Gluconobacter aidae sp. nov., an acetic acid bacteria isolated from tropical fruits in Thailand

Yukphan, Pattaraporn; Charoenyingcharoen, Piyanat; Malimas, Sukunphat; Muramatsu, Yuki; Nakagawa, Yasuyoshi; Tanasupawat, Somboon; Yamada, Yoshihiko

doi:10.1099/ijsem.0.004292

Cited by 11 publications

(7 citation statements)

References 48 publications

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“…( Salvetti et al 2018 ; Zheng et al 2020 ). Similarly, the evolutionary relationships between taxa of the Enterobacterales and Rhodospirillales were consistent with published data sets containing additional species from each order ( Matsutani et al 2011 ; Adeolu et al 2016 ; Baek et al 2020 ; Yukphan et al 2020 ).…”

Section: Resultssupporting

confidence: 85%

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome

McMullen

Bueno

Blow

et al. 2021

Genome Biology and Evolution

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Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species-level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation and nucleotide metabolism (Lactobacillales) and arginine, urea and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2-3 species in each order, were well-represented among the isolates and included ≥ 5 strains, permitting analysis of metabolic functions in the accessory genome (i.e. genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.

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Section: Resultssupporting

confidence: 85%

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome

McMullen

Bueno

Blow

et al. 2021

Genome Biology and Evolution

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“…All strains were Gram-stain-negative and shared the following characteristics: catalase activity, ethanol oxidation, ketogenesis from glycerol, formation of 2-keto- d -gluconic acid and glucuronic acid from glucose, acid production from d -arabinose, d -fructose, d -glucose, d -galactose, d -mannitol, d -mannose, d -ribose, d -xylose, ethanol, glycerol, melibiose and meso-erythritol. All results, except for the formation of 2-keto- d -gluconic acid and glucuronic acid from glucose for Gluconobacter aidae AC 10 T [29], were obtained in the present study. The following characteristics were uniformly absent: oxidase activity, growth in SM medium with 2 % NaCl and growth in 30 % d -glucose, growth on d -ribose, d -xylose, dulcitol, ethanol, l -arabitol, methanol, raffinose and sodium acetate as the sole carbon source.…”

Section: Physiology and Chemotaxonomysupporting

confidence: 55%

“… *Phenotypic tests for strains LMG 1744 T and LMG 1745, respectively. †Data taken from reference [29]. …”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Characterization of novel Gluconobacter species from fruits and fermented food products: Gluconobacter cadivus sp. nov., Gluconobacter vitians sp. nov. and Gluconobacter potus sp. nov

Sombolestani

Cleenwerck

Cnockaert

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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Strains LMG 1744T, LMG 1745, LMG 31484T, LMG 1764T and R-71646 were isolated from rotting fruits and fermented food products. A phylogenomic analysis based on 107 single-copy core genes revealed that they grouped in a Gluconobacter lineage comprising Gluconobacter oxydans , Gluconobacter roseus , Gluconobacter sphaericus, Gluconobacter kanchanaburiensis, Gluconobacter albidus, Gluconobacter cerevisiae, Gluconobacter kondonii and Gluconobacter aidae . OrthoANIu and digital DNA hybridization analyses demonstrated that these five strains represented three novel Gluconobacter species, which could be differentiated from the type strains of closely related Gluconobacter species by multiple phenotypic characteristics. We therefore propose to classify strains LMG 1744T and LMG 1745 in the novel species Gluconobacter cadivus sp. nov., with LMG 1744T (=CECT 30141T) as the type strain; to classify strain LMG 31484T as the novel species Gluconobacter vitians sp. nov., with LMG 31484T (=CECT 30132T) as the type strain; and to classify strains LMG 1764T and R-71646 in the novel species Gluconobacter potus sp. nov., with LMG 1764T (=CECT 30140T) as the type strain.

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“…In contrast, Gluconobacter spp. are acid-fast obligate aerobes that consume oxygen during growth and metabolism but do not produce CO 2 gas (Tanasupawat et al, 2004;Malimas et al, 2008Malimas et al, , 2009Noman et al, 2020;Yukphan et al, 2020). Therefore, Gluconobacter spp.…”

Section: Discussionmentioning

confidence: 99%

“…Gluconobacter spp. live mainly in fruits and orchard soil (Bevardi et al, 2013;Yukphan et al, 2020); hence, the source of the Gluconobacter spp. is most likely the strawberry jam.…”

Section: Discussionmentioning

confidence: 99%

16S ribosomal RNA-depletion PCR and its application in cause analysis of yogurt package shrinkage

Zhang

You

2022

Journal of Dairy Science

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Fermentative bacteria, the main microbiota in yogurt, interfere with the detection of unintended bacterial contaminants. The removal of fermentative bacteria and enrichment of unintended bacterial contaminants is a challenging task in bacterial detection. The present study developed a new 16S rRNA-depletion PCR for such enrichment and detection. Specifically, a singleguide RNA was designed and synthesized based on the 16S rRNA sequence of Streptococcus thermophilus, with the highest DNA abundance in the yogurt. The CRISPR-Cas9 system was used to specifically cleave and remove the genomic DNA of the fermentative bacteria, followed by PCR amplification. This method improved the detection sensitivity, simplified the operation steps, and reduced the detection cost of PCR analysis. We also used the 16S rRNA-depletion PCR to amplify and detect the unintended bacterial contaminants in yogurts with shrunken packages and analyzed the underlying reasons to prevent this issue of product quality.

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Gluconobacter aidae sp. nov., an acetic acid bacteria isolated from tropical fruits in Thailand

Cited by 11 publications

References 48 publications

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome

Characterization of novel Gluconobacter species from fruits and fermented food products: Gluconobacter cadivus sp. nov., Gluconobacter vitians sp. nov. and Gluconobacter potus sp. nov

16S ribosomal RNA-depletion PCR and its application in cause analysis of yogurt package shrinkage

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