Selection of Acetic Acid Bacterial Strains and Vinegar Production From Local Maltese Food Sources

This study investigates the isolation, identification, and fermentation performance of autochthonous acetic acid bacteria (AAB) from local niche habitats on the Island of Gozo (Malta) and their further use for vinegar production, employing local raw materials. The bacteria were isolated from grapevine berries and vinegar produced in the cottage industry. Following phenotype and genotype identification, the AAB were ascribed to the genera Acetobacter, Gluconobacter, and Komagataeibacter. A mixture of selected AAB was tested as an inoculum for vinegar production in bench fermenters, under different conditions and substrates, namely, grapes, honey, figs, onions, prickly pear, and tomatoes. The bench fermenters were operated under semi-continuous fermentation where working volumes were maintained by discharging and subsequent recharging accordingly to maintain the acidity in fermenters by adding 30-50 g/l of acetic acid for optimal Acetobacteraceae performance. Finally, the vinegar products obtained from the different substrates were evaluated for their quality, including organoleptic properties, which showed the superior quality of wood-treated vinegar samples with respect to neat vinegar samples.

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia . Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria . Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria , and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

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).

Proposal for transfer of Defluviimonas alba to the genus Frigidibacter as Frigidibacter mobilis nom. nov

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42^T of the species Defluviimonas alba Pan et al. 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42^T shared 99.6 and 99.7 % similarity to that of the type strain SP32^T of the species Frigidibacter albus and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42^T and SP32^T yielded a digital DNA-DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42^T and SP32^T shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of Defluviimonas alba into the genus Frigidibacter as Frigidibacter mobilis nom. nov. with the type strain cai42^T (=CGMCC 1.12518^T=LMG 27406^T).

Komagataeibacter cocois sp. nov., a novel cellulose-producing strain isolated from coconut milk

Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7^T, isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter. DNA-DNA correlation or average nucleotide identity analysis was performed between WE7^T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7^T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7^T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7^T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7^T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7^T (=CGMCC 1.15338^T=JCM 31140^T).

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales

Methane emissions from agriculture represent around 9 % of global anthropogenic greenhouse emissions. The single largest source of this methane is animal enteric fermentation, predominantly from ruminant livestock where it is produced mainly in their fermentative forestomach (or reticulo-rumen) by a group of archaea known as methanogens. In order to reduce methane emissions from ruminants, it is necessary to understand the role of methanogenic archaea in the rumen, and to identify their distinguishing characteristics that can be used to develop methane mitigation technologies. To gain insights into the role of methylotrophic methanogens in the rumen environment, the genome of a methanogenic archaeon has been sequenced. This isolate, strain ISO4-H5, was isolated from the ovine rumen and belongs to the order Methanomassiliicoccales. Genomic analysis suggests ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use methanol and methylamines as substrates for methanogenesis. Like other organisms within this order, ISO4-H5 does not possess genes required for the first six steps of hydrogenotrophic methanogenesis. Comparison between the genomes of different members of the order Methanomassiliicoccales revealed strong conservation in energy metabolism, particularly in genes of the methylotrophic methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine. Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not contain the genes required for production of coenzyme M, and so likely requires external coenzyme M to survive.

Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture

For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N2 is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth-promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth-promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.

Fruit peels support higher yield and superior quality bacterial cellulose production

Fruit peels, also known as rinds or skins, are wastes readily available in large quantities. Here, we have used pineapple (PA) and watermelon (WM) peels as substrates in the culture media (containing 5 % sucrose and 0.7 % ammonium sulfate) for production of bacterial cellulose (BC). The bacterial culture used in the study, Komagataeibacter hansenii produced BC under static conditions as a pellicle at the air-liquid interface in standard Hestrin and Schramm (HS) medium. The yield obtained was ~3.0 g/100 ml (on a wet weight basis). The cellulosic nature of the pellicle was confirmed by CO2, H2O, N2, and SO2 (CHNS) analysis and Fourier transform infrared (FT-IR) spectroscopy. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) of the pellicle revealed the presence of flat twisted ribbonlike fibrils (70-130 nm wide). X-ray diffraction analysis proved its crystalline nature (matching cellulose I) with a crystallinity index of 67 %. When K. hansenii was grown in PA and WM media, BC yields were threefolds or fourfolds higher than those obtained in HS medium. Interestingly, textural characterization tests (viz., SEM, crystallinity index, resilience, hardness, adhesiveness, cohesiveness, springiness, shear energy and stress, and energy required for puncturing the pellicle) proved that the quality of BC produced in PA and WM media was superior to the BC produced in HS medium. These findings demonstrate the utility of the newly designed media for getting higher yields and better quality of BC, which could make fermentative production of BC more attractive on a commercial scale.

