1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Shangpliang HNJ, Tamang JP. Metagenomics and metagenome-assembled genomes mining of health benefits in jalebi batter, a naturally fermented cereal-based food of India. Food Res Int 2023; 172:113130. [PMID: 37689895 DOI: 10.1016/j.foodres.2023.113130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 09/11/2023]
Abstract
Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional activities. Due to limited studies, information on microbial community structure in jalebi is unknown. Hence, the present study is aimed to profile the microbial community in jalebi by shotgun metagenomics and also to predict putative probiotic and functional genes by metagenome-assembled genome (MAG). Bacteria were the most abundant domain (91.91%) under which Bacillota was the most abundant phylum (82%). The most abundant species was Lapidilactobacillus dextrinicus followed by several species of lactic acid bacteria, acetic acid bacteria including few yeasts. Lap. dextrinicus was also significantly abundant in jalebi when compared to similar fermented wheat-based sourdough. Additionally, Lap. bayanensis, Pediococcus stilesii, and yeast- Candida glabrata, Gluconobacter japonicus, Pichia kudriavzevii, Wickerhamomyces anomalus were only detected in jalebi, which are not detected in sourdough. Few viruses and archaea were detected with < 1 % abundance. In silico screening of genes from the abundant species was mined using both KEGG and EggNOG database for putative health beneficial attributes. Circular genomes of five high-quality MAGs, identified as Lapidilactobacillus dextrinicus, Enterococcus hirae, Pediococcus stilesii, Acetobacter indonesiensis and Acetobacter cibinongensis, were constructed separately and putative genes were mapped and annotated. The CRISPR/Cas gene clusters in the genomes of four MAGs except Acetobacter cibinongensis were detected. MAGs also showed several secondary metabolites. Since, the identified MAGs have different putative genes for bio-functional properties, this may pave the way to selectively culture the uncultivated putative microbes for jalebi production. We believe this is the first report on metagenomic and MAGs of jalebi.
Collapse
Affiliation(s)
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Tadong, Gangtok 737102, Sikkim, India.
| |
Collapse
|
3
|
Raible KM, Algazaq JN, Papanicolaou G, Babady NE. Acetobacter tropicalis bacteraemia in an immunocompromised patient: case report. Access Microbiol 2022; 4:acmi000374. [PMID: 36644433 PMCID: PMC9833420 DOI: 10.1099/acmi.0.000374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction. The published literature characterizing the bacterial genus Acetobacter primarily explores the role of these organisms in the fermentation industry. Reports of human infections caused by Acetobacter species are rare and are primarily associated with immunocompromised patients. Case Presentation. A young patient with refractory acute myeloid leukaemia received a peripheral blood stem cell transplant at our institution. Both pre- and post-transplant courses were complicated by polymicrobial bloodstream infections. During this time a bacterium, later identified as Acetobacter tropicalis , was isolated from blood cultures. A. tropicalis was recovered in consecutive blood cultures for approximately 1 week; during this time the patient's condition deteriorated, ending in fatal cardiorespiratory failure. Conclusion. This case provides the first report of a human infection with A. tropicalis , although the significance of this finding in a complex patient is hard to establish. This illustrates how the routine implementation of molecular identification techniques by clinical microbiology laboratories will result in the reporting of more rare or novel micro-organisms involved in human infections.
Collapse
Affiliation(s)
- Kevin M. Raible
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jumanah N. Algazaq
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genovefa Papanicolaou
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N. Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
4
|
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).
Collapse
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
| |
Collapse
|
5
|
Yukphan P, Charoenyingcharoen P, Kingcha Y, Likhitrattanapisal S, Muangham S, Tanasupawat S, Yamada Y. Acetobacter garciniae sp. nov., an acetic acid bacterium isolated from fermented mangosteen peel in Thailand. Int J Syst Evol Microbiol 2021; 71. [PMID: 34662265 DOI: 10.1099/ijsem.0.005052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates, MS16-SU-2T and MS18-SU-3, obtained from fermented mangosteen peel in vinegar were suggested to constitute a new species assignable to the genus Acetobacter based on the results of 16S rRNA gene sequencing. The two isolates showed the highest sequence similarity (98.58%) to Acetobacter tropicalis NBRC 16470T and Acetobacter senegalensis LMG 23690T. However, the calculated similarity values were lower than the threshold for species demarcation. The phylogenetic analysis showed that the branches of the two isolates were separated from other Acetobacter species, and the two isolates constituted a new species in the genus Acetobacter. The genomic DNA of isolate MS16-SU-2T was sequenced. The assembled genome of the isolate was analysed, and the results showed that the highest average nucleotide identity value of 75.9 % was with Acetobacter papayae JCM 25143T and the highest digital DNA-DNA hybridization value of 25.1 % was with Acetobacter fallax LMG 1636T, which were lower than the cutoff values for species delineation. The phylogenetic tree based on the genome sequences showed that the lineage of isolate MS16-SU-2T was most closely related to A. papayae JCM 25143T and Acetobacter suratthaniensis TBRC 1719T, but separated from the branches of these two species. In addition, the two isolates could be distinguished from the type strains of closely related species by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, MS16-SU-2T (=TBRC 12339T=LMG 32243T) and MS18-SU-3 (=TBRC 12305), can be assigned to an independent species within the genus Acetobacter, and the name of Acetobacter garciniae sp. nov. is proposed for the two isolates.
