Nguyenibacter vanlangensis gen. nov., sp. nov., an unusual acetic acid bacterium in the -Proteobacteria (original) (raw)
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Molecular Biology
Acetobacteraceae family under the class Alpha Proteobacteria comprise of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria is economically the most significant group under this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain significantly low abundance in their natural habitats. Thus identification of the organisms in such environments are getting increasingly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly more among the Acetic Acid Bacteria than the whole of the Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.
16S rRNA gene sequences analysis of acetic acid bacteria isolated from Thailand
We determined the 16S rRNA gene sequences of 302 strains of acetic acid bacteria isolated from Thailand. The isolates were divided into 35 sequence groups based on differences in 16S rRNA gene sequences. A phylogenetic tree constructed from these sequences showed that 5 strains should be classified into new genera in the family Acetobacteraceae. The other 297 strains were assigned to 33 sequence groups of 4 known genera Acetobacter, Asaia, Gluconacetobacter, and Gluconobacter. Seventeen strains belonging to Acetobacter were divided into 8 sequence groups (AB1-AB8). Seven groups except for AB2 were closely related to known Acetobacter species. AB2 was remote from known Acetobacter species. We sorted 150 strains of Asaia into 11 sequence groups (AS1-AS11). AS11 was distinct from all known Asaia species. Nine strains assigned to Gluconacetobacter showed 100% sequence similarity to Gluconacetobacter liquefaciens NBRC 12388T. Further, 121 strains of Gluconobacter were divided into 13 sequence groups (GB1-GB13). Of these, GB1 and GB6 seemed to constitute 2 distinct lineages in the genus. Based on these results, 155 Thai strains were deposited from the BIOTEC culture collection (BCC) in the NITE Biological Resource Center (NBRC) for public use.
Gluconobacter japonicus sp. nov., an acetic acid bacterium in the Alphaproteobacteria
International Journal of Systematic and Evolutionary Microbiology, 2009
Five strains, NBRC 3271 T , NBRC 3272, NBRC 3263, NBRC 3260 and NBRC 3269 were examined genetically, phylogenetically, phenotypically and chemotaxonomically. The DNA G+C contents of the five strains were 55.1-56.4 mol%. The five strains had low levels of DNA-DNA hybridization of 13-51 % to the type strains of Gluconobacter frateurii, Gluconobacter thailandicus, Gluconobacter oxydans, Gluconobacter cerinus, Gluconobacter albidus and Gluconobacter kondonii and formed a cluster that was separate from the type strains of the six Gluconobacter species given above in phylogenetic trees based on 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences. The five strains weakly produced dihydroxyacetone from glycerol, but not 2,5-diketo-D-gluconate or a water-soluble brown pigment from D-glucose and contained ubiquinone-10. The five strains were assigned as representing a novel species of the genus Gluconobacter, for which the name Gluconobacter japonicus sp. nov. is proposed. The type strain is NBRC 3271 T (5BCC 14458 T 5strain 7 T , K. Kondo). Cells of the type strain are motile by means of polar flagella and the DNA G+C content is 56.4 mol%.
Acetobacter suratthanensis sp. nov., an acetic acid bacterium isolated in Thailand
Annals of Microbiology, 2016
A Gram-negative, rod-shaped, and non-motile bacterium, designated as AI32 T , was isolated from a fruit in Surat Thani, the southern district of Thailand. Phylogenetic analyses of the 16S rRNA gene, 16S-23S rRNA gene ITS, and groEL gene sequences showed that the isolate formed a quite independent cluster located outside the clusters of Acetobacter peroxydans and Acetobacter papayae. Analysis of 16S rRNA gene sequence showed that the isolate was related to the type strains of A. peroxydans and A. papayae, respectively, with 99.4 % and 99.3 % similarities. The DNA G + C content of the isolate was 59.6 mol%. The isolate was positive in catalase test and showed no growth on ethanol in the presence of ammonium sulfate. The isolate produced only D-gluconic acid from D-glucose. The predominant fatty acid of isolate AI32 T was C 18:1 ω7C. Based on the results obtained in physiological and biochemical tests and in genotypic differences between the isolate and the type strains of the validly named species of the genus Acetobacter, the isolate is classified as a novel species, for which the name of Acetobacter suratthanensis sp. nov. is introduced. The type strain of the species is AI32 T (= BCC 26087 T = NBRC 111399 T). Keywords Acetic acid bacterium. Acetobacter suratthanensis sp. nov.. groEL gene sequences. 16S rRNA gene sequences. 16S-23S rRNA gene ITS sequences
Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the a-Proteobacteria
2000
ABSTRACT Four bacterial strains were isolated from palm brown sugar and ragi collected in Bali and Yogyakarta, Indonesia, by an enrichment culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates constituted a cluster separate from the genera Acetobacter, Gluconobacter, Acidomonas, Gluconacetobacter and Asaia with a high bootstrap value in a phylogenetic tree. The isolates had high values of DNA-DNA similarity (78-100%) between one another and low values of the similarity (7-25%) to the type strains of Acetobacter aceti, Gluconobacter oxydans, Gluconacetobacter liquefaciens and Asaia bogorensis. The DNA base composition of the isolates ranged from 56.8 to 57.2 mol% G+C with a range of 0-4 mol%. The major quinone was Q-10. The isolates oxidized acetate and lactate to carbon dioxide and water, but the activity was weak, as with strains of Asaia bogorensis. The isolates differed from Asaia bogorensis strains in phenotypic characteristics. The name Kozakia baliensis gen. nov., sp. nov., is proposed for the four isolates. Strain Yo-3T (= NRIC 0488T = JCM 11301T = IFO 16664T = DSM 14400T) was isolated from palm brown sugar collected in Bali, Indonesia, and was designated as the type strain.
International journal of food microbiology, 2011
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.