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Han D, Yang Y, Guo Z, Dai S, Jiang M, Zhu Y, Wang Y, Yu Z, Wang K, Rong C, Yu Y. A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective. Foods 2024; 13:2534. [PMID: 39200461 PMCID: PMC11353490 DOI: 10.3390/foods13162534] [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: 07/17/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.
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Affiliation(s)
- Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yunsong Yang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Zhantong Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Shuwen Dai
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Mingchao Jiang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Chunchi Rong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China; (D.H.); (Z.G.)
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang 212004, China
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, García-Martínez T, Mauricio JC. Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications-A Comprehensive Review. Foods 2023; 12:3705. [PMID: 37835358 PMCID: PMC10572879 DOI: 10.3390/foods12193705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
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3
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Ibacache-Quiroga C, González-Pizarro K, Charifeh M, Canales C, Díaz-Viciedo R, Schmachtenberg O, Dinamarca MA. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods 2022; 11:foods11070900. [PMID: 35406987 PMCID: PMC8997647 DOI: 10.3390/foods11070900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.
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Affiliation(s)
- Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| | - Karoll González-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Mariam Charifeh
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Christian Canales
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción 4080871, Chile;
| | - Rodrigo Díaz-Viciedo
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
| | - Oliver Schmachtenberg
- Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2360102, Chile;
- Centro Interdisciplinario de Neurociencias (CINV), Universidad de Valparaíso, Valparaíso 2381850, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
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Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L. The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa. Microorganisms 2021; 9:microorganisms9081570. [PMID: 34442649 PMCID: PMC8399863 DOI: 10.3390/microorganisms9081570] [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: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
- Correspondence:
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Chun-Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
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Kumar MR, Yeap SK, Mohamad NE, Abdullah JO, Masarudin MJ, Khalid M, Leow ATC, Alitheen NB. Metagenomic and phytochemical analyses of kefir water and its subchronic toxicity study in BALB/c mice. BMC Complement Med Ther 2021; 21:183. [PMID: 34210310 PMCID: PMC8247212 DOI: 10.1186/s12906-021-03358-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In recent years, researchers are interested in the discovery of active compounds from traditional remedies and natural sources, as they reveal higher therapeutic efficacies and improved toxicological profiles. Among the various traditional treatments that have been widely studied and explored for their potential therapeutic benefits, kefir, a fermented beverage, demonstrates a broad spectrum of pharmacological properties, including antioxidant, anti-inflammation, and healing activities. These health-promoting properties of kefir vary among the kefir cultures found at the different part of the world as different media and culture conditions are used for kefir maintenance and fermentation. METHODS This study investigated the microbial composition and readily found bioactive compounds in water kefir fermented in Malaysia using 16S rRNA microbiome and UHPLC sequencing approaches. The toxicity effects of the kefir water administration in BALB/c mice were analysed based on the mice survival, body weight index, biochemistry profile, and histopathological changes. The antioxidant activities were evaluated using SOD, FRAP, and NO assays. RESULTS The 16S rRNA amplicon sequencing revealed the most abundant species found in the water kefir was Lactobacillus hilgardii followed by Lactobacillus harbinensis, Acetobacter lovaniensis, Lactobacillus satsumensis, Acetobacter tropicalis, Lactobacillus zeae, and Oenococcus oeni. The UHPLC screening showed flavonoid and phenolic acid derivatives as the most important bioactive compounds present in kefir water which has been responsible for its antioxidant activities. Subchronic toxicity study showed no toxicological signs, behavioural changes, or adverse effects by administrating 10 mL/kg/day and 2.5 mL/kg/day kefir water to the mice. Antioxidants assays demonstrated enhanced SOD and FRAP activities and reduced NO level, especially in the brain and kidney samples. CONCLUSIONS This study will help to intensify the knowledge on the water kefir microbial composition, available phytochemicals and its toxicological and antioxidant effects on BALB/c mice since there are very limited studies on the water kefir grain fermented in Malaysia.