Collapse
Affiliation(s)
- Pattaraporn Yukphan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Piyanat Charoenyingcharoen
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Yutthana Kingcha
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Somsak Likhitrattanapisal
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Supattra Muangham
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand.,Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Yuzo Yamada
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand.,Japan International Cooperation Agency (JICA Senior Overseas Volunteer), Shibuya-ku, Tokyo 151-8558, Japan.,Laboratory of Applied Microbiology (Professor Emeritus), Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| |
Collapse
|
6
|
Fortney NW, Hanson NJ, Rosa PRF, Donohue TJ, Noguera DR. Diverse Profile of Fermentation Byproducts From Thin Stillage. Front Bioeng Biotechnol 2021; 9:695306. [PMID: 34336807 PMCID: PMC8320890 DOI: 10.3389/fbioe.2021.695306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/02/2021] [Indexed: 12/25/2022] Open
Abstract
The economy of biorefineries is influenced not only by biofuel production from carbohydrates but also by the production of valuable compounds from largely underutilized industrial residues. Currently, the demand for many chemicals that could be made in a biorefinery, such as succinic acid (SA), medium-chain fatty acids (MCFAs), and lactic acid (LA), is fulfilled using petroleum, palm oil, or pure carbohydrates as raw materials, respectively. Thin stillage (TS), the residual liquid material following distillation of ethanol, is an underutilized coproduct from the starch biofuel industry. This carbon-rich material has the potential for chemical upgrading by microorganisms. Here, we explored the formation of different fermentation products by microbial communities grown on TS using different bioreactor conditions. At the baseline operational condition (6-day retention time, pH 5.5, 35°C), we observed a mixture of MCFAs as the principal fermentation products. Operation of a bioreactor with a 1-day retention time induced an increase in SA production, and a temperature increase to 55°C resulted in the accumulation of lactic and propionic acids. In addition, a reactor operated with a 1-day retention time at 55°C conditions resulted in LA accumulation as the main fermentation product. The prominent members of the microbial community in each reactor were assessed by 16S rRNA gene amplicon sequencing and phylogenetic analysis. Under all operating conditions, members of the Lactobacillaceae family within Firmicutes and the Acetobacteraceae family within Proteobacteria were ubiquitous. Members of the Prevotellaceae family within Bacteroidetes and Lachnospiraceae family within the Clostridiales order of Firmicutes were mostly abundant at 35°C and not abundant in the microbial communities of the TS reactors incubated at 55°C. The ability to adjust bioreactor operating conditions to select for microbial communities with different fermentation product profiles offers new strategies to explore and compare potentially valuable fermentation products from TS and allows industries the flexibility to adapt and switch chemical production based on market prices and demands.
Collapse
Affiliation(s)
- Nathaniel W Fortney
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Nathaniel J Hanson
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Wisconsin Youth Apprenticeship Program, Department of Workforce Development, Madison, WI, United States
| | - Paula R F Rosa
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Chemical Engineering, Federal University of São Carlos, São Carlos, Brazil
| | - Timothy J Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel R Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
7
|
ODFM, an omics data resource from microorganisms associated with fermented foods. Sci Data 2021; 8:113. [PMID: 33879798 PMCID: PMC8058077 DOI: 10.1038/s41597-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 11/08/2022] Open
Abstract
ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
Collapse
Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| |
Collapse
|
10
|
Kim KH, Cho GY, Chun BH, Weckx S, Moon JY, Yeo SH, Jeon CO. Corrigendum to “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. 41 (2018) 324–332]. Syst Appl Microbiol 2020; 43:126042. [DOI: 10.1016/j.syapm.2019.126042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
11
|
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
|
12
|
Oren A, Garrity G. Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2018; 68:3371-3376. [PMID: 30113302 DOI: 10.1099/ijsem.0.002958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes respectively regulate the elevation of a subspecies to the rank of a species and the lowering of a species to the rank of subspecies. The Code does not indicate that the resulting new names must be considered new combinations, as the cases described in Rules 50a and 50b are not covered by Rule 34a. Based on the rules of the Code, new combination events are applicable only at the identical rank, and therefore new combination events and new species/subspecies events are mutually exclusive. In spite of this there have been at least 44 cases in which the new names were described as comb. nov. during elevation in rank from subspecies to species and at least 30 such cases during lowering in rank from species to subspecies. To prevent confusion in the future we propose adding notes to Rules 50a and 50b to clarify the issue.
Collapse
Affiliation(s)
- Aharon Oren
- 1The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- 2Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|
13
|
Microbial Community Composition Reveals Spatial Variation and Distinctive Core Microbiome of the Weaver Ant Oecophylla smaragdina in Malaysia. Sci Rep 2018; 8:10777. [PMID: 30018403 PMCID: PMC6050294 DOI: 10.1038/s41598-018-29159-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 06/22/2018] [Indexed: 11/20/2022] Open
Abstract
The weaver ant Oecophylla smaragdina is an aggressive predator of other arthropods and has been employed as a biological control agent against many insect pests in plantations. Despite playing important roles in pest management, information about the microbiota of O. smaragdina is limited. In this work, a number of O. smaragdina colonies (n = 12) from Malaysia had been studied on their microbiome profile using Illumina 16S rRNA gene amplicon sequencing. We characterized the core microbiota associated with these O. smaragdina and investigated variation between colonies from different environments. Across all 12 samples, 97.8% of the sequences were assigned to eight bacterial families and most communities were dominated by families Acetobacteraceae and Lactobacillaceae. Comparison among colonies revealed predominance of Acetobacteraceae in O. smaragdina from forest areas but reduced abundance was observed in colonies from urban areas. In addition, our findings also revealed distinctive community composition in O. smaragdina showing little taxonomic overlap with previously reported ant microbiota. In summary, our work provides information regarding microbiome of O. smaragdina which is essential for establishing healthy colonies. This study also forms the basis for further study on microbiome of O. smaragdina from other regions.
