1
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Brandão PR, Crespo MTB, Nascimento FX. Phylogenomic and comparative analyses support the reclassification of several Komagataeibacter species as novel members of the Novacetimonas gen. nov. and bring new insights into the evolution of cellulose synthase genes. Int J Syst Evol Microbiol 2022; 72. [PMID: 35175916 DOI: 10.1099/ijsem.0.005252] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Komagataeibacter harbours bacteria presenting the ability to produce increased levels of crystalline nanocellulose, as well as strains used in the industrial production of fermented products and beverages. Still, most of the studies of this biotechnologically relevant genus were conducted based on limited phenotypic methodologies and taxonomical classifications. In this work, a detailed analysis of the currently described genus Komagataeibacter was conducted based on phylogenomic analysis, unveiling the phylogenomic relationships within the genus and allowing a detailed phylogenetic analysis of biotechnologically important genes such as those involved in cellulose biosynthesis (bcs genes). Phylogenomic and comparative genomic analysis revealed that several type strains formed an independent genomic group from those of other Komagataeibacter, prompting their reclassification as members of a novel genus, hereby termed Novacetimonas gen. nov. The results support the reclassification of Komagataeibacter hansenii, Komagataeibacter cocois, Komagataeibacter maltaceti and Komagataeibacter pomaceti as novel members of the genus Novacetimonas. The Novacetimonas hansenii species is the proposed representative of the novel genus. Importantly, phylogenetic analysis based on cellulose biosynthesis genes (bcsABCD, bcsAB2XYC2, bcsAB3C3, bcsAB4), showed that the evolutionary history of these genes is closely related to the strain's phylogenomic/taxonomic classification. Hence, the robust taxonomic classification of these bacteria will allow the better characterization and selection of strains for biotechnological applications.
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Affiliation(s)
- Pedro R Brandão
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Maria T B Crespo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Francisco X Nascimento
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
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2
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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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3
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Marič L, Cleenwerck I, Accetto T, Vandamme P, Trček J. Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar. Microorganisms 2020; 8:E1178. [PMID: 32756518 PMCID: PMC7465234 DOI: 10.3390/microorganisms8081178] [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: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 01/18/2023] Open
Abstract
Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206T (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515T (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C19:0 cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C18:1ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382T and AV436T represent novel species of the genus Komagataeibacter, for which the names Komagataeibactermelaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382T (= ZIM B1054T = LMG 31303T = CCM 8958T) and of Komagataeibacter melomenusus AV436T (= ZIM B1056T = LMG 31304T = CCM 8959T).
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Affiliation(s)
- Leon Marič
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia;
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, B-9000 Ghent, Belgium; (I.C.); (P.V.)
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, SI-1230 Domžale, Slovenia;
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, B-9000 Ghent, Belgium; (I.C.); (P.V.)
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia;
- Faculty of Chemistry and Chemical Engineering, University of Maribor, SI-2000 Maribor, Slovenia
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4
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Towards control of cellulose biosynthesis by Komagataeibacter using systems-level and strain engineering strategies: current progress and perspectives. Appl Microbiol Biotechnol 2020; 104:6565-6585. [PMID: 32529377 PMCID: PMC7347698 DOI: 10.1007/s00253-020-10671-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/29/2022]
Abstract
The strains of the Komagataeibacter genus have been shown to be the most efficient bacterial nanocellulose producers. Although exploited for many decades, the studies of these species focused mainly on the optimisation of cellulose synthesis process through modification of culturing conditions in the industrially relevant settings. Molecular physiology of Komagataeibacter was poorly understood and only a few studies explored genetic engineering as a strategy for strain improvement. Only since recently the systemic information of the Komagataeibacter species has been accumulating in the form of omics datasets representing sequenced genomes, transcriptomes, proteomes and metabolomes. Genetic analyses of the mutants generated in the untargeted strain modification studies have drawn attention to other important proteins, beyond those of the core catalytic machinery of the cellulose synthase complex. Recently, modern molecular and synthetic biology tools have been developed