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Affiliation(s)
- Muganti Rajah Kumar
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Malaysia
| | - Nurul Elyani Mohamad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah Malaysia
| | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Melati Khalid
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah Malaysia
| | - Adam Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Biomedical Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Darul Ehsan Malaysia
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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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7
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Casas-Acevedo A, Veana F, Montet D, Aguilar CN, Rutiaga-Quiñones OM, Rodríguez-Herrera R. Microbial and chemical changes during the production of sotol: a Mexican alcoholic beverage. FOOD BIOTECHNOL 2021. [DOI: 10.1080/08905436.2020.1869981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Aarón Casas-Acevedo
- Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, Mexic
| | - Fabiola Veana
- Engineering Department, Tecnológico Nacional De México/IT De Ciudad Valles, San Luis Potosí, Méxic
| | - Didier Montet
- Food Contaminants Department, Centre De Coopération Internationale En Recherche Agronomique Pour Le Développement, Montpellier, Francia
| | - Cristóbal N. Aguilar
- Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, Mexic
| | | | - Raúl Rodríguez-Herrera
- Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, Mexic
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8
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Landis EA, Oliverio AM, McKenney EA, Nichols LM, Kfoury N, Biango-Daniels M, Shell LK, Madden AA, Shapiro L, Sakunala S, Drake K, Robbat A, Booker M, Dunn RR, Fierer N, Wolfe BE. The diversity and function of sourdough starter microbiomes. eLife 2021; 10:e61644. [PMID: 33496265 PMCID: PMC7837699 DOI: 10.7554/elife.61644] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- North Carolina Museum of Natural SciencesRaleighUnited States
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Nicole Kfoury
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | | | - Leonora K Shell
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Lori Shapiro
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | | | - Kinsey Drake
- Department of Biology, Tufts UniversityMedfordUnited States
| | - Albert Robbat
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | - Matthew Booker
- Department of History, North Carolina State UniversityRaleighUnited States
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- Danish Natural History Museum, University of CopenhagenCopenhagenDenmark
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
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9
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Sombolestani AS, Cleenwerck I, Cnockaert M, Borremans W, Wieme AD, De Vuyst L, Vandamme P. Novel acetic acid bacteria from cider fermentations: Acetobacter conturbans sp. nov. and Acetobacter fallax sp. nov. Int J Syst Evol Microbiol 2020; 70:6163-6171. [PMID: 33052084 DOI: 10.1099/ijsem.0.004511] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains LMG 1627T, LMG 1636T and LMG 1637 were all isolated from cider fermentations in the 1940s and 1950s. A recent study based on MALDI-TOF MS and dnaK gene sequence analyses suggested they represented novel Acetobacter species. In the present study, we determined the whole-genome sequences of these strains and analysed their phenotypic and chemotaxonomic characteristics. A phylogenomic analysis based on 107 single-copy core genes revealed that they represented a single Acetobacter lineage with Acetobacter aceti, Acetobacter sicerae, Acetobacter musti and Acetobacter oeni, Acetobacter estunensis and with Acetobacter nitrogenifigens as an outgroup to this cluster. OrthoANIu value and dDDH analyses among these and other Acetobacter type strains confirmed that these three strains represented two novel Acetobacter species, which could be differentiated from other closely related type strains of Acetobacter by different phenotypic tests, such as ketogenesis from glycerol. We therefore propose to classify strain LMG 1627T in the novel species Acetobacter conturbans sp. nov., with LMG 1627T (=NCIMB 8945T) as the type strain, and to classify strains LMG 1636T and LMG 1637 in the novel species Acetobacter fallax sp. nov., with LMG 1636T (=NCIMB 8956T) as the type strain.