Collapse
|
14
|
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35:1547-1549. [PMID: 29722887 DOI: 10.1007/0-387-30745-1_9] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
Collapse
Affiliation(s)
- Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Glen Stecher
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Michael Li
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Christina Knyaz
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| |
Collapse
|
15
|
Sträuber H, Bühligen F, Kleinsteuber S, Dittrich-Zechendorf M. Carboxylic acid production from ensiled crops in anaerobic solid-state fermentation - trace elements as pH controlling agents support microbial chain elongation with lactic acid. Eng Life Sci 2018; 18:447-458. [PMID: 32624926 DOI: 10.1002/elsc.201700186] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/23/2018] [Accepted: 04/10/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND For the production of carboxylic acid platform chemicals like medium-chain fatty acids (MCFA) by anaerobic fermentation, pH control is required. However, adding buffer solutions is ineffective in leach-bed reactors. AIM In order to increase the MCFA production by maize silage fermentation and to engineer the process we investigated the effect of solid alkaline iron and manganese additives on the process performance and microbial community dynamics. RESULTS Without additives, the pH dropped to 3.9 and lactic acid bacteria were favored. Total product yields of 207 ± 5.4 g organic acids (C2-C6) and alcohols per kg volatile solids were reached. The addition of trace elements increased the pH value and the product spectrum and yields changed. With a commercial iron additive, the product yields were higher (293 ± 15.2 g/kgvolatile solids) and supposedly clostridia used lactic acid for microbial chain elongation of acetic acid producing n-butyric acid. With the addition of pure Fe(OH)3 or Mn(OH)2, the total product yields were lower than in the other reactors. However, increased production of MCFA and the occurrence of distinct bacterial taxa (Lachnospiraceae, Ruminococcaceae and Megasphaera) related to this metabolic function were observed. CONCLUSIONS The application of alkaline trace metal additives as pH stabilizing agents can mitigate spatial metabolic heterogeneities when trace metal deficient substrates like specific crops or residues thereof are applied.
Collapse
Affiliation(s)
- Heike Sträuber
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research - UFZ Leipzig Germany
| | - Franziska Bühligen
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research - UFZ Leipzig Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research - UFZ Leipzig Germany
| | - Michael Dittrich-Zechendorf
- Department Biochemical Conversion Deutsches Biomasseforschungszentrum gemeinnützige GmbH (DBFZ) Leipzig Germany
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Kohlmann R, Barenberg K, Anders A, Gatermann SG. Acetobacter indonesiensis Bacteremia in Child with Metachromatic Leukodystrophy. Emerg Infect Dis 2018; 22:1681-3. [PMID: 27533630 PMCID: PMC4994355 DOI: 10.3201/eid2209.160566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
18
|
Martínez-Torres A, Gutiérrez-Ambrocio S, Heredia-del-Orbe P, Villa-Tanaca L, Hernández-Rodríguez C. Inferring the role of microorganisms in water kefir fermentations. Int J Food Sci Technol 2016. [DOI: 10.1111/ijfs.13312] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Abigail Martínez-Torres
- Departamento de Microbiología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Prol. Carpio y Plan de Ayala; Col. Casco de Santo Tomás. Distrito Federal; CP 11340 Mexico, D.F. Mexico
| | - Sandra Gutiérrez-Ambrocio
- Departamento de Microbiología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Prol. Carpio y Plan de Ayala; Col. Casco de Santo Tomás. Distrito Federal; CP 11340 Mexico, D.F. Mexico
| | - Pamela Heredia-del-Orbe
- Departamento de Microbiología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Prol. Carpio y Plan de Ayala; Col. Casco de Santo Tomás. Distrito Federal; CP 11340 Mexico, D.F. Mexico
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Prol. Carpio y Plan de Ayala; Col. Casco de Santo Tomás. Distrito Federal; CP 11340 Mexico, D.F. Mexico
| | - César Hernández-Rodríguez
- Departamento de Microbiología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Prol. Carpio y Plan de Ayala; Col. Casco de Santo Tomás. Distrito Federal; CP 11340 Mexico, D.F. Mexico
| |
Collapse
|
19
|
Majid M, Rasoul S, Raziyeh Z, Allal H, Philippe T, Frank D, Mustapha IA. Optimization of biomass production of Acetobacter pasteurianus KU710511 as a potential starter for fruit vinegar production. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2016.15323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
20
|
|
21
|
|
22
|
Yetiman AE, Kesmen Z. Identification of acetic acid bacteria in traditionally produced vinegar and mother of vinegar by using different molecular techniques. Int J Food Microbiol 2015; 204:9-16. [PMID: 25828705 DOI: 10.1016/j.ijfoodmicro.2015.03.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 02/24/2015] [Accepted: 03/12/2015] [Indexed: 11/16/2022]
Abstract
Culture-dependent and culture-independent methods were combined for the investigation of acetic acid bacteria (AAB) populations in traditionally produced vinegars and mother of vinegar samples obtained from apple and grape. The culture-independent denaturing gradient gel electrophoresis (DGGE) analysis, which targeted the V7-V8 regions of the 16S rRNA gene, showed that Komagataeibacter hansenii and Komagataeibacter europaeus/Komagataeibacter xylinus were the most dominant species in almost all of the samples analyzed directly. The culture-independent GTG5-rep PCR fingerprinting was used in the preliminary characterization of AAB isolates and species-level identification was carried out by sequencing of the 16S rRNA gene, 16S-23S rDNA internally transcribed to the spacer (ITS) region and tuf gene. Acetobacter okinawensis was frequently isolated from samples obtained from apple while K. europaeus was identified as the dominant species, followed by Acetobacter indonesiensis in the samples originating from grape. In addition to common molecular techniques, real-time PCR intercalating dye assays, including DNA melting temperature (Tm) and high resolution melting analysis (HRM), were applied to acetic acid bacterial isolates for the first time. The target sequence of ITS region generated species-specific HRM profiles and Tm values allowed discrimination at species level.