Desulfovibrio legallii prosthetic shoulder joint infection and review of antimicrobial susceptibility and clinical characteristics of Desulfovibrio infections

We describe a case of shoulder hemiarthroplasty infection with Desulfovibrio legallii. Antimicrobial susceptibilities of 36 Desulfovibrio isolates are presented. Metronidazole and carbapenems exhibited reliable activity, although piperacillin-tazobactam did not. Eleven previous cases of Desulfovibrio infection are reviewed; most arose from a gastrointestinal tract-related source.

Transfer of Gluconacetobacter kakiaceti, Gluconacetobacter medellinensis and Gluconacetobacter maltaceti to the genus Komagataeibacter as Komagataeibacter kakiaceti comb. nov., Komagataeibacter medellinensis comb. nov. and Komagataeibacter maltaceti comb. nov

Gluconacetobacter kakiaceti, Gluconacetobacter medellinensis and Gluconacetobacter maltaceti are transferred to the genus Komagataeibacter as Komagataeibacter kakiaceti comb. nov. (type strain, G5-1T=JCM 25156T=NRIC 0798T=LMG 26206T), Komagataeibacter medellinensis comb. nov. (type strain, LMG 1693T=NBRC 3288T=Kondo 51T) and Komagataeibacter maltaceti comb. nov. (type strain, LMG 1529T=NBRC 14815T=NCIMB 8752T).

Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi

A Gram-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated MA-E2-3(T), was isolated from an ascidian (Halocynthia roretzi) collected from the South Sea, South Korea. Strain MA-E2-3(T) was found to grow optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MA-E2-3(T) fell within the clade comprising Ruegeria species, clustering consistently with the type strain of Ruegeria halocynthiae, with which it exhibited 98.2 % sequence similarity. Sequence similarities to the type strains of the other recognized Ruegeria species were 94.7-97.7 %. Strain MA-E2-3(T) was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c as the predominant fatty acid. The major polar lipids of strain MA-E2-3(T) were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA-E2-3(T) was determined to be 58.0 mol%. Mean DNA-DNA relatedness values between strain MA-E2-3(T) and the type strains of four phylogenetically closely related Ruegeria species were in the range of 13-23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MA-E2-3(T) is separated from other Ruegeria species. On the basis of the data presented, strain MA-E2-3(T) (=KCTC 32450(T) = CECT 8411(T)) represents a novel species of the genus Ruegeria, for which the name Ruegeria meonggei sp. nov. is proposed.

Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov., isolated from Takamatsuzuka Tumulus samples before and during the dismantling work in 2007

Ten strains of Gram-stain-negative, rod-shaped, non-spore-forming bacteria were isolated from the burial mound soil collected before the dismantling and samples collected during the dismantling work on the Takamatsuzuka Tumulus in Asuka village, Nara Prefecture, Japan in 2007. On the basis of the 16S rRNA gene sequence analysis of the isolates, they were accommodated in the genus Gluconacetobacter (class Alphaproteobacteria) and can be separated into four groups within the cluster containing the genus Gluconacetobacter. One of the groups demonstrated a phylogenetic position identical to that of Gluconacetobacter asukensis, which was isolated from small holes on plaster walls of the stone chamber interior of Kitora Tumulus in Asuka village, Nara Prefecture, Japan. The remaining three groups consisted of novel lineages within the genus Gluconacetobacter. A total of four isolates were selected from each group and carefully identified using a polyphasic approach. The isolates were characterized on the basis of their possessing Q-10 as the major ubiquinone system and C18 : 1ω7c (58.5-65.2 %) as the predominant fatty acid. A DNA-DNA hybridization test was used to determine that the three lineages represented novel species, for which the names Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov. are proposed. The type strains are T611xx-1-4a(T) ( = JCM 19097(T) = NCIMB 14861(T)), T61213-20-1a(T) ( = JCM 19094(T) = NCIMB 14859(T)) and T6203-4-1a(T) ( = JCM 19092(T) = NCIMB 14860(T)), respectively.