were compared, and the relationship between energy metabolism and acetic acid fermentation was analyzed. The results imply that proper oxygen supply can maintain the reasonable energy metabolism and cell tolerance to improve the acetic acid fermentation. Further, the transcriptions of genes that involve in the ethanol oxidation, TCA cycle, ATP synthesis and tolerance protein expression were analyzed to outline the effect of oxygen supply on cell metabolism of Acetobacter pasteurianus. Under the direction of energy metabolism framework a rational two-stage oxygen supply strategy was established to release the power consumption and substrates volatilization during acetic acid fermentation. As a result, the acetic acid production rate of 1.86 g/L/h was obtained, which were 20.78% higher than that of 0.1 vvm one-stage aerate rate. And the final acetic acid concentration and the stoichiometric yield were 88.5 g/L and 94.1%, respectively, which were 84.6 g/L and 89.5% for 0.15 vvm one-stage aerate rate.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yangang Chang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Renkuan Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Jia Song
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Ying Xu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Jing Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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31
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Zheng Y, Wang J, Bai X, Chang Y, Mou J, Song J, Wang M. Improving the acetic acid tolerance and fermentation of Acetobacter pasteurianus by nucleotide excision repair protein UvrA. Appl Microbiol Biotechnol 2018; 102:6493-6502. [PMID: 29785501 DOI: 10.1007/s00253-018-9066-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 01/20/2023]
Abstract
Acetic acid bacteria (AAB) are widely used in acetic acid fermentation due to their remarkable ability to oxidize ethanol and high tolerance against acetic acid. In Acetobacter pasteurianus, nucleotide excision repair protein UvrA was up-regulated 2.1 times by acetic acid when compared with that without acetic acid. To study the effects of UvrA on A. pasteurianus acetic acid tolerance, uvrA knockout strain AC2005-ΔuvrA, uvrA overexpression strain AC2005 (pMV24-uvrA), and the control strain AC2005 (pMV24), were constructed. One percent initial acetic acid was almost lethal to AC2005-ΔuvrA. However, the biomass of the UvrA overexpression strain was higher than that of the control under acetic acid concentrations. After 6% acetic acid shock for 20 and 40 min, the survival ratios of AC2005 (pMV24-uvrA) were 2 and 0.12%, respectively; however, they were 1.5 and 0.06% for the control strain AC2005 (pMV24). UvrA overexpression enhanced the acetification rate by 21.7% when compared with the control. The enzymes involved in ethanol oxidation and acetic acid tolerance were up-regulated during acetic acid fermentation due to the overexpression of UvrA. Therefore, in A. pasteurianus, UvrA could be induced by acetic acid and is related with the acetic acid tolerance by protecting the genome against acetic acid to ensure the protein expression and metabolism.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Xiaolei Bai
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Yangang Chang
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Jun Mou
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Jia Song
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
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32
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Wu X, Yao H, Liu Q, Zheng Z, Cao L, Mu D, Wang H, Jiang S, Li X. Producing Acetic Acid of Acetobacter pasteurianus by Fermentation Characteristics and Metabolic Flux Analysis. Appl Biochem Biotechnol 2018; 186:217-232. [PMID: 29552715 DOI: 10.1007/s12010-018-2732-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/28/2018] [Indexed: 02/07/2023]
Abstract
The acetic acid bacterium Acetobacter pasteurianus plays an important role in acetic acid fermentation, which involves oxidation of ethanol to acetic acid through the ethanol respiratory chain under specific conditions. In order to obtain more suitable bacteria for the acetic acid industry, A. pasteurianus JST-S screened in this laboratory was compared with A. pasteurianus CICC 20001, a current industrial strain in China, to determine optimal fermentation parameters under different environmental stresses. The maximum total acid content of A. pasteurianus JST-S was 57.14 ± 1.09 g/L, whereas that of A. pasteurianus CICC 20001 reached 48.24 ± 1.15 g/L in a 15-L stir stank. Metabolic flux analysis was also performed to compare the reaction byproducts. Our findings revealed the potential value of the strain in improvement of industrial vinegar fermentation.
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Affiliation(s)
- Xuefeng Wu
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Hongli Yao
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Qing Liu
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Zhi Zheng
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Lili Cao
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Dongdong Mu
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Hualin Wang
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Shaotong Jiang
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China
| | - Xingjiang Li
- School of Food Science and Engineering, Hefei University of Technology, No.193 Tunxi Road, Hefei City, 230009, Anhui Province, People's Republic of China.
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei, 230009, Anhui Province, People's Republic of China.
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Herschend J, Damholt ZBV, Marquard AM, Svensson B, Sørensen SJ, Hägglund P, Burmølle M. A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community. Sci Rep 2017; 7:16483. [PMID: 29184101 PMCID: PMC5705676 DOI: 10.1038/s41598-017-16633-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/15/2017] [Indexed: 01/11/2023] Open
Abstract
Microbial biofilms are omnipresent in nature and relevant to a broad spectrum of industries ranging from bioremediation and food production to biomedical applications. To date little is understood about how multi-species biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we apply a meta-proteomics approach to investigate the mechanisms influencing biofilm formation in a model consortium of four bacterial soil isolates; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. Protein abundances in community and single species biofilms were compared to describe occurring inter-species interactions and the resulting changes in active metabolic pathways. To obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for generating reduced reference proteomes for spectral database searches. Meta-proteomics profiling indicated that community development is dependent on cooperative interactions between community members facilitating cross-feeding on specific amino acids. Opposite regulation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, indicate that competition for limited resources also affects community development. Overall our results demonstrate the multitude of pathways involved in biofilm formation in mixed communities.