Collapse
Affiliation(s)
- Ahmet E Yetiman
- Erciyes University, Faculty of Engineering, Food Engineering Department, Kayseri, Turkey
| | - Zülal Kesmen
- Erciyes University, Faculty of Engineering, Food Engineering Department, Kayseri, Turkey.
| |
Collapse
|
23
|
|
24
|
Mei J, Guo Q, Wu Y, Li Y. Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods. PLoS One 2014; 9:e111648. [PMID: 25360757 PMCID: PMC4216126 DOI: 10.1371/journal.pone.0111648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/01/2014] [Indexed: 12/11/2022] Open
Abstract
The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.
Collapse
Affiliation(s)
- Jun Mei
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Qizhen Guo
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yan Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yunfei Li
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- * E-mail:
| |
Collapse
|
25
|
Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure. Appl Microbiol Biotechnol 2014; 98:6015-37. [DOI: 10.1007/s00253-014-5795-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/23/2014] [Accepted: 04/26/2014] [Indexed: 02/07/2023]
|
26
|
Acetobacter lambici sp. nov., isolated from fermenting lambic beer. Int J Syst Evol Microbiol 2014; 64:1083-1089. [DOI: 10.1099/ijs.0.057315-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An acetic acid bacterium, strain LMG 27439T, was isolated from fermenting lambic beer. The cells were Gram-stain-negative, motile rods, catalase-positive and oxidase-negative. Analysis of the 16S rRNA gene sequence revealed the strain was closely related to
Acetobacter okinawensis
(99.7 % 16S rRNA gene sequence similarity with the type strain of this species),
A. ghanensis
(99.6 %),
A. syzygii
(99.6 %),
A. fabarum
(99.4 %) and
A. lovaniensis
(99.2 %). DNA–DNA hybridization with the type strains of these species revealed moderate DNA–DNA hybridization values (31–45 %). Strain LMG 27439T was unable to grow on glycerol or methanol as the sole carbon source, on yeast extract with 10 % ethanol or on glucose-yeast extract medium at 37 °C. It did not produce acid from l-arabinose, d-galactose or d-mannose, nor did it produce 2-keto-d-gluconic acid, 5-keto-d-gluconic acid or 2,5-diketo-d-gluconic acid from d-glucose. It did not grow on ammonium as the sole nitrogen source and ethanol as the sole carbon source. These genotypic and phenotypic data distinguished strain LMG 27439T from established species of the genus
Acetobacter
, and therefore we propose this strain represents a novel species of the genus
Acetobacter
. The name Acetobacter lambici sp. nov. is proposed, with LMG 27439T ( = DSM 27328T) as the type strain.
Collapse
|
27
|
Thi Lan Vu H, Yukphan P, Chaipitakchonlatarn W, Malimas T, Muramatsu Y, Thi Tu Bui U, Tanasupawat S, Cong Duong K, Nakagawa Y, Thanh Pham H, Yamada Y. Nguyenibacter vanlangensis gen. nov., sp. nov., an unusual acetic acid bacterium in the α- Proteobacteria. J GEN APPL MICROBIOL 2013; 59:153-66. [DOI: 10.2323/jgam.59.2_153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Huong Thi Lan Vu
- Department of Microbiology, Faculty of Biology, University of Science, Vietnam National University-HCM City
| | - Pattaraporn Yukphan
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)
| | - Winai Chaipitakchonlatarn
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)
| | - Taweesak Malimas
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)
| | - Yuki Muramatsu
- NITE Biological Resource Center, National Institute of Technology and Evaluation
| | - Uyen Thi Tu Bui
- Department of Microbiology, Faculty of Biology, University of Science, Vietnam National University-HCM City
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University
| | - Kien Cong Duong
- Department of Microbiology, Faculty of Biology, University of Science, Vietnam National University-HCM City
| | - Yasuyoshi Nakagawa
- NITE Biological Resource Center, National Institute of Technology and Evaluation
| | - Ho Thanh Pham
- Department of Microbiology, Faculty of Biology, University of Science, Vietnam National University-HCM City
| | - Yuzo Yamada
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)
| |
Collapse
|
28
|
lino T, Suzuki R, Kosako Y, Ohkuma M, Komagata K, Uchimura T. Acetobacter okinawensis sp. nov., Acetobacter papayae sp. nov., and Acetobacter persicus sp. nov.; novel acetic acid bacteria isolated from stems of sugarcane, fruits, and a flower in Japan. J GEN APPL MICROBIOL 2012; 58:235-43. [DOI: 10.2323/jgam.58.235] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
29
|
