Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii

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.Acetic acid bacteria (AAB) are Gram-negative, coccoid or rod-shaped, obligate aerobic bacteria that have the ability to incompletely oxidize a wide range of carbohydrates, alcohols and sugar alcohols. They are involved in the production of several fermented foods and beverages, either in a beneficial (vinegars, cocoa-based products, Kombucha and nata de coco) or detrimental (spoilage of beer, wine and cider) manner and are also used in the production of commercially important fine chemicals and bacterial cellulose. Recently, some AAB have beenAbbreviations: AAB, acetic acid bacteria; AFLP, amplified fragment length polymorphism; ERIC enterobacterial repetitive intergenic consensus sequences; FAFLP, fluorescent amplified fragment length polymorphism; RAPD, randomly amplified polymorphic DNA; REP, Repetitive extragenic palindromic sequences.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of LMG 23726 T is AM999342.A supplementary figure showing the (GTG...

Description of Komagataeibacter gen. nov., with proposals of new combinations (Acetobacteraceae)

“…Microbiol. 57: 356, 2007. According to Cleenwerck et al (2009), this species is a later heterotypic synonym of Gluconacetobacter hansenii.…”

Transmission of Intestinal Bifidobacterium longum subsp. longum Strains from Mother to Infant, Determined by Multilocus Sequencing Typing and Amplified Fragment Length Polymorphism

“…AFLP analysis is based on the detection of genomic restriction fragments by PCR amplification (16,37). These methods have the capacity for high resolution and provide reproducible data, therefore being suitable for both species identification and strain typing (3,6,8).…”

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.

“…Taken together, these results suggest clearly that LMG 18788 represents a distinct species in the G. xylinus species group. LMG 18788 and other strains of the G. xylinus species group were subjected to (GTG) 5 -PCR and amplified fragment length polymorphism (AFLP) DNA fingerprinting, as described previously (De Vuyst et al, 2008;Cleenwerck et al, 2009), to obtain a more detailed view of their genomic relatedness. Cluster analysis of the DNA fingerprints obtained revealed a separate position for LMG 18788 (Fig.…”