Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry

Implementation of a Novel Method for Processing Proteins from Acetic Acid Bacteria via Liquid Chromatography Coupled with Tandem Mass Spectrometry

Acetic acid bacteria (AAB) and other members of the complex microbiotas, whose activity is essential for vinegar production, display biodiversity and richness that is difficult to study in depth due to their highly selective culture conditions. In recent years, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has emerged as a powerful tool for rapidly identifying thousands of proteins present in microbial communities, offering broader precision and coverage. In this work, a novel method based on LC-MS/MS was established and developed from previous studies. This methodology was tested in three studies, enabling the characterization of three submerged acetification profiles using innovative raw materials (synthetic alcohol medium, fine wine, and craft beer) while working in a semicontinuous mode. The biodiversity of existing microorganisms was clarified, and both the predominant taxa (Komagataeibacter, Acetobacter, Gluconacetobacter, and Gluconobacter) and others never detected in these media (Asaia and Bombella, among others) were identified. The key functions and adaptive metabolic strategies were determined using comparative studies, mainly those related to cellular material biosynthesis, energy-associated pathways, and cellular detoxification processes. This study provides the groundwork for a highly reliable and reproducible method for the characterization of microbial profiles in the vinegar industry.

Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas

Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products' pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community.

Recent advances in applying omic technologies for studying acetic acid bacteria in industrial vinegar production: A comprehensive review

Vinegar and related bioproducts containing acetic acid as the main component are among the most appreciated fermented foodstuffs in numerous European and Asian countries because of their exceptional organoleptic and bio-healthy properties. Regarding the acetification process and obtaining of final products, there is still a lack of knowledge on fundamental aspects, especially those related to the study of biodiversity and metabolism of the present microbiota. In this context, omic technologies currently allow for the massive analysis of macromolecules and metabolites for the identification and characterization of these microorganisms working in their natural media without the need for isolation. This review approaches comprehensive research on the application of omic tools for the identification of vinegar microbiota, mainly acetic acid bacteria, with subsequent emphasis on the study of the microbial diversity, behavior, and key molecular strategies used by the predominant groups throughout acetification. The current omics tools are enabling both the finding of new vinegar microbiota members and exploring underlying strategies during the elaboration process. The species Komagataeibacter europaeus may be a model organism for present and future research in this industry; moreover, the development of integrated meta-omic analysis may facilitate the achievement of numerous of the proposed milestones. This work might provide useful guidance for the vinegar industry establishing the first steps towards the improvement of the acetification conditions and the development of new products with sensory and bio-healthy profiles adapted to the agri-food market.

The Homologous Gene of Chromosomal Virulence D (chvD) Presents High Resolution as a Novel Biomarker in Mycobacterium Species Identification

Objective

To evaluate the resolution of chromosomal virulence D (chvD) as a novel marker for mycobacterial species identification.

Methods

A segment of chvD (652 bp) was amplified by PCR from 63 mycobacterial reference strains, 163 nontuberculous mycobacterial clinical isolates, and 16 M. tuberculosis complex (MTBC) clinical isolates. A phylogenetic tree based on the reference strains was constructed by the neighbor-joining and IQ-tree methods. Comparative sequence analysis of the homologous chvD gene efficiently differentiated the species within the genus Mycobacterium. Slowly growing Mycobacterium (SGM) and rapidly growing Mycobacterium (RGM) were separated in the phylogenetic tree based on the chvD gene.

Results

The sequence discrepancies were obvious between M. kansasii and M. gastri, M. chelonae and M. abscessus, and M. avium and M. intracellulare, none of which could be achieved by 16S ribosomal RNA (rRNA) homologous gene alignment. Furthermore, chvD manifested larger intraspecies diversity among members of M. intracellulare subspecies. A total of 174 of the 179 (97.21%) clinical isolates, consisting of 12 mycobacterial species, were identified correctly by chvD blast. Four M. abscessus subsp. abscessus were identified as M. abscessus subsp. bolletii by chvD. MTBC isolates were indistinguishable, because they showed 99.84%-100% homology.

Conclusion

Homologous chvD is a promising gene marker for identifying mycobacterial species, and could be used for highly accurate species identification among mycobacteria.

Comparative Genomics and Phenotypic Characterization of Gluconacetobacter entanii, a Highly Acetic Acid-Tolerant Bacterium from Vinegars

The bacterial species Gluconacetobacter entanii belongs to a group of acetic acid bacteria. In 2000, it was described as a primary species of submerged spirit vinegar-producing bioreactors with a strict requirement of acetic acid, ethanol, and glucose for growth. Over the years, the type-strain of G. entanii deposited in international culture collections has lost the ability for revitalization and is thus not available any more in a culturable form. Here, we have systematically characterized phenotypic features and genomes of recently isolated G. entanii strains and compared them with characteristics of the type-strain available from published data. Using the functional annotation, genes gmhB and psp were identified as unique for G. entanii genomes among species in the clade Novacetimonas. The genome stability of G. entanii was assessed after 28 and 43 months of preculturing the strain Gluconacetobacter entanii AV429 twice a week. The strain G. entanii AV429 did not accumulate giant insertions or deletions but a few gene mutations. To unify further research into acetic acid bacteria systematics and taxonomy, we propose G. entanii AV429 as the neotype strain.

Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS

Vinegars elaborated in southern Spain are highly valued all over the world because of their exceptional organoleptic properties and high quality. Among the factors which influence the characteristics of the final industrial products, the composition of the microbiota responsible for the process and the raw material used as acetification substrate have a crucial role. The current state of knowledge shows that few microbial groups are usually present throughout acetification, mainly acetic acid bacteria (AAB), although other microorganisms, present in smaller proportions, may also affect the overall activity and behavior of the microbial community. In the present work, the composition of a starter microbiota propagated on and subsequently developing three acetification profiles on different raw materials, an alcohol wine medium and two other natural substrates (a craft beer and fine wine), was characterized and compared. For this purpose, two different "omics" tools were combined for the first time to study submerged vinegar production: 16S rRNA amplicon sequencing, a culture-independent technique, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), a culture-dependent method. Analysis of the metagenome revealed numerous taxa from 30 different phyla and highlighted the importance of the AAB genus Komagataeibacter, which was much more frequent than the other taxa, and Acetobacter; interestingly, also archaea from the Nitrososphaeraceae family were detected by 16S rRNA amplicon sequencing. MALDI-TOF MS confirmed the presence of Komagataeibacter by the identification of K. intermedius. These tools allowed for identifying some taxonomic groups such as the bacteria genera Cetobacterium and Rhodobacter, the bacteria species Lysinibacillus fusiformis, and even archaea, never to date found in this medium. Definitely, the effect of the combination of these techniques has allowed first, to confirm the composition of the predominant microbiota obtained in our previous metaproteomics approaches; second, to identify the microbial community and discriminate specific species that can be cultivated under laboratory conditions; and third, to obtain new insights on the characterization of the acetification raw materials used. These first findings may contribute to improving the understanding of the microbial communities' role in the vinegar-making industry.

Screening and Characterization of New Acetobacter fabarum and Acetobacter pasteurianus Strains with High Ethanol−Thermo Tolerance and the Optimization of Acetic Acid Production

The production of vinegar on an industrial scale from different raw materials is subject to constraints, notably the low tolerance of acetic acid bacteria (AAB) to high temperatures and high ethanol concentrations. In this study, we used 25 samples of different fruits from seven Moroccan biotopes with arid and semi-arid environmental conditions as a basic substrate to isolate thermo- and ethanol-tolerant AAB strains. The isolation and morphological, biochemical and metabolic characterization of these bacteria allowed us to isolate a total number of 400 strains with characters similar to AAB, of which six strains (FAGD1, FAGD10, FAGD18 and GCM2, GCM4, GCM15) were found to be mobile and immobile Gram-negative bacteria with ellipsoidal rod-shaped colonies that clustered in pairs and in isolated chains. These strains are capable of producing acetic acid from ethanol, growing on peptone and oxidizing acetate to CO2 and H2O. Strains FAGD1, FAGD10 and FAGD18 show negative growth on YPG medium containing D-glucose > 30%, while strains GCM2, GCM4 and GCM15 show positive growth. These six strains stand out on CARR indicator medium as isolates of the genus Acetobacter ssp. Analysis of 16S rDNA gene sequencing allowed us to differentiate these strains as Acetobacter fabarum and Acetobacter pasteurianus. The study of the tolerance of these six isolates towards pH showed that most of the six strains are unable to grow at pH 3 and pH 9, with an ideal pH of 5. The behavior of the six strains at different concentrations of ethanol shows an optimal production of acetic acid after incubation at concentrations between 6% and 8% (v/v) of ethanol. All six strains tolerated an ethanol concentration of 16% (v/v). The resistance of the strains to acetic acid differs between the species of AAB. The optimum acetic acid production is obtained at a concentration of 1% (v/v) for the strains of FAGD1, FAGD10 and FAGD18, and 3% (v/v) for GCM2, GCM4 and GCM15. These strains are able to tolerate an acetic acid concentration of up to 6% (v/v). The production kinetics of the six strains show the highest levels of growth and acetic acid production at 30 °C. This rate of growth and acetic acid production is high at 35 °C, 37 °C and 40 °C. Above 40 °C, the production of acid is reduced. All six strains continue to produce acetic acid, even at high temperatures up to 48 °C. These strains can be used in the vinegar production industry to minimize the load on cooling systems, especially in countries with high summer temperatures.

Species-specific identification of Pseudomonas based on 16S-23S rRNA gene internal transcribed spacer (ITS) and its combined application with next-generation sequencing

Background

Pseudomonas species are widely distributed in the human body, animals, plants, soil, fresh water, seawater, etc. Pseudomonas aeruginosa is one of the main pathogens involved in nosocomial infections. It can cause endocarditis, empyema, meningitis, septicaemia and even death. However, the Pseudomonas classification system is currently inadequate and not well established.