Tanasupawat S, Kommanee J, Yukphan P, Muramatsu Y, Nakagawa Y, Yamada Y. Acetobacter farinalis sp. nov., an acetic acid bacterium in the α-Proteobacteria. J GEN APPL MICROBIOL 2011; 57:159-67. [PMID: 21817828 DOI: 10.2323/jgam.57.159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
| | | | | | | | | | | |
Collapse
|
30
|
Valera MJ, Laich F, González SS, Torija MJ, Mateo E, Mas A. Diversity of acetic acid bacteria present in healthy grapes from the Canary Islands. Int J Food Microbiol 2011; 151:105-12. [DOI: 10.1016/j.ijfoodmicro.2011.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/01/2011] [Accepted: 08/13/2011] [Indexed: 10/17/2022]
|
31
|
Tanasupawat S, Kommanee J, Yukphan P, Nakagawa Y, Yamada Y. Identification of Acetobacter strains from Thai fermented rice products based on the 16S rRNA gene sequence and 16S-23S rRNA gene internal transcribed spacer restriction analyses. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2011; 91:2652-2659. [PMID: 21717464 DOI: 10.1002/jsfa.4506] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 04/21/2011] [Accepted: 05/15/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Fermented rice flour (khao-khab, a non-glutinous rice) and related products are Thai traditional products. The types of acetic acid bacteria (AAB) microflora in khao-khab have not been reported. In this study, Acetobacter strains were isolated and identified based on the phenotypic and chemotaxonomic characteristics and molecular aspects. RESULTS Twenty-five acetic acid bacteria isolated from fermented rice products and a starter for sweetened rice in Thailand by an enrichment culture approach, were assigned to the genus Acetobacter by phenotypic and chemotaxonomic characterisations. On the basis of the 16S rRNA gene sequence and 16S-23S rRNA gene ITS restriction analyses, 25 isolates were divided into six groups and identified at the specific level: (1) Group 1 included five isolates, which were identified as A. indonesiensis; (2) Group 2 included two isolates, which were identified as A. lovaniensis; (3) Group 3 included one isolate, which was identified as A. orientalis; (4) Group 4 included eleven isolates, which were identified as A. pasteurianus; (5) Group 5 included three isolates, which were identified as A. syzygii and (6) Group 6 included three isolates, which were unidentified and considered to constitute a new species. CONCLUSION Results revealed that various Acetobacter species were distributed in Thai fermented rice flour and related products. A novel Acetobacter species was isolated from the product.
Collapse
MESH Headings
- Acetic Acid/metabolism
- Acetobacter/classification
- Acetobacter/genetics
- Acetobacter/isolation & purification
- Acetobacter/metabolism
- Base Sequence
- DNA, Ribosomal Spacer/genetics
- Diet/ethnology
- Fermentation
- Food Microbiology
- Lactic Acid/metabolism
- Molecular Typing
- Oryza/microbiology
- Phylogeny
- Polymorphism, Restriction Fragment Length
- Quinones/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- Seeds/microbiology
- Terpenes/metabolism
- Thailand
Collapse
Affiliation(s)
- Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Wangmai, Bangkok 10330, Thailand.
| | | | | | | | | |
Collapse
|
32
|
Iino T, Suzuki R, Tanaka N, Kosako Y, Ohkuma M, Komagata K, Uchimura T. Gluconacetobacter kakiaceti sp. nov., an acetic acid bacterium isolated from a traditional Japanese fruit vinegar. Int J Syst Evol Microbiol 2011; 62:1465-1469. [PMID: 21841006 DOI: 10.1099/ijs.0.031773-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel acetic acid bacteria, strains G5-1(T) and I5-1, were isolated from traditional kaki vinegar (produced from fruits of kaki, Diospyros kaki Thunb.), collected in Kumamoto Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains G5-1(T) and I5-1 formed a distinct subline in the genus Gluconacetobacter and were closely related to Gluconacetobacter swingsii DST GL01(T) (99.3% 16S rRNA gene sequence similarity). The isolates showed 96-100% DNA-DNA relatedness with each other, but <53% DNA-DNA relatedness with closely related members of the genus Gluconacetobacter. The isolates could be distinguished from closely related members of the genus Gluconacetobacter by not producing 2- and 5-ketogluconic acids from glucose, producing cellulose, growing without acetic acid and with 30% (w/v) d-glucose, and producing acid from sugars and alcohols. Furthermore, the genomic DNA G+C contents of strains G5-1(T) and I5-1 were a little higher than those of their closest phylogenetic neighbours. On the basis of the phenotypic characteristics and phylogenetic position, strains G5-1(T) and I5-1 are assigned to a novel species, for which the name Gluconacetobacter kakiaceti sp. nov. is proposed; the type strain is G5-1(T) (=JCM 25156(T)=NRIC 0798(T)=LMG 26206(T)).