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Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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10
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Comasio A, Verce M, Van Kerrebroeck S, De Vuyst L. Diverse Microbial Composition of Sourdoughs From Different Origins. Front Microbiol 2020; 11:1212. [PMID: 32760353 PMCID: PMC7374928 DOI: 10.3389/fmicb.2020.01212] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 01/04/2023] Open
Abstract
Hundreds of sourdoughs have been investigated in the last decades. However, many studies used a culture-dependent and/or culture-independent microbiological approach [mainly based on denaturing gradient gel electrophoresis (DGGE) of PCR amplicons], seldomly combined with a metabolite target analysis, to characterize the microbial species communities of the sourdoughs examined. Moreover, attention was mainly paid on lactic acid bacteria (LAB) and yeast species. In the present study, distinct household-scale (including an artisan lambic brewery) and artisan bakery-scale backslopped sourdoughs (17 in total), obtained from different regions (Belgium, France, United Kingdom, and USA), were examined through a multiphasic approach, encompassing a culture-dependent analysis [targeting LAB, acetic acid bacteria (AAB), and yeasts], different culture-independent techniques [rRNA-PCR-DGGE, metagenetics, and metagenomics (four bakery sourdoughs)], and metabolite target analysis. It turned out that the microbial species diversity of the sourdoughs was influenced by the house microbiota of the producer. Further, when the producer made use of different flours, the sourdoughs harbored similar microbial communities, independent of the flour used. AAB were only present in the Belgian sourdoughs, which might again be related to the processing environment. Fructilactobacillus sanfranciscensis (formerly known as Lactobacillus sanfranciscensis) was the prevalent LAB species of the eight sourdoughs produced by two of the three bakeries of different countries analyzed. These sourdoughs were characterized by the presence of either Saccharomyces cerevisiae or Kazachstania humilis. Moreover, the presence of Fl. sanfranciscensis was positively correlated with the production of mannitol and negatively correlated with the presence of other LAB or AAB species. Sourdoughs produced in an artisan lambic brewery were characterized by the presence of the yeast species Dekkera anomala and Pichia membranifaciens. One household sourdough was characterized by the presence of uncommon species, such as Pediococcus parvulus and Pichia fermentans. Metagenomic sequencing allowed the detection of many more LAB and AAB species than the other methods applied, which opened new frontiers for the understanding of the microbial communities involved during sourdough production processes.
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Affiliation(s)
| | | | | | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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11
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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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12
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Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01497-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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13
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Huang CH, Li SW, Huang L, Watanabe K. Identification and Classification for the Lactobacillus casei Group. Front Microbiol 2018; 9:1974. [PMID: 30186277 PMCID: PMC6113361 DOI: 10.3389/fmicb.2018.01974] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.,Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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14
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Kim KH, Cho GY, Chun BH, Weckx S, Moon JY, Yeo SH, Jeon CO. Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov. Syst Appl Microbiol 2018; 41:324-332. [PMID: 29655875 DOI: 10.1016/j.syapm.2018.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 02/07/2023]
Abstract
Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590T and LMG 1591 (previously classified as the type strains of A. pasteurianus subsp. ascendens and paradoxus, respectively) and strain SLV-7T do not belong to A. pasteurianus. Strain SLV-7T, isolated from Korean traditional vinegar, shared low ANI (<91.0%) and in silico DDH (44.2%) values with all other Acetobacter type strains analyzed in this study, indicating that strain SLV-7T represents a new Acetobacter species. The phenotypic and chemotaxonomic analyses confirmed these results and therefore a new species named Acetobacter oryzifermentans sp. nov. is proposed with SLV-7T (=KACC 19301T=JCM 31096T) as the type strain. Strains LMG 1590T and LMG 1591 shared high ANI (99.4%) and in silico DDH (96.0%) values between them, but shared low ANI (<92.3%) and in silico DDH (<49.0%) values with other type strains analyzed in this study, indicating that strains LMG 1590T and LMG 1591 should be reclassified into a new single species that should be named Acetobacter ascendens sp. nov., comb. nov., with LMD 51.1T (=LMG 1590T=NCCB 51001T) as its type strain.
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Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ga Youn Cho
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - 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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15
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De Roos J, De Vuyst L. Acetic acid bacteria in fermented foods and beverages. Curr Opin Biotechnol 2018; 49:115-119. [DOI: 10.1016/j.copbio.2017.08.007] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/03/2017] [Accepted: 08/14/2017] [Indexed: 11/29/2022]
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16
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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17
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Bourrie BCT, Willing BP, Cotter PD. The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir. Front Microbiol 2016; 7:647. [PMID: 27199969 PMCID: PMC4854945 DOI: 10.3389/fmicb.2016.00647] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/18/2016] [Indexed: 01/04/2023] Open
Abstract
Kefir is a complex fermented dairy product created through the symbiotic fermentation of milk by lactic acid bacteria and yeasts contained within an exopolysaccharide and protein complex called a kefir grain. As with other fermented dairy products, kefir has been associated with a range of health benefits such as cholesterol metabolism and angiotensin-converting enzyme (ACE) inhibition, antimicrobial activity, tumor suppression, increased speed of wound healing, and modulation of the immune system including the alleviation of allergy and asthma. These reports have led to increased interest in kefir as a focus of research and as a potential probiotic-containing product. Here, we review those studies with a particular emphasis on the microbial composition and the health benefits of the product, as well as discussing the further development of kefir as an important probiotic product.