which showed the potential for improving targeted strain engineering. Taking the advantage of the gathered knowledge should allow for better understanding of the genotype–phenotype relationship which is necessary for robust modelling of metabolism as well as selection and testing of new molecular engineering targets. In this review, we discuss the current progress in the area of Komagataeibacter systems biology and its impact on the research aimed at scaled-up cellulose synthesis as well as BNC functionalisation.Key points • The accumulated omics datasets advanced the systemic understanding of Komagataeibacter physiology at the molecular level. • Untargeted and targeted strain modification approaches have been applied to improve nanocellulose yield and properties. • The development of modern molecular and synthetic biology tools presents a potential for enhancing targeted strain engineering. • The accumulating omic information should improve modelling of Komagataeibacter’s metabolism as well as selection and testing of new molecular engineering targets. |
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Characterization and optimization of production of bacterial cellulose from strain CGMCC 17276 based on whole-genome analysis. Carbohydr Polym 2020; 232:115788. [DOI: 10.1016/j.carbpol.2019.115788] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022]
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Naloka K, Yukphan P, Matsutani M, Matsushita K, Theeragool G. Komagataeibacter diospyri sp. nov., a novel species of thermotolerant bacterial nanocellulose-producing bacterium. Int J Syst Evol Microbiol 2020; 70:251-258. [PMID: 31622229 DOI: 10.1099/ijsem.0.003745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermotolerant bacterial nanocellulose-producing strains, designated MSKU 9T and MSKU 15, were isolated from persimmon and sapodilla fruits, respectively. These strains were aerobic, Gram-stain-negative, had rod-shaped cells, were non-motile and formed white-cream colonies. Phylogeny based on the 16S rRNA gene sequences revealed that MSKU 9T and MSKU 15 represented members of the genus Komagataeibacter and formed a monophyletic branch with K. swingsii JCM 17123T and K. europaeus DSM 6160T. The genomic analysis revealed that overall genomic relatedness index values of MSKU 9T with K. swingsii JCM 17123T and K. europaeus DSM 6160T were ~90 % average nucleotide identity (ANI) and ≤58.2 % digital DNA-DNA hybridization (dDDH), respectively. MSKU 9T and MSKU 15 can be differentiated from the closely related K. swingsii JCM 17123T by their growth on 30 % d-glucose and ability to utilize and to form acid from raffinose and sucrose as carbon sources, and from K. europaeus DSM 6160T by their ability to grow without acetic acid. The genomic DNA G+C contents of MSKU 9T and MSKU 15 were 60.4 and 60.2 mol%, respectively. The major fatty acids of MSKU 9T and MSKU 15 were summed feature 8 (C18 : 1 ω7c and/or C18 : 1ω6c). The respiratory quinone was determined to be Q10. On the basis of the results of the polyphasic taxonomic analysis, MSKU 9T (=TBRC 9844T=NBRC 113802T) represents a novel species of the genus Komagataeibacter, for which the name Komagataeibacter diospyri sp. nov. is proposed.
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Affiliation(s)
- Kallayanee Naloka
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pattaraporn Yukphan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Minenosuke Matsutani
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kazunobu Matsushita
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan.,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Gunjana Theeragool
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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7
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Raiszadeh-Jahromi Y, Rezazadeh-Bari M, Almasi H, Amiri S. Optimization of bacterial cellulose production by Komagataeibacter xylinus PTCC 1734 in a low-cost medium using optimal combined design. Journal of Food Science and Technology 2020; 57:2524-2533. [PMID: 32549603 DOI: 10.1007/s13197-020-04289-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/22/2020] [Accepted: 01/29/2020] [Indexed: 11/28/2022]
Abstract
This study was aimed to optimize the production of bacterial cellulose (BC) by Komagataeibacter xylinus PTCC 1734 using mixture of date syrup and cheese whey as carbon sources as well as ascorbic acid as a supplementary agent and to characterize the properties of produced BC. The results showed the highest BC production on the 10th day. The 50:50 ratio of date syrup and cheese whey lead to the highest BC production. Three samples were selected in optimal cultivation conditions until the 10th day, with different ascorbic acid concentrations (0, 0.1 and 0.4%). SEM results showed no difference in the morphology of BC product in the optimal samples, where the average diameter of cellulose nanofibers produced was in the range of nanometer. The FTIR test results showed no difference in the chemical structure of cellulose product in different ascorbic acid concentrations. According to XRD and TGA analyses, the highest degree of BC crystallinity and thermal resistance was obtained at maximum ascorbic acid concentration (0.04%). Consequently, the 50:50 ratio of date syrup and cheese whey and 10th day of fermentation time were selected as the best conditions for BC production. Though ascorbic acid reduced production efficiency, it improved the physical properties of the BC product.