Collapse
Affiliation(s)
- Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Rei Suzuki
- Laboratory of General and Applied Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Yoshimasa Kosako
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuo Komagata
- Laboratory of General and Applied Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Tai Uchimura
- Laboratory of General and Applied Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| |
Collapse
|
33
|
Subdivision of the genus Gluconacetobacter Yamada, Hoshino and Ishikawa 1998: the proposal of Komagatabacter gen. nov., for strains accommodated to the Gluconacetobacter xylinus group in the α-Proteobacteria. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0288-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
34
|
Matsutani M, Hirakawa H, Yakushi T, Matsushita K. Genome-wide phylogenetic analysis of Gluconobacter, Acetobacter, and Gluconacetobacter. FEMS Microbiol Lett 2010; 315:122-8. [DOI: 10.1111/j.1574-6968.2010.02180.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
35
|
Suzuki R, Zhang Y, Iino T, Kosako Y, Komagata K, Uchimura T. Asaia astilbes sp. nov., Asaia platycodi sp. nov., and Asaia prunellae sp. nov., novel acetic acid bacteria isolated from flowers in Japan. J GEN APPL MICROBIOL 2010; 56:339-46. [PMID: 20953098 DOI: 10.2323/jgam.56.339] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Rei Suzuki
- Laboratory of General and Applied Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
36
|
Abstract
Recent research in microbe-insect symbiosis has shown that acetic acid bacteria (AAB) establish symbiotic relationships with several insects of the orders Diptera, Hymenoptera, Hemiptera, and Homoptera, all relying on sugar-based diets, such as nectars, fruit sugars, or phloem sap. To date, the fruit flies Drosophila melanogaster and Bactrocera oleae, mosquitoes of the genera Anopheles and Aedes, the honey bee Apis mellifera, the leafhopper Scaphoideus titanus, and the mealybug Saccharicoccus sacchari have been found to be associated with the bacterial genera Acetobacter, Gluconacetobacter, Gluconobacter, Asaia, and Saccharibacter and the novel genus Commensalibacter. AAB establish symbiotic associations with the insect midgut, a niche characterized by the availability of diet-derived carbohydrates and oxygen and by an acidic pH, selective factors that support AAB growth. AAB have been shown to actively colonize different insect tissues and organs, such as the epithelia of male and female reproductive organs, the Malpighian tubules, and the salivary glands. This complex topology of the symbiosis indicates that AAB possess the keys for passing through body barriers, allowing them to migrate to different organs of the host. Recently, AAB involvement in the regulation of innate immune system homeostasis of Drosophila has been shown, indicating a functional role in host survival. All of these lines of evidence indicate that AAB can play different roles in insect biology, not being restricted to the feeding habit of the host. The close association of AAB and their insect hosts has been confirmed by the demonstration of multiple modes of transmission between individuals and to their progeny that include vertical and horizontal transmission routes, comprising a venereal one. Taken together, the data indicate that AAB represent novel secondary symbionts of insects.
Collapse
|
37
|
Bacterial and β-proteobacterial diversity in Olea europaea var. mastoidis- and O. europaea var. koroneiki-generated olive mill wastewaters: influence of cultivation and harvesting practice on bacterial community structure. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0426-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
38
|
Torija M, Mateo E, Guillamón J, Mas A. Identification and quantification of acetic acid bacteria in wine and vinegar by TaqMan–MGB probes. Food Microbiol 2010; 27:257-65. [DOI: 10.1016/j.fm.2009.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/28/2009] [Accepted: 10/05/2009] [Indexed: 11/29/2022]
|
39
|
Microbial communities and chemical changes during fermentation of sugary Brazilian kefir. World J Microbiol Biotechnol 2010; 26:1241-50. [DOI: 10.1007/s11274-009-0294-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 12/17/2009] [Indexed: 10/20/2022]
|
40
|
Characterization of thermotolerant Acetobacter pasteurianus strains and their quinoprotein alcohol dehydrogenases. Appl Microbiol Biotechnol 2009; 85:741-51. [DOI: 10.1007/s00253-009-2203-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/13/2009] [Accepted: 08/13/2009] [Indexed: 10/20/2022]
|
41
|
Suzuki R, Lisdiyanti P, Komagata K, Uchimura T. MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase in and false growth of acetic acid bacteria on methanol. J GEN APPL MICROBIOL 2009; 55:101-10. [PMID: 19436127 DOI: 10.2323/jgam.55.101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase, was investigated for acetic acid bacteria, and growth on methanol was examined for the bacteria by using various media. Of 21 strains of acetic acid bacteria studied, Acidomonas methanolica strains showed the presence of mxaF gene exclusively, and grew on a defined medium containing methanol. Further, none of the strains tested of which the growth on methanol had been previously reported, except for Acidomonas methanolica, showed the presence of mxaF gene or the growth on methanol. Precautions were taken against false growth on compounds used for identification of bacteria.