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Affiliation(s)
- Benjamin C T Bourrie
- Agricultural, Food and Nutritional Sciences, University of AlbertaEdmonton, AB, Canada; Teagasc Food Research CentreFermoy, Ireland
| | - Benjamin P Willing
- Agricultural, Food and Nutritional Sciences, University of Alberta Edmonton, AB, Canada
| | - Paul D Cotter
- Teagasc Food Research CentreFermoy, Ireland; APC Microbiome InstituteCork, Ireland
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18
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19
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Dzieciol M, Schornsteiner E, Muhterem-Uyar M, Stessl B, Wagner M, Schmitz-Esser S. Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment. Int J Food Microbiol 2016; 223:33-40. [PMID: 26881738 DOI: 10.1016/j.ijfoodmicro.2016.02.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 02/01/2023]
Abstract
Sanitation protocols are applied on a daily basis in food processing facilities to prevent the risk of cross-contamination with spoilage organisms. Floor drain water serves along with product-associated samples (slicer dust, brine or cheese smear) as an important hygiene indicator in monitoring Listeria monocytogenes in food processing facilities. Microbial communities of floor drains are representative for each processing area and are influenced to a large degree by food residues, liquid effluents and washing water. The microbial communities of drain water are steadily changing, whereas drain biofilms provide more stable niches. Bacterial communities of four floor drains were characterized using 16S rRNA gene pyrosequencing to better understand the composition and exchange of drain water and drain biofilm communities. Furthermore, the L. monocytogenes contamination status of each floor drain was determined by applying cultivation-independent real-time PCR quantification and cultivation-dependent detection according to ISO11290-1. Pyrosequencing of 16S rRNA genes of drain water and drain biofilm bacterial communities yielded 50,611 reads, which were clustered into 641 operational taxonomic units (OTUs), affiliated to 16 phyla dominated by Proteobacteria, Firmicutes and Bacteroidetes. The most abundant OTUs represented either product- (Lactococcus lactis) or fermentation- and food spoilage-associated phylotypes (Pseudomonas mucidolens, Pseudomonas fragi, Leuconostoc citreum, and Acetobacter tropicalis). The microbial communities in DW and DB samples were distinct in each sample type and throughout the whole processing plant, indicating the presence of indigenous specific microbial communities in each processing compartment. The microbiota of drain biofilms was largely different from the microbiota of the drain water. A sampling approach based on drain water alone may thus only provide reliable information on planktonic bacterial cells but might not allow conclusions on the bacterial composition of the microbiota in biofilms.
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Affiliation(s)
- Monika Dzieciol
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Elisa Schornsteiner
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Meryem Muhterem-Uyar
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Beatrix Stessl
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Stephan Schmitz-Esser
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria.
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20
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Wang B, Shao Y, Chen T, Chen W, Chen F. Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics. Sci Rep 2015; 5:18330. [PMID: 26691589 PMCID: PMC4686929 DOI: 10.1038/srep18330] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/16/2015] [Indexed: 12/11/2022] Open
Abstract
Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.
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Affiliation(s)
- Bin Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Tao Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Wanping Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Fusheng Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China.,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068, Hubei Province, P. R. China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
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21
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Ferrer S, Mañes-Lázaro R, Benavent-Gil Y, Yépez A, Pardo I. Acetobacter musti sp. nov., isolated from Bobal grape must. Int J Syst Evol Microbiol 2015; 66:957-961. [PMID: 26637821 DOI: 10.1099/ijsem.0.000818] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An acetic acid bacterium (strain Bo7T), obtained during a study of the microbial diversity of spontaneous fermentations of Bobal grape must, was subjected to a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain Bo7T to the genus Acetobacter, and revealed Acetobacter aceti and Acetobacter oeni to be nearest neighbours (99.57 % 16S rRNA gene sequence similarity between strain Bo7T and A. oeni CECT 5830T, and 98.76 % between strain Bo7T and A. aceti CECT 298T). Cells of strain Bo7T are Gram-negative, motile rods, catalase-positive and oxidase-negative. The DNA G+C content of strain Bo7T was 58.0 mol%. DNA-DNA hybridizations demonstrated that strain Bo7T belongs to a single novel genospecies that can be differentiated from its nearest phylogenetic neighbours by the following phenotypic characteristics: no production of 5-keto-d-gluconic acid from d-glucose, growth with glycerol but not with methanol or maltose as sole carbon sources, and growth on yeast extract with 30 % d-glucose. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c (summed feature 8; approx. 56 %); other fatty acids in significant amounts (>5 %) were C16 : 0 2-OH (11 %), C16 : 0 (7 %), C14 : 0 2-OH (7 %) and C14 : 0 3-OH/iso-C16 : 1 I (summed feature 2; 6 %). The results obtained indicate that strain Bo7T represents a novel species of the genus Acetobacter, for which the name Acetobacter musti sp. nov. is proposed. The type strain is Bo7T ( = DSM 23824T = CECT 7722T).