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Affiliation(s)
| | - Mahmoud Rezazadeh-Bari
- Department of Food Science and Technology, Factually of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Almasi
- Department of Food Science and Technology, Factually of Agriculture, Urmia University, Urmia, Iran
| | - Saber Amiri
- Department of Food Science and Technology, Factually of Agriculture, University of Tabriz, Tabriz, Iran
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8
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Gullo M, La China S, Petroni G, Di Gregorio S, Giudici P. Exploring K2G30 Genome: A High Bacterial Cellulose Producing Strain in Glucose and Mannitol Based Media. Front Microbiol 2019; 10:58. [PMID: 30761107 PMCID: PMC6363697 DOI: 10.3389/fmicb.2019.00058] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022] Open
Abstract
Demands for renewable and sustainable biopolymers have rapidly increased in the last decades along with environmental issues. In this context, bacterial cellulose, as renewable and biodegradable biopolymer has received considerable attention. Particularly, acetic acid bacteria of the Komagataeibacter xylinus species can produce bacterial cellulose from several carbon sources. To fully exploit metabolic potential of cellulose producing acetic acid bacteria, an understanding of the ability of producing bacterial cellulose from different carbon sources and the characterization of the genes involved in the synthesis is required. Here, K2G30 (UMCC 2756) was studied with respect to bacterial cellulose production in mannitol, xylitol and glucose media. Moreover, the draft genome sequence with a focus on cellulose related genes was produced. A pH reduction and gluconic acid formation was observed in glucose medium which allowed to produce 6.14 ± 0.02 g/L of bacterial cellulose; the highest bacterial cellulose production obtained was in 1.5% (w/v) mannitol medium (8.77 ± 0.04 g/L), while xylitol provided the lowest (1.35 ± 0.05 g/L) yield. Genomic analysis of K2G30 revealed a peculiar gene sets of cellulose synthase; three bcs operons and a fourth copy of bcsAB gene, that encodes the catalytic core of cellulose synthase. These features can explain the high amount of bacterial cellulose produced by K2G30 strain. Results of this study provide valuable information to industrially exploit acetic acid bacteria in producing bacterial cellulose from different carbon sources including vegetable waste feedstocks containing mannitol.
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Affiliation(s)
- Maria Gullo
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | | | | | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
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9
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Liu LX, Liu SX, Wang YM, Bi JC, Chen HM, Deng J, Zhang C, Hu QS, Li CF. Komagataeibacter cocois sp. nov., a novel cellulose-producing strain isolated from coconut milk. Int J Syst Evol Microbiol 2018; 68:3125-3131. [PMID: 30132753 DOI: 10.1099/ijsem.0.002947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7T, isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter. DNA-DNA correlation or average nucleotide identity analysis was performed between WE7T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7T (=CGMCC 1.15338T=JCM 31140T).
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Affiliation(s)
- Long-Xiang Liu
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Si-Xin Liu
- 2College of Materials and Chemical Engineering, Hainan University, Haikou 570228, PR China.,1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Yan-Mei Wang
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Ji-Cai Bi
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Hua-Mei Chen
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Jian Deng
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Cui Zhang
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Qi-Song Hu
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Cong-Fa Li
- 1College of Food Science and Technology, Hainan University, Haikou 570228, PR China
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10
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Škraban J, Cleenwerck I, Vandamme P, Fanedl L, Trček J. Genome sequences and description of novel exopolysaccharides producing species Komagataeibacter pomaceti sp. nov. and reclassification of Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al., 2013 as a later heterotypic synonym of Komagataeibacter hansenii (Gosselé et al. 1983) Yamada et al., 2013. Syst Appl Microbiol 2018; 41:581-592. [PMID: 30177404 DOI: 10.1016/j.syapm.2018.08.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022]
Abstract
Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529T and Gluconacetobacter entanii LTH 4560T. Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S-23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA-DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA-DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer-Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150T [=CCM 8723T=ZIM B1029T] as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii.
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Affiliation(s)
- Jure Škraban
- University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, Ghent, Belgium
| | - Lijana Fanedl
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Janja Trček
- University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia; University of Maribor, Faculty of Chemistry and Chemical Engineering, Maribor, Slovenia.
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11
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De Filippis F, Troise AD, Vitaglione P, Ercolini D. Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation. Food Microbiol 2018. [DOI: 10.1016/j.fm.2018.01.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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12
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Florea M, Hagemann H, Santosa G, Abbott J, Micklem CN, Spencer-Milnes X, de Arroyo Garcia L, Paschou D, Lazenbatt C, Kong D, Chughtai H, Jensen K, Freemont PS, Kitney R, Reeve B, Ellis T. Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain. Proc Natl Acad Sci U S A 2016; 113:E3431-40. [PMID: 27247386 PMCID: PMC4914174 DOI: 10.1073/pnas.1522985113] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Bacterial cellulose is a strong and ultrapure form of cellulose produced naturally by several species of the Acetobacteraceae Its high strength, purity, and biocompatibility make it of great interest to materials science; however, precise control of its biosynthesis has remained a challenge for biotechnology. Here we isolate a strain of Komagataeibacter rhaeticus (K. rhaeticus iGEM) that can produce cellulose at high yields, grow in low-nitrogen conditions, and is highly resistant to toxic chemicals. We achieved external control over its bacterial cellulose production through development of a modular genetic toolkit that enables rational reprogramming of the cell. To further its use as an organism for biotechnology, we sequenced its genome and demonstrate genetic circuits that enable functionalization and patterning of heterologous gene expression within the cellulose matrix. This work lays the foundations for using genetic engineering to produce cellulose-based materials, with numerous applications in basic science, materials engineering, and biotechnology.