Collapse
Affiliation(s)
- Rei Suzuki
- Laboratory of General and Applied Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | | | | | | |
Collapse
|
42
|
Cleenwerck I, De Wachter M, González A, De Vuyst L, De Vos P. Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii. Int J Syst Evol Microbiol 2009; 59:1771-86. [PMID: 19542117 DOI: 10.1099/ijs.0.005157-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) DNA fingerprinting was investigated as a tool for fast and accurate identification of acetic acid bacteria (AAB) to the species level. One hundred and thirty five reference strains and 15 additional strains, representing 50 recognized species of the family Acetobacteraceae, were subjected to AFLP analysis using the restriction enzyme combination ApaI/TaqI and the primer combination A03/T03. The reference strains had been previously subjected to either DNA-DNA hybridization or 16S-23S rRNA spacer region gene sequence analysis and were regarded as being accurately classified at the species level. The present study revealed that six of these strains should be reclassified, namely Gluconacetobacter europaeus LMG 1518 and Gluconacetobacter xylinus LMG 1510 as Gluconacetobacter xylinus and Gluconacetobacter europaeus, respectively; Gluconacetobacter kombuchae LMG 23726(T) as Gluconacetobacter hansenii; and Acetobacter orleanensis strains LMG 1545, LMG 1592 and LMG 1608 as Acetobacter cerevisiae. Cluster analysis of the AFLP DNA fingerprints of the reference strains revealed one cluster for each species, showing a linkage level below 50 % with other clusters, except for Acetobacter pasteurianus, Acetobacter indonesiensis and Acetobacter cerevisiae. These three species were separated into two, two, and three clusters, respectively. At present, confusion exists regarding the taxonomic status of Gluconacetobacter oboediens and Gluconacetobacter intermedius; the AFLP data from this study supported their classification as separate taxa. The 15 additional strains could all be identified at the species level. AFLP analysis further revealed that some species harboured genetically diverse strains, whereas other species consisted of strains showing similar banding patterns, indicating a more limited genetic diversity. It can be concluded that AFLP DNA fingerprinting is suitable for accurate identification and classification of a broad range of AAB, as well as for the determination of intraspecific genetic diversity.
Collapse
Affiliation(s)
- Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | | | | | | | | |
Collapse
|
43
|
Cleenwerck I, Gonzalez A, Camu N, Engelbeen K, De Vos P, De Vuyst L. Acetobacter fabarum sp. nov., an acetic acid bacterium from a Ghanaian cocoa bean heap fermentation. Int J Syst Evol Microbiol 2008; 58:2180-5. [PMID: 18768626 DOI: 10.1099/ijs.0.65778-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six acetic acid bacterial isolates, obtained during a study of the microbial diversity of spontaneous fermentations of Ghanaian cocoa beans, were subjected to a polyphasic taxonomic study. (GTG)(5)-PCR fingerprinting grouped the isolates together, but they could not be identified using this method. Phylogenetic analysis based on 16S rRNA gene sequences allocated the isolates to the genus Acetobacter and revealed Acetobacter lovaniensis, Acetobacter ghanensis and Acetobacter syzygii to be nearest neighbours. DNA-DNA hybridizations demonstrated that the isolates belonged to a single novel genospecies that could be differentiated from its phylogenetically nearest neighbours by the following phenotypic characteristics: no production of 2-keto-D-gluconic acid from D-glucose; growth on methanol and D-xylose, but not on maltose, as sole carbon sources; no growth on yeast extract with 30% D-glucose; and weak growth at 37 degrees C. The DNA G+C contents of four selected strains were 56.8-58.0 mol%. The results obtained prove that the isolates should be classified as representatives of a novel Acetobacter species, for which the name Acetobacter fabarum sp. nov. is proposed. The type strain is strain 985(T) (=R-36330(T) =LMG 24244(T) =DSM 19596(T)).
Collapse
Affiliation(s)
- Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | | | | | | | | | | |
Collapse
|
44
|
Bittar F, Reynaud-Gaubert M, Thomas P, Boniface S, Raoult D, Rolain JM. Acetobacter indonesiensis pneumonia after lung transplant. Emerg Infect Dis 2008; 14:997-8. [PMID: 18507930 PMCID: PMC2600273 DOI: 10.3201/eid1406.071236] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Fadi Bittar
- Unité de Research sur les Maladies Infectieuses et Tropicales Emergentes, Marseille, France
| | | | | | | | - Didier Raoult
- Unité de Research sur les Maladies Infectieuses et Tropicales Emergentes, Marseille, France
| | - Jean-Marc Rolain
- Unité de Research sur les Maladies Infectieuses et Tropicales Emergentes, Marseille, France
| |
Collapse
|
45
|
De Vero L, Giudici P. Genus-specific profile of acetic acid bacteria by 16S rDNA PCR-DGGE. Int J Food Microbiol 2008; 125:96-101. [DOI: 10.1016/j.ijfoodmicro.2007.02.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 02/15/2007] [Accepted: 02/27/2007] [Indexed: 10/22/2022]
|
46
|
Acetic acid bacteria spoilage of bottled red wine—A review. Int J Food Microbiol 2008; 125:60-70. [DOI: 10.1016/j.ijfoodmicro.2007.10.016] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Revised: 09/11/2007] [Accepted: 10/04/2007] [Indexed: 11/18/2022]
|
47
|
Cleenwerck I, De Vos P. Polyphasic taxonomy of acetic acid bacteria: An overview of the currently applied methodology. Int J Food Microbiol 2008; 125:2-14. [DOI: 10.1016/j.ijfoodmicro.2007.04.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 03/15/2007] [Accepted: 04/05/2007] [Indexed: 10/22/2022]
|
48
|
Yamada Y, Yukphan P. Genera and species in acetic acid bacteria. Int J Food Microbiol 2007; 125:15-24. [PMID: 18199517 DOI: 10.1016/j.ijfoodmicro.2007.11.077] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 09/26/2007] [Accepted: 11/27/2007] [Indexed: 10/22/2022]
Abstract
Taxonomic studies of acetic acid bacteria were historically surveyed. The genus Acetobacter was first introduced in 1898 with a single species, Acetobacter aceti. The genus Gluconobacter was proposed in 1935 for strains with intense oxidation of glucose to gluconic acid rather than oxidation of ethanol to acetic acid and no oxidation of acetate. The genus "Acetomonas" was described in 1954 for strains with polar flagellation and no oxidation of acetate. The proposals of the two generic names were due to confusion, and "Acetomonas" was a junior subjective synonym of Gluconobacter. The genus Acetobacter was in 1984 divided into two subgenera, Acetobacter and Gluconoacetobacter. The latter was elevated to the genus Gluconacetobacter in 1998. In the acetic acid bacteria, ten genera are presently recognized and accommodated to the family Acetobacteraceae, the Alphaproteobacteria: Acetobacteer, Gluconobacter, Acidomonas, Gluconacetobacter, Asaia, Kozakia, Swaminathania, Saccharibacter, Neoasaia and Granulibacter. In contrast, the genus Frateuria, strains of which were once named 'pseudacetic acid bacteria', was classified into the Gammaproteobacteria. The genus Gluconacetobacter was phylogenetically divided into two groups: the Gluconacetobacter liquefaciens group and the Gluconacetobacter xylinus group. The two groups were discussed taxonomically.