Results

In this study, the whole genomes of 103 Pseudomonas strains belonging to 62 species available in GenBank were collected and the specificity of the 16S–23S ribosomal RNA internal transcribed spacer (ITS) sequence was analysed. Secondary structures of ITS transcripts determining where the diversity bases were located were predicted. The alignment results using BLAST indicated that the ITS sequence is specific for most species in the genus. The remaining species were identified by additional frequency analyses based on BLAST results. A double-blind experiment where 200 ITS sequences were randomly selected indicated that this method could identify Pseudomonas species with 100% sensitivity and specificity. In addition, we applied a universal primer to amplify the Pseudomonas ITS of DNA extracts from fish samples with next-generation sequencing. The ITS analysis results were utilized to species-specifically identify the proportion of Pseudomonas species in the samples.

Conclusions

The present study developed a species-specific method identification and classification of Pseudomonas based on ITS sequences combined NGS. The method showed its potential application in other genera.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02607-w.

Oxidative Fermentation of Acetic Acid Bacteria and Its Products

Acetic acid bacteria (AAB) are a group of Gram-negative, strictly aerobic bacteria, including 19 reported genera until 2021, which are widely found on the surface of flowers and fruits, or in traditionally fermented products. Many AAB strains have the great abilities to incompletely oxidize a large variety of carbohydrates, alcohols and related compounds to the corresponding products mainly including acetic acid, gluconic acid, gulonic acid, galactonic acid, sorbose, dihydroxyacetone and miglitol via the membrane-binding dehydrogenases, which is termed as AAB oxidative fermentation (AOF). Up to now, at least 86 AOF products have been reported in the literatures, but no any monograph or review of them has been published. In this review, at first, we briefly introduce the classification progress of AAB due to the rapid changes of AAB classification in recent years, then systematically describe the enzymes involved in AOF and classify the AOF products. Finally, we summarize the application of molecular biology technologies in AOF researches.

Bio-Based Processes for Material and Energy Production from Waste Streams under Acidic Conditions

The revolutionary transformation from petrol-based production to bio-based production is becoming urgent in line with the rapid industrialization, depleting resources, and deterioration of the ecosystem. Bio-based production from waste-streams is offering a sustainable and environmentally friendly solution. It offers several advantages, such as a longer operation period, less competition for microorganisms, higher efficiency, and finally, lower process costs. In the current study, several bio-based products (organic acids, biomethane, biohydrogen, and metal leachates) produced under acidic conditions are reviewed regarding their microbial pathways, processes, and operational conditions. Furthermore, the limitations both in the production process and in the scale-up are evaluated with future recommendations.

Molecular biology: Fantastic toolkits to improve knowledge and application of acetic acid bacteria

Acetic acid bacteria (AAB) are a group of gram-negative, obligate aerobic bacteria within the Acetobacteraceae family of the alphaproteobacteria class, which are distributed in a wide variety of different natural sources that are rich in sugar and alcohols, as well as in several traditionally fermented foods. Their capabilities are not limited to the production of acetic acid and the brewing of vinegar, as their names suggest. They can also fix nitrogen and produce various kinds of aldehydes, ketones and other organic acids by incomplete oxidation (also referred to as oxidative fermentation) of the corresponding alcohols and/or sugars, as well as pigments and exopolysaccharides (EPS). In order to gain more insight into these organisms, molecular biology techniques have been extensively applied in almost all aspects of AAB research, including their identification and classification, acid resistance mechanisms, oxidative fermentation, EPS production, thermotolerance and so on. In this review, we mainly focus on the application of molecular biological technologies in the advancement of research into AAB while presenting the progress of the latest studies using these techniques.

Antimicrobial Resistance of Acetobacter and Komagataeibacter Species Originating from Vinegars

Consumers' preference towards healthy and novel foods dictates the production of organic unfiltered bottled vinegar that still contains acetic acid bacteria. After ingesting vinegar, the bacteria come into close contact with the human microbiota, creating the possibility of horizontal gene transfer, including genetic determinants for antibiotic resistance. Due to the global spread of antimicrobial resistance (AMR), we analyzed the AMR of Acetobacter and Komagataeibacter species originating mainly from vinegars. Six antibiotics from different structural groups and mechanisms of action were selected for testing. The AMR was assessed with the disk diffusion method using various growth media. Although the number of resistant strains differed among the growth media, 97.4%, 74.4%, 56.4%, and 33.3% of strains were resistant to trimethoprim, erythromycin, ciprofloxacin, and chloramphenicol, respectively, on all three media. Moreover, 17.9% and 53.8% of all strains were resistant to four and three antibiotics of different antimicrobial classes, respectively. We then looked for antimicrobial resistance genes in the genome sequences of the reference strains. The most common genetic determinant potentially involved in AMR encodes an efflux pump. Since these genes pass through the gastrointestinal tract and may be transferred to human microbiota, further experiments are needed to analyze the probability of this scenario in more detail.