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Affiliation(s)
- Michael Florea
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Henrik Hagemann
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Gabriella Santosa
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James Abbott
- Bioinformatics Support Service, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom; Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chris N Micklem
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xenia Spencer-Milnes
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Laura de Arroyo Garcia
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Despoina Paschou
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Christopher Lazenbatt
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Deze Kong
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Haroon Chughtai
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kirsten Jensen
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Richard Kitney
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Benjamin Reeve
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tom Ellis
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom;
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Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582. Sci Rep 2016; 6:23635. [PMID: 27010592 PMCID: PMC4806288 DOI: 10.1038/srep23635] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 03/10/2016] [Indexed: 12/27/2022] Open
Abstract
Bacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in addition to the previously described cellulose synthase operon, ATCC 53582 contains two additional cellulose synthase operons and several previously undescribed genes associated with cellulose production. In parallel, we also develop optimized protocols and identify plasmid backbones suitable for transformation of ATCC 53582, albeit with low efficiencies. Together, these results provide important information for further studies into cellulose synthesis and for future studies aiming to genetically engineer G. hansenii ATCC 53582 for increased cellulose productivity.
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Reis VM, Teixeira KRDS. Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture. J Basic Microbiol 2015; 55:931-49. [PMID: 25736602 PMCID: PMC7166518 DOI: 10.1002/jobm.201400898] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/27/2015] [Indexed: 11/17/2022]
Abstract
For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N2 is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth-promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth-promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.
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15
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Microbial diversity and their roles in the vinegar fermentation process. Appl Microbiol Biotechnol 2015; 99:4997-5024. [DOI: 10.1007/s00253-015-6659-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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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: 33] [Impact Index Per Article: 3.3] [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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Physical, structural, mechanical and thermal characterization of bacterial cellulose by G. hansenii NCIM 2529. Carbohydr Polym 2014; 106:132-41. [DOI: 10.1016/j.carbpol.2014.02.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 11/20/2022]
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18
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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]
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19
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Lin D, Lopez-Sanchez P, Li R, Li Z. Production of bacterial cellulose by Gluconacetobacter hansenii CGMCC 3917 using only waste beer yeast as nutrient source. BIORESOURCE TECHNOLOGY 2014; 151:113-9. [PMID: 24212131 DOI: 10.1016/j.biortech.2013.10.052] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 05/11/2023]
Abstract
In order to improve the use of waste beer yeast (WBY) for bacterial cellulose production by Gluconacetobacter hansenii CGMCC 3917, a two-step pre-treatment was designed. First WBY was treated by 4 methods: 0.1M NaOH treatment, high speed homogenizer, ultrasonication and microwave treatment followed by hydrolysis (121°C, 20 min) under mild acid condition (pH 2). The optimal pre-treatment conditions were evaluated by the reducing sugar yield after hydrolysis. 15% WBY treated by ultrasonication for 40 min had the highest reducing sugar yield (29.19%), followed by NaOH treatment (28.98%), high speed homogenizer (13.33%) and microwaves (13.01%). Treated WBY hydrolysates were directly supplied as only nutrient source for BC production. A sugar concentration of 3% WBY hydrolysates treated by ultrasonication gave the highest BC yield (7.02 g/L), almost 6 times as that from untreated WBY (1.21 g/L). Furthermore, the properties of the BC were as good as those obtained from the conventional chemical media.
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Affiliation(s)
- Dehui Lin
- College of Food Science and Engineering, Northwest A&F University, No. 28 Xinong Road, 712100 Yangling, Shaanxi, China.
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20
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Valera MJ, Torija MJ, Mas A, Mateo E. Acetobacter malorum and Acetobacter cerevisiae identification and quantification by Real-Time PCR with TaqMan-MGB probes. Food Microbiol 2013; 36:30-9. [PMID: 23764217 DOI: 10.1016/j.fm.2013.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/06/2013] [Accepted: 03/27/2013] [Indexed: 10/27/2022]
Abstract
The identification and quantification of Acetobacter malorum and Acetobacter cerevisiae in wine and vinegar were performed using the Real-Time PCR (RT-PCR) with two TaqMan-MGB probes designed to amplify the internal transcribed spacer (ITS) region between the 16S-23S rRNA genes. The primers and probes were highly specific, with a detection limit of 10² cells/ml for both species, and the efficiency of the technique was >80%. The RT-PCR technique with these two new TaqMan-MGB probes, together with the five (Acetobacter aceti, Acetobacter pasteurianus, Gluconobacter oxydans, Gluconacetobacter hansenii and Gluconacetobacter europaeus) that are already available (Torija et al., 2010), were validated on known concentrations of Acetic Acid Bacteria (AAB) grown in glucose medium (GY) and in inoculated matrices of wine and vinegar. Furthermore, this technique was applied to evaluate the AAB population in real wine samples collected in the Canary Islands. PCR enrichment performed prior to RT-PCR increased the accuracy of quantification and produced results similar to those detected with SYBR-Green. In real wine samples, the total AAB enumeration ranged from 9 × 10² to 10⁶ cells/ml, and the seven AAB species tested were detected in more than one sample. However, AAB recovery on plates was poor; the isolates obtained on plates were A. malorum, G. oxydans, A. cerevisiae and A. pasteurianus species. RT-PCR with TaqMan-MGB probes is an accurate, specific and fast method for the identification and quantification of AAB species commonly found in wine and vinegar.