Collapse
Affiliation(s)
- Yuzo Yamada
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand.
| | | |
Collapse
|
49
|
Influence of turning and environmental contamination on the dynamics of populations of lactic acid and acetic acid bacteria involved in spontaneous cocoa bean heap fermentation in Ghana. Appl Environ Microbiol 2007; 74:86-98. [PMID: 17993565 DOI: 10.1128/aem.01512-07] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The influence of turning and environmental contamination on six spontaneous cocoa bean heap fermentations performed in Ghana was studied through a multiphasic approach, encompassing both microbiological (culture-dependent and culture-independent techniques) and metabolite target analyses. A sensory analysis of chocolate made from the fermented, dried beans was performed as well. Only four clusters were found among the isolates of acetic acid bacteria (AAB) identified: Acetobacter pasteurianus, Acetobacter ghanensis, Acetobacter senegalensis, and a potential new Acetobacter lovaniensis-like species. Two main clusters were identified among the lactic acid bacteria (LAB) isolated, namely, Lactobacillus plantarum and Lactobacillus fermentum. No differences in biodiversity of LAB and AAB were seen for fermentations carried out at the farm and factory sites, indicating the cocoa pod surfaces and not the general environment as the main inoculum for spontaneous cocoa bean heap fermentation. Turning of the heaps enhanced aeration and increased the relative population size of AAB and the production of acetic acid. This in turn gave a more sour taste to chocolate made from these beans. Bitterness was reduced through losses of polyphenols and alkaloids upon fermentation and cocoa bean processing.
Collapse
|
50
|
Cleenwerck I, Camu N, Engelbeen K, De Winter T, Vandemeulebroecke K, De Vos P, De Vuyst L. Acetobacter ghanensis sp. nov., a novel acetic acid bacterium isolated from traditional heap fermentations of Ghanaian cocoa beans. Int J Syst Evol Microbiol 2007; 57:1647-1652. [PMID: 17625210 DOI: 10.1099/ijs.0.64840-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twenty-three acetic acid bacteria, isolated from traditional heap fermentations of Ghanaian cocoa beans, were subjected to a polyphasic taxonomic study. The isolates were catalase-positive, oxidase-negative, Gram-negative rods. They oxidized ethanol to acetic acid and were unable to produce 2-ketogluconic acid, 5-ketogluconic acid and 2,5-diketogluconic acid from glucose; therefore, they were tentatively identified as Acetobacter species. 16S rRNA gene sequencing and phylogenetic analysis confirmed their position in the genus Acetobacter, with Acetobacter syzygii and Acetobacter lovaniensis as their closest phylogenetic neighbours. (GTG)(5)-PCR fingerprinting grouped the strains in a cluster that did not contain any type strains of members of the genus Acetobacter. DNA-DNA hybridization with the type strains of all recognized Acetobacter species revealed DNA-DNA relatedness values below the species level. The DNA G+C contents of three selected strains were 56.9-57.3 mol%. The novel strains had phenotypic characteristics that enabled them to be differentiated from phylogenetically related Acetobacter species, i.e. they were motile, did not produce 2-ketogluconic acid or 5-ketogluconic acid from glucose, were catalase-positive and oxidase-negative, grew on yeast extract with 30 % glucose, grew on glycerol (although weakly) but not on maltose or methanol as carbon sources, and did not grow with ammonium as sole nitrogen source and ethanol as carbon source. Based on the genotypic and phenotypic data, the isolates represent a novel species of the genus Acetobacter for which the name Acetobacter ghanensis sp. nov. is proposed. The type strain is R-29337(T) (=430A(T)=LMG 23848(T)=DSM 18895(T)).
Collapse
MESH Headings
- Acetic Acid/metabolism
- Acetobacter/chemistry
- Acetobacter/classification
- Acetobacter/isolation & purification
- Acetobacter/physiology
- Bacterial Typing Techniques
- Base Composition
- Cacao/microbiology
- Catalase/analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Ethanol/metabolism
- Fermentation
- Food Microbiology
- Genes, rRNA
- Glucose/metabolism
- Locomotion
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Oxidation-Reduction
- Oxidoreductases/analysis
- Phylogeny
- Polymerase Chain Reaction/methods
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Nicholas Camu
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Katrien Engelbeen
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Tom De Winter
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Katrien Vandemeulebroecke
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| |
Collapse
|