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Affiliation(s)
- Sergi Ferrer
- ENOLAB - Laboratori de Microbiologia Enològica, ERI-ISIC BioTecMed, Universitat de València, c/ Dr. Moliner 50 E46100, Burjassot-València, Spain
| | - Rosario Mañes-Lázaro
- ENOLAB - Laboratori de Microbiologia Enològica, ERI-ISIC BioTecMed, Universitat de València, c/ Dr. Moliner 50 E46100, Burjassot-València, Spain
| | - Yaiza Benavent-Gil
- ENOLAB - Laboratori de Microbiologia Enològica, ERI-ISIC BioTecMed, Universitat de València, c/ Dr. Moliner 50 E46100, Burjassot-València, Spain
| | - Alba Yépez
- ENOLAB - Laboratori de Microbiologia Enològica, ERI-ISIC BioTecMed, Universitat de València, c/ Dr. Moliner 50 E46100, Burjassot-València, Spain
| | - Isabel Pardo
- ENOLAB - Laboratori de Microbiologia Enològica, ERI-ISIC BioTecMed, Universitat de València, c/ Dr. Moliner 50 E46100, Burjassot-València, Spain
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22
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23
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Li L, Praet J, Borremans W, Nunes OC, Manaia CM, Cleenwerck I, Meeus I, Smagghe G, De Vuyst L, Vandamme P. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop. Int J Syst Evol Microbiol 2015; 65:267-273. [DOI: 10.1099/ijs.0.068049-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as
Asaia astilbis
or as ‘Commensalibacter intestini’, except for two isolates (R-52486 and LMG 28161T) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161T was determined and showed the highest pairwise similarity to
Saccharibacter floricola
S-877T (96.5 %), which corresponded with genus level divergence in the family
Acetobacteraceae
. Isolate LMG 28161T was subjected to whole-genome shotgun sequencing; a 16S–23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family
Acetobacteraceae
. The DNA G+C content of strain LMG 28161T was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161T were similar to those of established AAB species [with C18 : 1ω7c (43.1 %) as the major component], but the amounts of fatty acids such as C19 : 0 cyclo ω8c, C14 : 0 and C14 : 0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161T ( = DSM 28636T = R-52487T) as the type strain of the type species.
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Affiliation(s)
- Leilei Li
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Jessy Praet
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Olga C. Nunes
- LEPAE – Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
| | - Célia M. Manaia
- CBQF – Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4200-072 Porto, Portugal
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ivan Meeus
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Trček J, Barja F. Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry. Int J Food Microbiol 2014; 196:137-44. [PMID: 25589227 DOI: 10.1016/j.ijfoodmicro.2014.12.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
Acetic acid bacteria have attracted much attention over the past few years, due mainly to their metabolic traits that are of interest to the biotechnology industry. In addition, it turns out that their ecological habitats are almost unlimited since they have been found as symbionts in different insects and also as emerging opportunistic human pathogens. Very surprising is the finding that they colonize niches considered anaerobic, disproving the generalized statement that they are strict aerobes. Since they have taken on different biological roles in our environment, more and more people are charged with the task of identifying them. However, this turns out to be not always easy, especially if we are using phenotypic approaches for identification. A substantial step forward in making the identification of acetic acid bacteria easier was made possible using molecular biological methods, which have been extensively tested since 2000. However, some molecular methods require expensive machines and experienced staff, and moreover the level of their discrimination varies. All these factors must be considered when selecting the most appropriate approach for identifying acetic acid bacteria. With this objective in mind, this review article discusses the benefits and drawbacks of molecular biological methods for identification of acetic acid bacteria, with a focus on the 16S-23S rRNA gene ITS regions and the recently described alternative method for identification of acetic acid bacteria, MALDI-TOF MS.
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Affiliation(s)
- Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia; Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Jussy-Geneva, Switzerland
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