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Strains LMG 1627T, LMG 1636T and LMG 1637 were all isolated from cider fermentations in the 1940s and 1950s. A recent study based on MALDI-TOF MS and dnaK gene sequence analyses suggested they represented novel Acetobacter species. In the present study, we determined the whole-genome sequences of these strains and analysed their phenotypic and chemotaxonomic characteristics. A phylogenomic analysis based on 107 single-copy core genes revealed that they represented a single Acetobacter lineage with Acetobacter aceti , Acetobacter sicerae , Acetobacter musti and Acetobacter oeni , Acetobacter estunensis and with Acetobacter nitrogenifigens as an outgroup to this cluster. OrthoANIu value and dDDH analyses among these and other Acetobacter type strains confirmed that these three strains represented two novel Acetobacter species, which could be differentiated from other closely related type strains of Acetobacter by different phenotypic tests, such as ketogenesis from glycerol. We therefore propose to classify strain LMG 1627T in the novel species Acetobacter conturbans sp. nov., with LMG 1627T (=NCIMB 8945T) as the type strain, and to classify strains LMG 1636T and LMG 1637 in the novel species Acetobacter fallax sp. nov., with LMG 1636T (=NCIMB 8956T) as the type strain.

Strains LMG 1744

Strains LMG 1744T, LMG 1745, LMG 31484T, LMG 1764T and R-71646 were isolated from rotting fruits and fermented food products. A phylogenomic analysis based on 107 single-copy core genes revealed that they grouped in a Gluconobacter lineage comprising Gluconobacter oxydans , Gluconobacter roseus , Gluconobacter sphaericus, Gluconobacter kanchanaburiensis, Gluconobacter albidus, Gluconobacter cerevisiae, Gluconobacter kondonii and Gluconobacter aidae . OrthoANIu and digital DNA hybridization analyses demonstrated that these five strains represented three novel Gluconobacter species, which could be differentiated from the type strains of closely related Gluconobacter species by multiple phenotypic characteristics. We therefore propose to classify strains LMG 1744T and LMG 1745 in the novel species Gluconobacter cadivus sp. nov., with LMG 1744T (=CECT 30141T) as the type strain; to classify strain LMG 31484T as the novel species Gluconobacter vitians sp. nov., with LMG 31484T (=CECT 30132T) as the type strain; and to classify strains LMG 1764T and R-71646 in the novel species Gluconobacter potus sp. nov., with LMG 1764T (=CECT 30140T) as the type strain.

A phylogenomic analysis based on 107 single-copy core genes revealed that three strains from sugar-rich environments, i.e. LMG 1728T, LMG 1731 and LMG 22058, represented a single, novel Gluconacetobacter lineage with Gluconacetobacter liquefaciens as nearest validly named neighbour. OrthoANIu and digital DNA–DNA hybridization analyses among these strains and Gluconacetobacter type strains confirmed that the three strains represented a novel Gluconacetobacter species. Biochemical characteristics and MALDI-TOF mass spectra allowed differentiation of this novel species from the type strains of G. liquefaciens and other closely related Gluconacetobacter species. We therefore propose to classify strains LMG 1728T, LMG 1731 and LMG 22058 in the novel species Gluconacetobacter dulcium sp. nov., with LMG 1728T (=CECT 30142T) as the type strain.

Strains LMG 1627

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

Cooked pork products, i.e., sliced cooked hams maintained under modified-atmosphere-packaging (MAP), were analysed both microbiologically and with respect to volatile levels during storage. Three storage temperature ranges were compared (4–6 °C, 7–9 °C, and 11–13 °C), representing different refrigeration conditions at household level. The microbial loads were determined by plating samples on six different agar media, followed by (GTG)5-PCR fingerprinting of genomic DNA of selected isolates, and identification of representative isolates by 16S rRNA, pheS, and rpoA gene sequencing. Carnobacterium maltaromaticum, Lactobacillus sakei, and Serratia proteamaculans were the major bacterial species found among the 619 isolates identified. The volatiles produced during storage were followed by selected ion flow tube-mass spectrometry (SIFT-MS) and the identity of the volatiles was confirmed by headspace solid-phase microextraction combined with gas chromatography and time-of-flight mass spectrometry (HS-SPME-GC-TOF-MS). SIFT-MS analysis showed that volatiles, such as 2,3-butanediol, acetoin, and ethanol, may serve as potential markers for spoilage development. Differences in volatile production between samples were likely due to discrepancies in the initial microbial load and the effect of storage conditions. In conclusion, this study combines the use of new mass spectrometric techniques to examine volatile production during spoilage as an additional source of information during microbiological community analysis.

The whole-genome sequence of Bombella intestini LMG 28161(T), an endosymbiotic acetic acid bacterium (AAB) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. The draft genome sequence of B. intestini LMG 28161(T) was 2.02 Mb. Metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, D-glucose, D-fructose and D-mannitol, but not ethanol and glycerol. The results of the fermentation experiments also demonstrated that the lack of effective aeration in small-scale carbohydrate consumption experiments may be responsible for the lack of reproducibility of such results in taxonomic studies of AAB. Finally, compared to the genome sequences of its nearest phylogenetic neighbor and of three other insect associated AAB strains, the B. intestini LMG 28161(T) genome lost 69 orthologs and included 89 unique genes. Although many of the latter were hypothetical they also included several type IV secretion system proteins, amino acid transporter/permeases and membrane proteins which might play a role in the interaction with the bumble bee host.

The ability of coagulase-negative staphylococci (CNS) to convert amino acids into volatile compounds and biogenic amines was investigated after 24 h and 48 h of incubation in a rich medium (brain heart infusion). Volatile compounds were measured with static-headspace gas chromatography and mass spectrometry (SH-GC–MS); biogenic amine measurements were carried out with a newly developed method based on ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC–MS/MS). In total, 56 CNS strains from five different species were used, namely Staphylococcus carnosus , Staphylococcus epidermidis , Staphylococcus equorum , Staphylococcus saprophyticus , and Staphylococcus xylosus . With respect to the production of volatile compounds, the leucine-derived 3-methyl butanol was produced over time by most CNS strains, up to 52 μM for S. xylosus W1-1 after 48 h of incubation. The average production by strains of S. xylosus was significantly higher than for strains of S. carnosus , whereas strains of S. epidermidis turned out to be poor producers. Yet, differences between species were blurred to a large degree because of the high strain variability. A few strains also produced 3-methyl butanal on top of the amount that was already present in the medium background, although most CNS led to a decrease of this compound. Concerning biogenic amines, the average total concentrations per species remained below 100 μM after 48 h of incubation. The most abundant variant was 2-phenylethylamine (PEA), especially within S. carnosus (average of 65 μM after 48 h of incubation). Yet, some individual strains were able to produce higher concentrations, as found for the PEA production of 295 μM by S. epidermidis ATCC 12228 after 48 h of incubation. The insights obtained during this study indicate heterogeneity and are of importance in view of both starter culture development and the evaluation of a spontaneously established CNS microbiota in artisan-type meat fermentations.