Dehydrogenases of acetic acid bacteria

Acetic acid bacteria (AAB) are a group of bacteria that can oxidize many substrates such as alcohols and sugar alcohols and play important roles in industrial biotechnology. A majority of industrial processes that involve AAB are related to their dehydrogenases, including PQQ/FAD-dependent membrane-bound dehydrogenases and NAD(P)⁺-dependent cytoplasmic dehydrogenases. These cofactor-dependent dehydrogenases must effectively regenerate their cofactors in order to function continuously. For PQQ, FAD and NAD(P)⁺ alike, regeneration is directly or indirectly related to the electron transport chain (ETC) of AAB, which plays an important role in energy generation for aerobic cell growth. Furthermore, in changeable natural habitats, ETC components of AAB can be regulated so that the bacteria survive in different environments. Herein, the progressive cascade in an application of AAB, including key dehydrogenases involved in the application, regeneration of dehydrogenase cofactors, ETC coupling with cofactor regeneration and ETC regulation, is systematically reviewed and discussed. As they have great application value, a deep understanding of the mechanisms through which AAB function will not only promote their utilization and development but also provide a reference for engineering of other industrial strains.

Impacts of type II toxin-antitoxin systems on cell physiology and environmental behavior in acetic acid bacteria

Acetic acid bacteria (AAB) are a group of Gram-negative and strictly aerobic microorganisms widely used in vinegar industry, especially the species belonging to the genera Acetobacter and Komagataeibacter. The environments inhabited by AAB during the vinegar fermentation, in particular those natural traditional bioprocesses, are complex and dynamically changed, usually accompanied by diverse microorganisms, bacteriophages, and the increasing acetic acid concentration. For this reason, how AAB survive to such harsh niches has always been an interesting research field. Previous omic analyses (e.g., genomics, proteomics, and transcriptomics) have provided abundant clues for the metabolic pathways and bioprocesses indispensable for the acid stress adaptation of AAB. Nevertheless, it is far from fully understanding what factors regulate these modular mechanisms overtly and covertly upon shifting environments. Bacterial toxin-antitoxin systems (TAS), usually consisting of a pair of genes encoding a stable toxin and an unstable antitoxin that is capable of counteracting the toxin, have been uncovered to have a variety of biological functions. Recent studies focusing on the role of TAS in Acetobacter pasteurianus suggest that TAS contribute substantially to the acid stress resistance. In this mini review, we discuss the biological functions of type II TAS in the context of AAB with regard to the acid stress resistance, persister formation and resuscitation, genome stability, and phage immunity. KEY POINTS: • Type II TAS act as regulators in the acid stress resistance of AAB. • Type II TAS are implicated in the formation of acid-tolerant persister cells in AAB. • Type II TAS are potential factors responsible for phage immunity and genome stability.

Biotechnological Processes in Fruit Vinegar Production

The production of fruit vinegars as a way of making use of fruit by-products is an option widely used by the food industry, since surplus or second quality fruit can be used without compromising the quality of the final product. The acetic nature of vinegars and its subsequent impact on the organoleptic properties of the final product allows almost any type of fruit to be used for its elaboration. A growing number of scientific research studies are being carried out on this matrix, and they are revealing the importance of controlling the processes involved in vinegar elaboration. Thus, in this review, we will deal with the incidence of technological and biotechnological processes on the elaboration of fruit vinegars other than grapes. The preparation and production of the juice for the elaboration of the vinegar by means of different procedures is an essential step for the final quality of the product, among which crushing or pressing are the most employed. The different conditions and processing methods of both alcoholic and acetic fermentation also affect significantly the final characteristics of the vinegar produced. For the alcoholic fermentation, the choice between spontaneous or inoculated procedure, together with the microorganisms present in the process, have special relevance. For the acetic fermentation, the type of acetification system employed (surface or submerged) is one of the most influential factors for the final physicochemical properties of fruit vinegars. Some promising research lines regarding fruit vinegar production are the use of commercial initiators to start the acetic fermentation, the use of thermotolerant bacteria that would allow acetic fermentation to be carried out at higher temperatures, or the use of innovative technologies such as high hydrostatic pressure, ultrasound, microwaves, pulsed electric fields, and so on, to obtain high-quality fruit vinegars.

Classification of acetic acid bacteria and their acid resistant mechanism

Acetic acid bacteria (AAB) are obligate aerobic Gram-negative bacteria that are commonly used in vinegar fermentation because of their strong capacity for ethanol oxidation and acetic acid synthesis as well as their acid resistance. However, low biomass and low production rate due to acid stress are still major challenges that must be overcome in industrial processes. Although acid resistance in AAB is important to the production of high acidity vinegar, the acid resistance mechanisms of AAB have yet to be fully elucidated. In this study, we discuss the classification of AAB species and their metabolic processes and review potential acid resistance factors and acid resistance mechanisms in various strains. In addition, we analyze the quorum sensing systems of Komagataeibacter and Gluconacetobacter to provide new ideas for investigation of acid resistance mechanisms in AAB in the form of signaling pathways. The results presented herein will serve as an important reference for selective breeding of high acid resistance AAB and optimization of acetic acid fermentation processes.

