Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods.

Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization.

Acetobacter malorum and Acetobacter cerevisiae identification and quantification by Real-Time PCR with TaqMan-MGB probes.

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.

Analysis of several methods for the extraction of high quality DNA from acetic acid bacteria in wine and vinegar for characterization by PCR-based methods.

Acetic acid bacteria (AAB) are fastidious microorganisms with poor recovery in culture. Culture-independent methods are currently under examination. Good DNA extraction is a strict requirement of these methods. We compared five methods for extracting the DNA of AAB directly from wine and vinegar samples. Four matrices (white wine, red wine, superficial vinegar and submerged vinegar) contaminated with two AAB strains belonging to Acetobacter pasteurianus and Gluconacetobacter hansenii were assayed. To improve the yield and quality of the extracted DNA, a sample treatment (washing with polyvinyl pyrrolidone or NaCl) was also tested. DNA quality was measured by amplification of the 16S rRNA gene with conventional PCR. DNA recovery rate was assessed by real-time PCR. DNA amplification was always successful with the Wizard method though DNA recovery was poor. A CTAB-based method and NucleoSpin protocol extracted the highest DNA recoveries from wine and vinegar samples. Both of these methods require treatment to recover suitable DNA for amplification with maximum recovery. Both may therefore be good solutions for DNA extraction in wine and vinegar samples. DNA extraction of Ga hansenii was more effective than that of A. pasteurianus. The fastest and cheapest method we evaluated (the Thermal shock protocol) produced the worst results both for DNA amplification and DNA recovery.

The enumeration and identification of acetic acid bacteria from South African red wine fermentations.

Acetic acid bacteria are microorganisms that can profoundly influence the quality of wine. Surprisingly, little research has been done on these microorganisms in the winemaking field. The object of this study was to investigate the occurrence of acetic acid bacteria in South African red wine fermentations and to identify the dominant species occurring. Acetic acid bacteria were isolated and enumerated from small-scale and commercial red must fermentations in 1998 and 1999, respectively. The initial occurrence of acetic acid bacteria in the must was shown to vary with cell numbers ranging from 10(6)-10(7) to 10(4)-10(5) cfu/ml for the 1998 and 1999 musts, respectively. The acetic acid bacteria decreased to 10(2)-10(3) cfu/ml in musts having a low pH (< or = 3.6), whereas in some musts having a high pH (> or = 3.7), the cell numbers increased during fermentation. During the process of cold soaking, the cell numbers of acetic acid bacteria also increased until inoculation with commercial wine yeast. Gluconobacter oxydans dominated in the fresh must and Acetobacter pasteurianus and A. liquefaciens during fermentation. This study showed that A. liquefaciens and A. hansenii were present in significant numbers, which has not been reported before.

Identification of acetic acid bacteria by restriction fragment length polymorphism analysis of a PCR-amplified fragment of the gene coding for 16S rRNA.

Acetic acid bacteria (AAB) irreversibly spoil wines and represent a serious problem. Limited studies on the ecology of AAB during winemaking have been done due to the lack of rapid and precise techniques for their identification. RFLP analysis of PCR-amplified fragment of 16S rDNA was performed on AAB reference strains. The amplified rDNAs were approximately 870-bp long for all AAB species while no amplicons were detected for lactic acid bacteria and yeasts. Out of the four restriction enzymes tested, TaqI was the most efficient one and divided the studied AAB into six groups. However, complete differentiation among collection strains of Acetobacter pasteurianus and Gluconoacetobacter hansenii was not possible.

Gluconacetobacter entanii sp. nov., isolated from submerged high-acid industrial vinegar fermentations.

Acetic acid bacteria have been isolated from submerged high-acid spirit vinegar fermentations in the Southern part of Germany. Four strains (LTH 4560T, LTH 4341, LTH 4551 and LTH 4637) were characterized in more detail and it was revealed that they have in common certain properties such as requirement of acetic acid, ethanol and glucose for growth, and no over-oxidation of acetate. Growth occurs only at total concentrations (sum of acetic acid and ethanol) exceeding 6.0%. A method for their preservation was developed. Comparative analysis of the 16S rRNA revealed sequence similarities of >99% between strain LTH 4560T and the type strains of the related species Gluconacetobacter hansenii. However, low levels of DNA relatedness (<41 %) were determined in DNA-DNA similarity studies. In addition, specific physiological characteristics permitted a clear identification of the strains within established species of acetic acid bacteria. The strains could also be differentiated on the basis of the distribution of IS element 1031 C within the chromosome. Based on these results, the new species Gluconacetobacter entanii sp. nov. is proposed for strain LTH 4560T ( = DSM 13536T). A 16S-rRNA-targeted oligonucleotide probe was constructed that was specific for G. entanii, and the phylogenetic position of the new species was derived from a 16S-rRNA-based tree.

Transfer of Acetobacter oboediens Sokollek et al 1998 and Acetobacter intermedius Boesch et al. 1998 to the genus Gluconacetobacter as Gluconacetobacter oboediens comb. nov. and Gluconacetobacter intermedius comb. nov.

Acetobacter oboediens Sokollek et al. 1998 and Acetobacter intermedius Boesch et al. 1998 are transferred to the genus Gluconacetobacter as Gluconacetobacter oboediens comb. nov. and Gluconacetobacter intermedius comb. nov. because, on the basis of their 16S rRNA gene sequences, the type strains of both species are located in the cluster of the genus Gluconacetobacter along with those of Gluconacetobacter xylinus, Gluconacetobacter europaeus, Gluconacetobacter hansenii, Gluconacetobacter liquefaciens (the type species) and Gluconacetobacter diazotrophicus. The significance of growth on mannitol agar and the presence of a ubiquinone isoprenologue composed of Q-10 is discussed for characterization of the genus Gluconacetobacter.

Acetobacter intermedius, sp. nov.

Strains of a new species in the genus Acetobacter, for which we propose the name A. intermedius sp. nov., were isolated and characterized in pure culture from different sources (Kombucha beverage, cider vinegar, spirit vinegar) and different countries (Switzerland, Slovenia). The isolated strains grow in media with 3% acetic acid and 3% ethanol as does A. europaeus, do, however, not require acetic acid for growth. These characteristics phenotypically position A. intermedius between A. europaeus and A. xylinus, DNA-DNA hybridizations of A. intermedius-DNA with DNA of the type strains of Acetobacter europaeus, A. xylinus, A. aceti, A. hansenii, A. liquefaciens, A. methanolicus, A. pasteurianus, A. diazotrophicus, Gluconobacter oxydans and Escherichia coli HB 101 indicated less than 60% DNA similarity. The important features of the new species are described. Acetobacter intermedius strain TF2 (DSM11804) isolated from the liquid phase of a tea fungus beverage (Kombucha) is the type strain.