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Affiliation(s)
- Maria José Valera
- Biotecnologia Enológica, Dept. Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, C/ Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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Vegas C, González Á, Mateo E, Mas A, Poblet M, Torija MJ. Evaluation of representativity of the acetic acid bacteria species identified by culture-dependent method during a traditional wine vinegar production. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.12.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Enhanced Production of Bacterial Cellulose by Using Gluconacetobacter hansenii NCIM 2529 Strain Under Shaking Conditions. Appl Biochem Biotechnol 2013; 169:1497-511. [DOI: 10.1007/s12010-013-0092-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 01/01/2013] [Indexed: 11/25/2022]
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23
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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)
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Slapšak N, Cleenwerck I, De Vos P, Trček J. Gluconacetobacter maltaceti sp. nov., a novel vinegar producing acetic acid bacterium. Syst Appl Microbiol 2012; 36:17-21. [PMID: 23273842 DOI: 10.1016/j.syapm.2012.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 11/29/2022]
Abstract
Comparison of HaeIII- and HpaII-restriction profiles of PCR-amplified 16S-23S rDNA ITS regions of Gluconacetobacter sp. LMG 1529(T) and SKU 1109 with restriction profiles of reference strains of acetic acid bacteria described by Trček and Teuber [34] revealed the same but unique restriction profiles for LMG 1529(T) and SKU 1109. Further analyses of nearly complete 16S rRNA gene sequences, nearly complete 16S-23S rDNA ITS sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, allocated both strains to a single phylogenetic cluster well separated from the other species of the genus Gluconacetobacter. DNA-DNA hybridizations confirmed their novel species identity by 73% DNA-DNA relatedness between both strains, and values below the species level (<70%) between SKU 1109 and the type strains of the closest phylogenetic neighbors. The classification of strains LMG 1529(T) and SKU 1109 into a single novel species was confirmed also by AFLP and (GTG)(5)-PCR DNA fingerprinting data, as well as by phenotypic data. Strains LMG 1529(T) and SKU 1109 can be differentiated from their closely related Gluconacetobacter species, Gluconacetobacter entanii and Gluconacetobacter hansenii, by their ability to form 2-keto-d-gluconic acid from d-glucose, their ability to use d-mannitol, d-gluconate and glycerol as carbon source and form acid from d-fructose, and their ability to grow without acetic acid. The major fatty acid of LMG 1529(T) and SKU 1109 is C(18:1ω7c) (60.2-64.8%). The DNA G+C content of LMG 1529(T) and SKU 1109 is 62.5 and 63.3mol% respectively. The name Gluconacetobacter maltaceti sp. nov. is proposed. The type strain is LMG 1529(T) (=NBRC 14815(T)=NCIMB 8752(T)).
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Affiliation(s)
- Nina Slapšak
- University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia
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25
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Castro C, Cleenwerck I, Trček J, Zuluaga R, De Vos P, Caro G, Aguirre R, Putaux JL, Gañán P. Gluconacetobacter medellinensis sp. nov., cellulose- and non-cellulose-producing acetic acid bacteria isolated from vinegar. Int J Syst Evol Microbiol 2012; 63:1119-1125. [PMID: 22729025 DOI: 10.1099/ijs.0.043414-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic position of a cellulose-producing acetic acid bacterium, strain ID13488, isolated from commercially available Colombian homemade fruit vinegar, was investigated. Analyses using nearly complete 16S rRNA gene sequences, nearly complete 16S-23S rRNA gene internal transcribed spacer (ITS) sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, allocated the micro-organism to the genus Gluconacetobacter, and more precisely to the Gluconacetobacter xylinus group. Moreover, the data suggested that the micro-organism belongs to a novel species in this genus, together with LMG 1693(T), a non-cellulose-producing strain isolated from vinegar by Kondo and previously classified as a strain of Gluconacetobacter xylinus. DNA-DNA hybridizations confirmed this finding, revealing a DNA-DNA relatedness value of 81 % between strains ID13488 and LMG 1693(T), and values <70 % between strain LMG 1693(T) and the type strains of the closest phylogenetic neighbours. Additionally, the classification of strains ID13488 and LMG 1693(T) into a single novel species was supported by amplified fragment length polymorphism (AFLP) and (GTG)5-PCR DNA fingerprinting data, as well as by phenotypic data. Strains ID13488 and LMG 1693(T) could be differentiated from closely related species of the genus Gluconacetobacter by their ability to produce 2- and 5-keto-d-gluconic acid from d-glucose, their ability to produce acid from sucrose, but not from 1-propanol, and their ability to grow on 3 % ethanol in the absence of acetic acid and on ethanol, d-ribose, d-xylose, sucrose, sorbitol, d-mannitol and d-gluconate as carbon sources. The DNA G+C content of strains ID13488 and LMG 1693(T) was 58.0 and 60.7 mol%, respectively. The major ubiquinone of LMG 1693(T) was Q-10. Taken together these data indicate that strains ID13488 and LMG 1693(T) represent a novel species of the genus Gluconacetobacter for which the name Gluconacetobacter medellinensis sp. nov. is proposed. The type strain is LMG 1693(T) ( = NBRC 3288(T) = Kondo 51(T)).