Deciphering the succession patterns of bacterial community and their correlations with environmental factors and flavor compounds during the fermentation of Zhejiang rosy vinegar

Zhejiang Rosy Vinegar (ZRV) is a traditional condiment in Southeast China, produced using semi-solid-state fermentation techniques under an open environment, yet little is known about the functional microbiota involved in the flavor formation of ZRV. In this study, 43 kinds of volatile flavor substances were identified by HS-SPME/GC-MS, mainly including ethyl acetate (relative content at the end of fermentation: 1104.1 mg/L), phenylethyl alcohol (417.6 mg/L) and acetoin (605.2 mg/L). The most abundant organic acid was acetic acid (59.6 g/L), which kept rising during the fermentation, followed by lactic acid (7.0 g/L), which showed a continuously downward trend. Amplicon sequencing analysis revealed that the richness and diversity of bacterial community were the highest at the beginning and then maintained decreasing during the fermentation. The predominant bacteria were scattered in Acetobacter (average relative abundance: 63.7%) and Lactobacillus (19.8%). Both sequencing and culture-dependent analysis showed Lactobacillus dominated the early stage (day 10 to 30), and Acetobacter kept highly abundant from day 40 to the end. Spearman correlation analysis displayed that the potential major groups involved in the formation of flavor compounds were Acetobacter and Lactobacillus, which were also showed strong relationships with other bacteria through co-occurrence network analysis (edges attached to Acetobacter: 61.7%; Lactobacillus: 14.0%). Moreover, structural equation model showed that the contents of ethanol, titratable acid and reducing sugar were the major environmental factors playing essential roles in influencing the succession of bacterial community and their metabolism during the fermentation. Overall, these findings illuminated the dynamic profiles of bacterial community and flavor compounds and the potential functional microbes, which were expected to help us understand the formation of flavor substances in ZRV.

Modulating microbiota metabolism via bioaugmentation with Lactobacillus casei and Acetobacter pasteurianus to enhance acetoin accumulation during cereal vinegar fermentation

Acetoin, giving a creamy yogurt aroma and buttery taste, exists in cereal vinegar as an important flavor substance and is mainly produced by the metabolism of Lactobacillus and Acetobacter during multispecies solid-state acetic acid fermentation. However, the impacts of Lactobacillus-Acetobacter interactions on acetoin accumulation and the microbial metabolism during acetic acid fermentation are not completely clear. Here, six strains isolated from vinegar fermentation culture and associated with acetoin metabolism, namely, Lactobacillus reuteri L-0, L. buchneri F2-6, L. brevis 4-20, L. fermentum M10-7, L. casei M1-6 and Acetobacter pasteurianus G3-2, were selected for microbial growth and metabolism analysis in monoculture and coculture fermentations. Lactobacillus sp. and A. pasteurianus G3-2 respectively utilized glucose and ethanol preferentially. In monocultures, L. casei M1-6 (183.7 mg/L) and A. pasteurianus G3-2 (121.0 mg/L) showed better acetoin-producing capacity than the others. In the bicultures with Lactobacillus sp. and A. pasteurianus G3-2, biomass analysis in the stationary phase demonstrated that significant growth depressions of Lactobacillus sp. occurred compared with monocultures, possibly due to intolerance to acetic acid produced by A. pasteurianus G3-2. Synergistic effect between Lactobacillus sp. and A. pasteurianus G3-2 on enhanced acetoin accumulation was identified, however, cocultures of two Lactobacillus strains could not apparently facilitate acetoin accumulation. Coculture of L. casei M1-6 and A. pasteurianus G3-2 showed the best performance in acetoin production amongst all mono-, bi- and triculture combinations, and the yield of acetoin increased from 1827.7 to 7529.8 mg/L following optimization of culture conditions. Moreover, the interactions of L. casei M1-6 and A. pasteurianus G3-2 regulated the global metabolism of vinegar microbiota during fermentation through performing in situ bioaugmentation, which could accelerate the production of acetic acid, lactic acid, acetoin, ethyl acetate, ethyl lactate, ligustrazine and other important flavoring substances. This work provides a promising strategy for the production of acetoin-rich vinegar through Lactobacillus sp.-A. pasteurianus joint bioaugmentation.

A novel strain of acetic acid bacteria Gluconobacter oxydans FBFS97 involved in riboflavin production

A novel bacterial strain of acetic acid bacteria capable of producing riboflavin was isolated from the soil sample collected in Wuhan, China. The isolated strain was identified as Gluconobacter oxydans FBFS97 based on several phenotype characteristics, biochemicals tests, and 16S rRNA gene sequence conducted. Furthermore, the complete genome sequencing of the isolated strain has showed that it contains a complete operon for the biosynthesis of riboflavin. In order to obtain the maximum concentration of riboflavin production, Gluconobacter oxydans FBFS97 was optimized in shake flask cultures through response surface methodology employing Plackett–Burman design (PBD), and Central composite design (CCD). The results of the pre-experiments displayed that fructose and tryptone were found to be the most suitable sources of carbon and nitrogen for riboflavin production. Then, PBD was conducted for initial screening of eleven minerals (FeSO₄, FeCl₃, KH₂PO₄, K₂HPO₄, MgSO₄, ZnSO₄, NaCl, CaCl₂, KCl, ZnCl₂, and AlCl₃.6H₂O) for their significances on riboflavin production by Gluconobacter oxydans strain FBFS97. The most significant variables affecting on riboflavin production are K₂HPO₄ and CaCl₂, the interaction affects and levels of these variables were optimized by CCD. After optimization of the medium compositions for riboflavin production were determined as follows: fructose 25 g/L, tryptone 12.5 g/L, K₂HPO₄ 9 g/L, and CaCl₂ 0.06 g/L with maximum riboflavin production 23.24 mg/L.

Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar

Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206T (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515T (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C19:0 cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C18:1ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382T and AV436T represent novel species of the genus Komagataeibacter, for which the names Komagataeibactermelaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382T (= ZIM B1054T = LMG 31303T = CCM 8958T) and of Komagataeibacter melomenusus AV436T (= ZIM B1056T = LMG 31304T = CCM 8959T).

Bacterial Cellulose as a Versatile Platform for Research and Development of Biomedical Materials

The unique pool of features found in intracellular and extracellular bacterial biopolymers attracts a lot of research, with bacterial cellulose (BC) being one of the most versatile and common. BC is an exopolysaccharide consisting solely of cellulose, and the variation in the production process can vary its shape or even its composition when compounding is applied in situ. Together with ex situ modification pathways, including specialised polymers, particles or exclusively functional groups, BC provides a robust platform that yields complex multifunctional compounds that go far beyond ultra-high purity, intrinsic hydrophilicity, mechanical strength and biocompatibility to introduce bioactive, (pH, thermal, electro) responsive, conductive and ‘smart’ properties. This review summarises the research outcomes in BC-medical applications, focusing mainly on data from the past decade (i.e., 2010–2020), with special emphasis on BC nanocomposites as materials and devices applicable in medicine. The high purity and unique structural/mechanical features, in addition to its capacity to closely adhere to irregular skin surfaces, skin tolerance, and demonstrated efficacy in wound healing, all stand as valuable attributes advantageous in topical drug delivery. Numerous studies prove BC compatibility with various human cells, with modifications even improving cell affinity and viability. Even BC represents a physical barrier that can reduce the penetration of bacteria into the tissue, but in its native form does not exhibit antimicrobial properties, therefore carious modifications have been made or specific compounds added to confer antimicrobial or anti-inflammatory properties. Progress in the use of BC-compounds as wound dressings, vascular grafts, and scaffolds for the treatment of cartilage, bone and osteochondral defects, the role as a basement membrane in blood-brain barrier models and many more are discussed to particular extent, emphasising the need for BC compounding to meet specific requirements.

Bacterial Cellulose: Production, Modification and Perspectives in Biomedical Applications

Bacterial cellulose (BC) is ultrafine, nanofibrillar material with an exclusive combination of properties such as high crystallinity (84%-89%) and polymerization degree, high surface area (high aspect ratio of fibers with diameter 20-100 nm), high flexibility and tensile strength (Young modulus of 15-18 GPa), high water-holding capacity (over 100 times of its own weight), etc. Due to high purity, i.e., absence of lignin and hemicellulose, BC is considered as a non-cytotoxic, non-genotoxic and highly biocompatible material, attracting interest in diverse areas with hallmarks in medicine. The presented review summarizes the microbial aspects of BC production (bacterial strains, carbon sources and media) and versatile in situ and ex situ methods applied in BC modification, especially towards bionic design for applications in regenerative medicine, from wound healing and artificial skin, blood vessels, coverings in nerve surgery, dura mater prosthesis, arterial stent coating, cartilage and bone repair implants, etc. The paper concludes with challenges and perspectives in light of further translation in highly valuable medical products.

Characterization and comparative analysis of toxin-antitoxin systems in Acetobacter pasteurianus

Bacterial toxin-antitoxin (TA) systems play important roles in diverse cellular regulatory processes. Here, we characterize three putative type II TA candidates from Acetobacter pasteurianus and investigate the profile of type II TA systems in the genus Acetobacter. Based on the gene structure and activity detection, two-pairs loci were identified as the canonical hicAB and higAB TA systems, respectively, and DB34_01190-DB34_01195 as a putative new one without a canonical TA architecture. Physiologically, the expression of the three pairs conferred E. coli with additional plasmid maintenance and survival when under acetic acid stress. Chromosomal TA systems can be horizontally transferred within an ecological vinegar microbiota by co-option, and there was a tendency for toxin module loss. The antitoxin retention in the genome is suggested to have a broad role in bacterial physiology. Furthermore, A. pasteurianus strains, universally domesticated and used for industrial vinegar fermentation, showed a higher number of type II TA loci compared to the host-associated ones. The amount of TA loci per genome showed little positive relationship to insertion sequences, although its prevalence was species-associated, to the extent of even being strain-associated. The TA system is a candidate of studying the resistant mechanistic network, the TAs-dependent translatome affords a real-time profile to explore stress adaptation of A. pasteurianus, promoting industrial development.

Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE

The production of traditional vinegar is usually carried out using the so-called "seed vinegar" or "mother of vinegar" that is composed of an undefined and complex pool of microorganisms deriving from a previous vinegar production. To date, there have been relatively few studies on the microbiota of seed vinegars. The present study was carried out to discover the bacterial biota of seed vinegar samples used in the homemade production of local vinegars obtained from the acetic fermentation of white wine. The seed vinegar samples were subjected to viable counting and advanced molecular analyses, namely, Illumina sequencing and PCR-DGGE. The adopted polyphasic approach allowed the bacterial diversity of the analyzed samples to be profiled, thus revealing the presence of acetic acid bacteria ascribed to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. Moreover, other microbial genera as Pseudomonas, Bacillus and Clostridium were abundantly found in almost all the samples, together with other minority genera. The results of viable counting confirmed the well-acknowledged limitations inherent with acetic acid bacteria recovery on plate growth media. The overall results confirmed that seed vinegars have a complex and heterogeneous biodiversity, thus encouraging their exploitation for the isolation and future technological characterization of cultures to be selected for the manufacture of mixed starter cultures.

Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov

Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590^T and LMG 1591 (previously classified as the type strains of A. pasteurianus subsp. ascendens and paradoxus, respectively) and strain SLV-7^T do not belong to A. pasteurianus. Strain SLV-7^T, isolated from Korean traditional vinegar, shared low ANI (<91.0%) and in silico DDH (44.2%) values with all other Acetobacter type strains analyzed in this study, indicating that strain SLV-7^T represents a new Acetobacter species. The phenotypic and chemotaxonomic analyses confirmed these results and therefore a new species named Acetobacter oryzifermentans sp. nov. is proposed with SLV-7^T (=KACC 19301^T=JCM 31096^T) as the type strain. Strains LMG 1590^T and LMG 1591 shared high ANI (99.4%) and in silico DDH (96.0%) values between them, but shared low ANI (<92.3%) and in silico DDH (<49.0%) values with other type strains analyzed in this study, indicating that strains LMG 1590^T and LMG 1591 should be reclassified into a new single species that should be named Acetobacter ascendens sp. nov., comb. nov., with LMD 51.1^T (=LMG 1590^T=NCCB 51001^T) as its type strain.

Acetic Acid Bacteria in the Food Industry: Systematics, Characteristics and Applications

The group of Gram-negative bacteria capable of oxidising ethanol to acetic acid is called acetic acid bacteria (AAB). They are widespread in nature and play an important role in the production of food and beverages, such as vinegar and kombucha. The ability to oxidise ethanol to acetic acid also allows the unwanted growth of AAB in other fermented beverages, such as wine, cider, beer and functional and soft beverages, causing an undesirable sour taste. These bacteria are also used in the production of other metabolic products, for example, gluconic acid, l-sorbose and bacterial cellulose, with potential applications in the food and biomedical industries. The classification of AAB into distinct genera has undergone several modifications over the last years, based on morphological, physiological and genetic characteristics. Therefore, this review focuses on the history of taxonomy, biochemical aspects and methods of isolation, identification and quantification of AAB, mainly related to those with important biotechnological applications.

16S rRNA in situ Hybridization Followed by Flow Cytometry for Rapid Identification of Acetic Acid Bacteria Involved in Submerged Industrial Vinegar Production

Acetic acid bacteria are involved in many biotechnological processes such as vitamin C, gluconic acid, miglitol or acetic acid production, and others. For a technologist trying to control the industrial process, the ability to follow the microbiological development of the process is thus of importance. During the past few years hybridization in a combination with flow cytometry has often been used for this purpose. Since vinegar is a liquid, it is an ideal matrix for flow cytometry analysis. In this work we have constructed a specific probe for highly acetic acid-resistant species of the acetic acid bacteria and a protocol for in situ hybridization, which in combination with flow cytometry enables direct monitoring of bacteria producing vinegar with >10% of acetic acid. The approach was successfully applied for monitoring microbiota during industrial vinegar production.

Effect of ammonium and amino acids on the growth of selected strains of Gluconobacter and Acetobacter

Acetic acid bacteria (AAB) are a group of microorganisms highly used in the food industry. However, its use can be limited by the insufficient information known about the nutritional requirements of AAB for optimal growth. The aim of this work was to study the effects of different concentrations and sources of nitrogen on the growth of selected AAB strains and to establish which nitrogen source best encouraged their growth. Two strains of three species of AAB, Gluconobacter japonicus, Gluconobacter oxydans and Acetobacter malorum, were grown in three different media with diverse nitrogen concentrations (25, 50, 100, and 300mgN/L and 1gN/L) as a complete solution of amino acids and ammonium. With this experiment, the most favourable medium and the lowest nitrogen concentration beneficial for the growth of each strain was selected. Subsequently, under these conditions, single amino acids or ammonium were added to media individually to determine the best nitrogen sources for each AAB strain. The results showed that nitrogen requirements are highly dependent on the nitrogen source, the medium and the AAB strain. Gluconobacter strains were able to grow in the lowest nitrogen concentration tested (25mgN/L); however, one of the G. oxydans strains and both A. malorum strains required a higher concentration of nitrogen (100-300mgN/L) for optimal growth. In general, single nitrogen sources were not able to support the growth of these AAB strains as well as the complete solution of amino acids and ammonium.

