Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis

Li, Leilei; Wieme, Anneleen D.; Spitaels, Freek; Balzarini, Tom; Nunes, Olga C.; Manaia, Célia M.; Landschoot, Anita Van; Vuyst, Luc De; Cleenwerck, Ilse; Vandamme, Peter

doi:10.1099/ijs.0.058354-0

Cited by 34 publications

(13 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Yet, the finding of A. tropicalis through metagenomic recruitment plotting was not in accordance with the culture-dependently isolated and identified A. senegalensis (both 16S rRNA and dnaK gene sequencing). However, both species differ only 4 and 10 nucleotides in their 16S rRNA and dnaK genes, respectively (this study; Li et al, 2014). Hence, the present study showed not only the complementarity of the combined use of culture-dependent and culture-independent methods regarding species detection and identification, which has been commonly employed since more than 20 years, but also the provision of both qualitative and quantitative data regarding species distribution.…”

Section: Sourdough Samplesupporting

confidence: 50%

Diverse Microbial Composition of Sourdoughs From Different Origins

et al. 2020

Self Cite

View full text Add to dashboard Cite

Section: Sourdough Samplesupporting

confidence: 50%

Diverse Microbial Composition of Sourdoughs From Different Origins

et al. 2020

Self Cite

View full text Add to dashboard Cite

“…Detecting and describing taxonomic novelty and reclassifying microbes has also been accomplished using MALDI-TOF MS ( Kudo et al, 2012 ; Wieme et al, 2012 ; Li L. et al, 2014 ; Praet et al, 2015 ; Yanokura et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Identification and Classification for the Lactobacillus casei Group

Huang

et al. 2018

Front. Microbiol.

View full text Add to dashboard Cite

Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.

show abstract

“…Acetic acid bacteria are Gram-stain-negative, obligately aerobic bacteria that produce acetic acid by ethanol oxidation and the genus Acetobacter is a representative acetic acid bacteria [1]. At the time of writing, the genus Acetobacter includes 28 validated published species that have been isolated from various alcoholic fermentation products such as in grapes, wine, water kefir, kombucha, beer, rice wine and cocoa bean and their vinegar products [2][3][4][5][6][7][8][9]. Cells of Acetobacter are motile or non-motile ellipsoidal to short rods usually showing catalase-positive and oxidase-negative activities and containing ubiquinone-9 (Q-9) as the predominant respiratory quinone.…”

mentioning

confidence: 99%

Acetobacter oryzoeni sp. nov., isolated from Korean rice wine vinegar

Baek

Kim

Moon

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

A Gram-stain-negative, obligately aerobic bacterium, designated strain B6T, was isolated from rice wine vinegar in the Republic of Korea. Cells were non-motile and oval short rods showing catalase-positive and oxidase-negative activities. Growth was observed at 15–45 °C (optimum, 30 °C) and pH 3.5–8.0 (optimum, pH 5.5–6.5). Strain B6T contained summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1 ω6c), and C16 : 0 as major fatty acids and ubiquinone-9 was identified as the sole isoprenoid quinone. The G+C content of the genomic DNA calculated from the whole genome was 53.1 mol%. Strain B6T was most closely related to Acetobacter pasteurianus LMG 1262T with very high 16S rRNA gene sequence similarity (100 %) and the strains formed a very close phylogenetic lineage together in phylogenetic trees based on 16S rRNA gene sequences. However, relatedness analyses based on concatenated amino acid sequences of 354 core genes and whole-cell MALDI-TOF profiles showed that strain B6T may form a distinct phyletic lineage from Acetobacter species. In addition, average nucleotide identity and in silico DNA–DNA hybridization values between strain B6T and the type strains of Acetobacter species were less than 93.3 and 51.4 %, respectively. The genomic features of strain B6T were also differentiated from those of closely related Acetobacter type strains. Based on the phenotypic, chemotaxonomic and genomic features, strain B6T clearly represents a novel species of the genus Acetobacter , for which the name Acetobacter oryzoeni sp. nov. is proposed. The type strain is B6T (=KACC 21201T=JCM 33371T).

show abstract

Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis

Cited by 34 publications

References 43 publications

Diverse Microbial Composition of Sourdoughs From Different Origins

Diverse Microbial Composition of Sourdoughs From Different Origins

Identification and Classification for the Lactobacillus casei Group

Acetobacter oryzoeni sp. nov., isolated from Korean rice wine vinegar

Contact Info

Product

Resources

About