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Affiliation(s)
- Cristina Castro
- Faculty of Textile Engineering, Universidad Pontificia Bolivariana, Circular 1 # 70-01, Medellín, Colombia
| | - Ilse Cleenwerck
- BCCM/LMG Bacterial Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Janja Trček
- University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Koroška cesta 160, 2000 Maribor, Slovenia
| | - Robin Zuluaga
- Faculty of Agroindustrial Engineering, Universidad Pontificia Bolivariana, Circular 1 # 70-01, Medellín, Colombia
| | - Paul De Vos
- BCCM/LMG Bacterial Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Gloria Caro
- Faculty of Textile Engineering, Universidad Pontificia Bolivariana, Circular 1 # 70-01, Medellín, Colombia
| | - Ricardo Aguirre
- School of Medicine, Universidad Pontificia Bolivariana, Cll 78b # 72a-109, Medellín, Colombia
| | - Jean-Luc Putaux
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041 Grenoble cedex 9, France (affiliated with Université Joseph Fourier and member of the Institut de Chimie Moléculaire de Grenoble)
| | - Piedad Gañán
- Faculty of Chemical Engineering, Universidad Pontificia Bolivariana, Circular 1 # 70-01, Medellín, Colombia
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Barata A, Malfeito-Ferreira M, Loureiro V. Changes in sour rotten grape berry microbiota during ripening and wine fermentation. Int J Food Microbiol 2012; 154:152-61. [PMID: 22277696 DOI: 10.1016/j.ijfoodmicro.2011.12.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 11/18/2011] [Accepted: 12/22/2011] [Indexed: 11/17/2022]
Abstract
This study investigated the microbiota of sour rotten wine grapes and its impact on wine fermentations. Yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) were enumerated and identified on sound and sour rot grapes during the ripening stage. The alteration of the ecological balance induced by sour rot was particularly evidenced by the unequivocal increase of yeast and AAB counts on rotten grapes, since the beginning of ripening. Yeast and AAB species diversity in rotten grape samples were much higher than those found in sound grapes. LAB populations were low detected from both healthy and sour rotten grapes. The yeast species Issatchenkia occidentalis, Zygoascus hellenicus and Zygosaccharomyces bailii and the AAB species Gluconacetobacter hansenii, Gluconacetobacter intermedius and Acetobacter malorum, were recovered from damaged grapes and resulting grape juices in the winery. Acetobacter orleaniensis and Acetobacter syzygii were only recovered from sour rotten grapes. Dekkera bruxellensis and Oenococcus oeni were only recovered after wine fermentation induced by starter inoculation, irrespective of grape health, probably originating from cellar environment. After malolactic fermentation, racking and sulphur dioxide addition the only remaining species were the yeast Trigonopsis cantarellii and Saccharomyces cerevisiae, independently of the grape health status.
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Affiliation(s)
- André Barata
- Laboratório de Microbiologia, Departamento de Recursos Naturais Ambiente e Território, Centro de Botânica Aplicada à Agricultura, Instituto Superior de Agronomia, Technical University of Lisbon, Lisboa, Portugal.
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27
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Yamada Y, Yukphan P, Lan Vu HT, Muramatsu Y, Ochaikul D, Tanasupawat S, Nakagawa Y. Description of Komagataeibacter gen. nov., with proposals of new combinations (Acetobacteraceae). J GEN APPL MICROBIOL 2012; 58:397-404. [DOI: 10.2323/jgam.58.397] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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28
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Valepyn E, Berezina N, Paquot M. Optimization of Production and Preliminary Characterization of New Exopolysaccharides from <i>Gluconacetobacter hansenii</i> LMG1524. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/aim.2012.24062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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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]
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30
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Gluconacetobacter hansenii subsp. nov., a High-Yield Bacterial Cellulose Producing Strain Induced by High Hydrostatic Pressure. Appl Biochem Biotechnol 2011; 165:1519-31. [DOI: 10.1007/s12010-011-9372-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
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31
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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)).