Comparison of D-gluconic acid production in selected strains of acetic acid bacteria

The oxidative metabolism of acetic acid bacteria (AAB) can be exploited for the production of several compounds, including D-gluconic acid. The production of D-gluconic acid in fermented beverages could be useful for the development of new products without glucose. In the present study, we analyzed nineteen strains belonging to eight different species of AAB to select those that could produce D-gluconic acid from D-glucose without consuming D-fructose. We tested their performance in three different media and analyzed the changes in the levels of D-glucose, D-fructose, D-gluconic acid and the derived gluconates. D-Glucose and D-fructose consumption and D-gluconic acid production were heavily dependent on the strain and the media. The most suitable strains for our purpose were Gluconobacter japonicus CECT 8443 and Gluconobacter oxydans Po5. The strawberry isolate Acetobacter malorum (CECT 7749) also produced D-gluconic acid; however, it further oxidized D-gluconic acid to keto-D-gluconates.

Vinegar Production from Jabuticaba (Myrciaria jaboticaba) Fruit Using Immobilized Acetic Acid Bacteria

Cell immobilization comprises the retention of metabolically active cells inside a polymeric matrix. In this study, the production of jabuticaba (Myrciaria jaboticaba) vinegar using immobilized Acetobacter aceti and Gluconobacter oxydans cells is proposed as a new method to prevent losses of jabuticaba fruit surplus. The pulp of jabuticaba was processed and Saccharomyces cerevisiae CCMA 0200 was used to ferment the must for jabuticaba wine production. Sugars, alcohols (ethanol and glycerol) and organic acids were assayed by high-performance liquid chromatography. Volatile compounds were determined by gas chromatography-flame ionization detector. The ethanol content of the produced jabuticaba wine was approx. 74.8 g/L (9.5% by volume) after 168 h of fermentation. Acetic acid fermentation for vinegar production was performed using a mixed culture of immobilized A. aceti CCT 0190 and G. oxydans CCMA 0350 cells. The acetic acid yield was 74.4% and productivity was 0.29 g/(L·h). The vinegar had particularly high concentrations of citric (6.67 g/L), malic (7.02 g/L) and succinic (5.60 g/L) acids. These organic acids give a suitable taste and flavour to the vinegar. Seventeen compounds (aldehydes, higher alcohols, terpene, acetate, diether, furans, acids, ketones and ethyl esters) were identified in the jabuticaba vinegar. In conclusion, vinegar was successfully produced from jabuticaba fruits using yeast and immobilized mixed cultures of A. aceti and G. oxydans. To the best of our knowledge, this is the first study to use mixed culture of immobilized cells for the production of jabuticaba vinegar.

Comparison of Cultivable Acetic Acid Bacterial Microbiota in Organic and Conventional Apple Cider Vinegar

Organic apple cider vinegar is produced from apples that go through very restricted treatment in orchard. During the first stage of the process, the sugars from apples are fermented by yeasts to cider. The produced ethanol is used as a substrate by acetic acid bacteria in a second separated bioprocess. In both, the organic and conventional apple cider vinegars the ethanol oxidation to acetic acid is initiated by native microbiota that survived alcohol fermentation. We compared the cultivable acetic acid bacterial microbiota in the production of organic and conventional apple cider vinegars from a smoothly running oxidation cycle of a submerged industrial process. In this way we isolated and characterized 96 bacteria from organic and 72 bacteria from conventional apple cider vinegar. Using the restriction analysis of the PCR-amplified 16S-23S rRNA gene ITS regions, we identified four different HaeIII and five different HpaII restriction profiles for bacterial isolates from organic apple cider vinegar. Each type of restriction profile was further analyzed by sequence analysis of the 16S-23S rRNA gene ITS regions, resulting in identification of the following species: Acetobacter pasteurianus (71.90%), Acetobacter ghanensis (12.50%), Komagataeibacter oboediens (9.35%) and Komagataeibacter saccharivorans (6.25%). Using the same analytical approach in conventional apple cider vinegar, we identified only two different HaeIII and two different HpaII restriction profiles of the 16S‒23S rRNA gene ITS regions, which belong to the species Acetobacter pasteurianus (66.70%) and Komagataeibacter oboediens (33.30%). Yeasts that are able to resist 30 g/L of acetic acid were isolated from the acetic acid production phase and further identified by sequence analysis of the ITS1-5.8S rDNA‒ITS2 region as Candida ethanolica, Pichia membranifaciens and Saccharomycodes ludwigii. This study has shown for the first time that the bacterial microbiota for the industrial production of organic apple cider vinegar is clearly more heterogeneous than the bacterial microbiota for the industrial production of conventional apple cider vinegar. Further chemical analysis should reveal if a difference in microbiota composition influences the quality of different types of apple cider vinegar.

Asaia lannensis bacteremia in a 'needle freak' patient

The genus Asaia has gained much interest lately owing to constant new species discoveries and its role as a potential opportunistic pathogen to humans. Here we describe a transient bacteremia due to Asaia lannensis in a patient with a psychiatric disorder (compulsive self-injection of different substances). Common phenotypic methods of identification failed to identify this organism, and only restriction fragment lenght polymorphism of PCR-amplified 16S rRNA gene allowed for proper identification. The isolate was highly resistant to most antibiotics. The paper also discusses the currently available medical literature, acknowledges the potential problems linked to the isolation of these strains and proposes an approach to species identification that can be applied in a clinical microbiology laboratory.