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Affiliation(s)
- Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zacharias B V Damholt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Andrea M Marquard
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Per Hägglund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production. Sci Rep 2017; 7:7911. [PMID: 28801647 PMCID: PMC5554229 DOI: 10.1038/s41598-017-06918-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 06/21/2017] [Indexed: 02/07/2023] Open
Abstract
Bacterial cellulose (BC) is widely used in industries owing to its high purity and strength. Although Komagataeibacter nataicola is a representative species for BC production, its intracellular metabolism leading to BC secretion is unclear. In the present study, a genome-scale metabolic network of cellulose-producing K. nataicola strain RZS01 was reconstructed to understand its metabolic behavior. This model iHZ771 comprised 771 genes, 2035 metabolites, and 2014 reactions. Constraint-based analysis was used to characterize and evaluate the critical intracellular pathways. The analysis revealed that a total of 71 and 30 genes are necessary for cellular growth in a minimal medium and complex medium, respectively. Glycerol was identified as the optimal carbon source for the highest BC production. The minimization of metabolic adjustment algorithm identified 8 genes as potential targets for over-production of BC. Overall, model iHZ771 proved to be a useful platform for understanding the physiology and BC production of K. nataicola.
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Zheng Y, Zhang R, Yin H, Bai X, Chang Y, Xia M, Wang M. Acetobacter pasteurianus metabolic change induced by initial acetic acid to adapt to acetic acid fermentation conditions. Appl Microbiol Biotechnol 2017; 101:7007-7016. [DOI: 10.1007/s00253-017-8453-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 11/29/2022]
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36
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Jia B, Chun BH, Cho GY, Kim KH, Moon JY, Yeo SH, Jeon CO. Complete Genome Sequences of Two Acetic Acid-Producing Acetobacter pasteurianus Strains (Subsp. ascendens LMG 1590 T and Subsp. paradoxus LMG 1591 T). Front Bioeng Biotechnol 2017; 5:33. [PMID: 28567373 PMCID: PMC5434130 DOI: 10.3389/fbioe.2017.00033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 04/27/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul, Korea (Republic of).,School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul, Korea (Republic of)
| | - Ga Youn Cho
- Department of Life Science, Chung-Ang University, Seoul, Korea (Republic of)
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul, Korea (Republic of)
| | - Ji Young Moon
- Department of Agrofood Resources, National Institute of Agricultural Sciences, RDA, Wanju-gun, Korea (Republic of)
| | - Soo-Hwan Yeo
- Department of Agrofood Resources, National Institute of Agricultural Sciences, RDA, Wanju-gun, Korea (Republic of)
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea (Republic of)
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37
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Xia K, Zang N, Zhang J, Zhang H, Li Y, Liu Y, Feng W, Liang X. New insights into the mechanisms of acetic acid resistance in Acetobacter pasteurianus using iTRAQ-dependent quantitative proteomic analysis. Int J Food Microbiol 2016; 238:241-251. [PMID: 27681379 DOI: 10.1016/j.ijfoodmicro.2016.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 12/01/2022]
Abstract
Acetobacter pasteurianus is the main starter in rice vinegar manufacturing due to its remarkable abilities to resist and produce acetic acid. Although several mechanisms of acetic acid resistance have been proposed and only a few effector proteins have been identified, a comprehensive depiction of the biological processes involved in acetic acid resistance is needed. In this study, iTRAQ-based quantitative proteomic analysis was adopted to investigate the whole proteome of different acidic titers (3.6, 7.1 and 9.3%, w/v) of Acetobacter pasteurianus Ab3 during the vinegar fermentation process. Consequently, 1386 proteins, including 318 differentially expressed proteins (p<0.05), were identified. Compared to that in the low titer circumstance, cells conducted distinct biological processes under high acetic acid stress, where >150 proteins were differentially expressed. Specifically, proteins involved in amino acid metabolic processes and fatty acid biosynthesis were differentially expressed, which may contribute to the acetic acid resistance of Acetobacter. Transcription factors, two component systems and toxin-antitoxin systems were implicated in the modulatory network at multiple levels. In addition, the identification of proteins involved in redox homeostasis, protein metabolism, and the cell envelope suggested that the whole cellular system is mobilized in response to acid stress. These findings provide a differential proteomic profile of acetic acid resistance in Acetobacter pasteurianus and have potential application to highly acidic rice vinegar manufacturing.
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Affiliation(s)
- Kai Xia
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Ning Zang
- Medical Scientific Research Center, Guangxi Medical University, Nanning 530021, China
| | - Junmei Zhang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Hong Zhang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Yudong Li
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Ye Liu
- Zhejiang Wuweihe Food Co. Ltd., Huzhou 313213, China
| | - Wei Feng
- Zhejiang Wuweihe Food Co. Ltd., Huzhou 313213, China
| | - Xinle Liang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China.
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