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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
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32
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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
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34
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González A, Mas A. Differentiation of acetic acid bacteria based on sequence analysis of 16S-23S rRNA gene internal transcribed spacer sequences. Int J Food Microbiol 2011; 147:217-22. [PMID: 21543129 DOI: 10.1016/j.ijfoodmicro.2011.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/25/2011] [Accepted: 04/06/2011] [Indexed: 11/29/2022]
Abstract
The 16S-23S gene internal transcribed spacer sequence of sixty-four strains belonging to different acetic acid bacteria genera were analyzed, and phylogenetic trees were generated for each genera. The topologies of the different trees were in accordance with the 16S rRNA gene trees, although the similarity percentages obtained between the species was shown to be much lower. These values suggest the usefulness of including the 16S-23S gene internal transcribed spacer region as a part of the polyphasic approach required for the further classification of acetic acid bacteria. Furthermore, the region could be a good target for primer and probe design. It has also been validated for use in the identification of unknown samples of this bacterial group from wine vinegar and fruit condiments.
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Affiliation(s)
- Angel González
- Departament de Bioquímica i Biotecnología, Facultat de Enologia, Universitat Rovira i Virgili, Tarragona, Spain
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35
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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
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36
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Cleenwerck I, De Vos P, De Vuyst L. Phylogeny and differentiation of species of the genus Gluconacetobacter and related taxa based on multilocus sequence analyses of housekeeping genes and reclassification of Acetobacter xylinus subsp. sucrofermentans as Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov. Int J Syst Evol Microbiol 2010; 60:2277-2283. [DOI: 10.1099/ijs.0.018465-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three housekeeping genes (dnaK, groEL and rpoB) of strains belonging to the genus Gluconacetobacter (37 strains) or related taxa (38 strains) were sequenced. Reference strains of the 15 species of the genus Gluconacetobacter were included. Phylogenetic trees generated using these gene sequences confirmed the existence of two phylogenetic groups within the genus Gluconacetobacter. These groups clustered separately in trees constructed using concatenated sequences of the three genes, indicating that the genus Gluconacetobacter should not remain a single genus and should be split, as suggested previously. Multilocus sequence analysis (MLSA) of the three housekeeping genes also proved useful for species differentiation in the family Acetobacteraceae. It also suggested that Gluconacetobacter xylinus LMG 18788, better known as the type and only strain of Acetobacter xylinus subsp. sucrofermentans, represents a distinct species in the genus Gluconacetobacter, and is not a true G. xylinus strain. In previous studies, this strain showed less than 70 % DNA relatedness to the type strains of G. xylinus and Gluconacetobacter nataicola, the phylogenetically nearest relatives, and could be distinguished from them phenotypically. Additionally, AFLP and (GTG)5-PCR DNA fingerprinting data supported its reclassification within a distinct species. The name Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov. is proposed.
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Affiliation(s)
- Ilse Cleenwerck
- 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, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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37
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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.
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38
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Genome sequence of a cellulose-producing bacterium, Gluconacetobacter hansenii ATCC 23769. J Bacteriol 2010; 192:4256-7. [PMID: 20543071 DOI: 10.1128/jb.00588-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Gluconacetobacter hansenii is considered a model organism for studying cellulose synthesis. We have determined the genome sequence of strain ATCC 23769.
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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.
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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
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40
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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.
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Affiliation(s)
- Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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41
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Ludwig W. Reprint of “Nucleic acid techniques in bacterial systematics and identification" [Int. J. Food Microbiol., 120 (2007) 225–236]. Int J Food Microbiol 2008; 125:I-XII. [DOI: 10.1016/s0168-1605(08)00293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 05/08/2007] [Accepted: 06/04/2007] [Indexed: 10/22/2022]
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42
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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]
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43
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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.
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Affiliation(s)
- Yuzo Yamada
- BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand.
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44
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Ludwig W. Nucleic acid techniques in bacterial systematics and identification. Int J Food Microbiol 2007; 120:225-36. [PMID: 17961780 DOI: 10.1016/j.ijfoodmicro.2007.06.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 05/08/2007] [Accepted: 06/04/2007] [Indexed: 12/27/2022]
Abstract
Systematics and identification play central roles in any discipline of microbiology. The current prokaryotic taxonomic framework as proposed in Bergey's Manual of Systematic Bacteriology is mainly based on small subunit rRNA data. Alternative markers representing the conserved core of the prokaryotic genomes roughly support rRNA based phylogenetic inference. Consequently, many of the nucleic acid based techniques for identification target these molecules: i.e. comparative sequencing, specific probing, diagnostic PCR, and pattern techniques. For studies at species and lower taxonomic ranks, however, alternative less conserved targets have to be chosen. An overview of commonly used targets and methods for identification or differentiation is given below.
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Affiliation(s)
- Wolfgang Ludwig
- Lehrstuhl für Mikrobiologie, Technical University Munich, Am Hochanger 4, 85354 Freising, Germany.
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45
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De Vuyst L, Camu N, De Winter T, Vandemeulebroecke K, Van de Perre V, Vancanneyt M, De Vos P, Cleenwerck I. Validation of the (GTG)(5)-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans. Int J Food Microbiol 2007; 125:79-90. [PMID: 17920717 DOI: 10.1016/j.ijfoodmicro.2007.02.030] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 01/19/2007] [Accepted: 02/27/2007] [Indexed: 11/19/2022]
Abstract
Amplification of repetitive bacterial DNA elements through the polymerase chain reaction (rep-PCR fingerprinting) using the (GTG)(5) primer, referred to as (GTG)(5)-PCR fingerprinting, was found a promising genotypic tool for rapid and reliable speciation of acetic acid bacteria (AAB). The method was evaluated with 64 AAB reference strains, including 31 type strains, and 132 isolates from Ghanaian, fermented cocoa beans, and was validated with DNA:DNA hybridization data. Most reference strains, except for example all Acetobacter indonesiensis strains and Gluconacetobacter liquefaciens LMG 1509, grouped according to their species designation, indicating the usefulness of this technique for identification to the species level. Moreover, exclusive patterns were obtained for most strains, suggesting that the technique can also be used for characterization below species level or typing of AAB strains. The (GTG)(5)-PCR fingerprinting allowed us to differentiate four major clusters among the fermented cocoa bean isolates, namely A. pasteurianus (cluster I, 100 isolates), A. syzygii- or A. lovaniensis-like (cluster II, 23 isolates), and A. tropicalis-like (clusters III and IV containing 4 and 5 isolates, respectively). A. syzygii-like and A. tropicalis-like strains from cocoa bean fermentations were reported for the first time. Validation of the method and indications for reclassifications of AAB species and existence of new Acetobacter species were obtained through 16S rRNA sequencing analyses and DNA:DNA hybridizations. Reclassifications refer to A. aceti LMG 1531, Ga. xylinus LMG 1518, and Ga. xylinus subsp. sucrofermentans LMG 18788(T).
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Affiliation(s)
- 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.
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46
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Dutta D, Gachhui R. Nitrogen-fixing and cellulose-producing Gluconacetobacter kombuchae sp. nov., isolated from Kombucha tea. Int J Syst Evol Microbiol 2007; 57:353-357. [PMID: 17267978 DOI: 10.1099/ijs.0.64638-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A few members of the family Acetobacteraceae are cellulose-producers, while only six members fix nitrogen. Bacterial strain RG3T, isolated from Kombucha tea, displays both of these characteristics. A high bootstrap value in the 16S rRNA gene sequence-based phylogenetic analysis supported the position of this strain within the genus Gluconacetobacter, with Gluconacetobacter hansenii LMG 1527T as its nearest neighbour (99.1 % sequence similarity). It could utilize ethanol, fructose, arabinose, glycerol, sorbitol and mannitol, but not galactose or xylose, as sole sources of carbon. Single amino acids such as l-alanine, l-cysteine and l-threonine served as carbon and nitrogen sources for growth of strain RG3T. Strain RG3T produced cellulose in both nitrogen-free broth and enriched medium. The ubiquinone present was Q-10 and the DNA base composition was 55.8 mol% G+C. It exhibited low values of 5.2–27.77 % DNA–DNA relatedness to the type strains of related gluconacetobacters, which placed it within a separate taxon, for which the name Gluconacetobacter kombuchae sp. nov. is proposed, with the type strain RG3T (=LMG 23726T=MTCC 6913T).
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MESH Headings
- Amino Acids/metabolism
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- Cellulose/biosynthesis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Food Microbiology
- Genes, rRNA
- Gluconacetobacter/classification
- Gluconacetobacter/genetics
- Gluconacetobacter/isolation & purification
- Gluconacetobacter/physiology
- Molecular Sequence Data
- Nitrogen Fixation
- Nucleic Acid Hybridization
- Phylogeny
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Tea/microbiology
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Affiliation(s)
- Debasree Dutta
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Ratan Gachhui
- Department of Life Science & Biotechnology, Jadavpur University, Kolkata 700032, West Bengal, India
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