Leuconostoc falkenbergense sp. nov., isolated from a lactic culture, fermentating string beans and traditional yogurt

Draft genome sequence of Leuconostoc falkenbergense isolated from naturally fermented buffalo milk curd

This study reports the draft genome of Leuconostoc falkenbergense strain BSMRAU-M1L5, isolated from artisanal buffalo milk curd in Bangladesh. The draft genome spans 1,776,471 bp, with 50× coverage and 96 contigs.

Sulfurovum mangrovi sp. nov., an obligately chemolithoautotrophic, hydrogen-oxidizing bacterium isolated from coastal marine sediments

A novel mesophilic, chemolithoautotrophic, hydrogen-oxidizing bacterium, designated strain ST1-3T, was isolated from mud sediment samples collected from mangroves in Jiulong River estuary. The cells were Gram-stain-negative, non-motile and rod-shaped. The temperature, pH and salinity ranges for growth of strain ST1-3T were 4-45 °C (optimum, 35 °C), pH 5.0-8.5 (optimum, pH 7.0) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen as the only energy source, and molecular oxygen, thiosulphate and elemental sulphur as electron acceptors. The major cellular fatty acids of strain ST1-3T were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c). The major polar lipids were phosphatidylethanolamine, phosphatidyldimethyl ethanolamine and phosphatidylglycerol. The respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurovum and was most closely related to Sulfurovum lithotrophicum 42BKTT (94.7 % sequence identity). The average nucleotide identity and digital DNA-DNA hybridization values between ST1-3T and S. lithotrophicum 42BKTT were 74.6 and 16.3 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain ST1-3T represents a novel species of the genus Sulfurovum, for which the name Sulfurovum mangrovi sp. nov. is proposed, with the type strain ST1-3T (=MCCC M25234T=KCTC 25639T).

Epiphytic microbiota in Swedish grass-clover herbage and the effect of silage additives on fermentation profiles and bacterial community compositions of the resulting silages

AIMS

To investigate the epiphytic microbiota in grass-clover herbage harvested at different sites and occasions and to explore the effect of different silage additives on the resulting silage microbiota.

METHODS AND RESULTS

Herbage was harvested from grass-clover leys at geographically distributed sites in a long-term field experiment in Sweden, in early and late season of two consecutive years. Different silages were made from the herbage using: (1) no additive, (2) acid-treatment, and (3) inoculation by starter culture. Herbages were analysed for botanical and chemical composition, and the resulting silages for products of fermentation. Bacterial DNA was extracted from herbage and silage samples, followed by sequencing using Illumina 16S rRNA amplicon sequencing. Herbage microbiota showed no clear correlation to site or harvesting time. Silage additives had a major effect on the ensiling process; inoculation resulted in well fermented silages comprising a homogenous microbiota dominated by the genera Lactobacillus and Pediococcus. A minor effect of harvest time was also observed, with generally a more diverse microbiota in second-harvest silages. Untreated silages showed a higher relative abundance (RA) from non-lactic acid bacteria compared to acid-treated silages. In most silages, only a few bacterial amplicon sequence variants contributed to most of the RA.

CONCLUSIONS

The epiphytic microbiota in grass-clover herbage were found to be random and not dependent on site. From a microbial point of view, the most predictable and preferable silage outcome was obtained by inoculation with a starter culture. Acid-treatment with formic- and propionic acid surprisingly resulted in a less preferable silage. Silage making without additives cannot be recommended based on our results.

Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods

Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods.

Phylogenomic analysis of the genus Leuconostoc

Leuconostoc is a genus of saccharolytic heterofermentative lactic acid bacteria that inhabit plant-derived matrices and a variety of fermented foods (dairy products, dough, milk, vegetables, and meats), contributing to desired fermentation processes or playing a role in food spoilage. At present, the genus encompasses 17 recognized species. In total, 216 deposited genome sequences of Leuconostoc were analyzed, to check the delineation of species and to infer their evolutive genealogy utilizing a minimum evolution tree of Average Nucleotide Identity (ANI) and the core genome alignment. Phylogenomic relationships were compared to those obtained from the analysis of 16S rRNA, pheS, and rpoA genes. All the phylograms were subjected to split decomposition analysis and their topologies were compared to check the ambiguities in the inferred phylogenesis. The minimum evolution ANI tree exhibited the most similar topology with the core genome tree, while single gene trees were less adherent and provided a weaker phylogenetic signal. In particular, the 16S rRNA gene failed to resolve several bifurcations and Leuconostoc species. Based on an ANI threshold of 95%, the organization of the genus Leuconostoc could be amended, redefining the boundaries of the species L. inhae, L. falkenbergense, L. gelidum, L. lactis, L. mesenteroides, and L. pseudomesenteroides. Two strains currently recognized as L. mesenteroides were split into a separate lineage representing a putative species (G16), phylogenetically related to both L. mesenteroides (G18) and L. suionicum (G17). Differences among the four subspecies of L. mesenteroides were not pinpointed by ANI or by the conserved genes. The strains of L. pseudomesenteroides were ascribed to two putative species, G13 and G14, the former including also all the strains presently belonging to L. falkenbergense. L. lactis was split into two phylogenetically related lineages, G9 and G10, putatively corresponding to separate species and both including subgroups that may correspond to subspecies. The species L. gelidum and L. gasicomitatum were closely related but separated into different species, the latter including also L. inhae strains. These results, integrating information of ANI, core genome, and housekeeping genes, complemented the taxonomic delineation with solid information on the phylogenetic lineages evolved within the genus Leuconostoc.

Rejection of the reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum based on whole genome analysis

In 2014, Rahkila et al. transferred Leuconostoc gasicomitatum to Leuconostoc gelidum as L. gelidum subsp. gasicomitatum comb. nov. based on a 75 % DNA-DNA hybridization value. In the present study, the taxonomic status of L. gelidum subsp. gasicomitatum is re-evaluated by a polyphasic approach, including 16S rRNA, pheS, rpoA, recA, and atpA gene sequence analyses, phylogenomic treeing, analyses of ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization), fatty acid methyl ester analysis and a phenotypic characterization. On the basis of the ANI and dDDH values, we propose to reject the proposal of Rahkila et al. to reclassify L. gasicomitatum as L. gelidum subsp. gasicomitatum.

Lactic Acid Bacteria Isolated from Fermented Doughs in Spain Produce Dextrans and Riboflavin

Many lactic acid bacteria (LAB) produce metabolites with applications in the food industry, such as dextran-type exopolysaccharides (EPS) and riboflavin (vitamin B₂). Here, 72 bacteria were isolated from sourdoughs made by Spanish bread-makers. In the presence of sucrose, colonies of 22 isolates showed a ropy phenotype, and NMR analysis of their EPS supported that 21 of them were dextran producers. These isolates were identified by their random amplified polymorphic DNA (RAPD) patterns and their rrs and pheS gene sequences as LAB belonging to four species (Weissella cibaria, Leuconostoc citreum, Leuconostoc falkenbergense and Leuconostoc mesenteroides). Six selected strains from the Leuconostoc (3) and Weissella (3) genera grew in the absence of riboflavin and synthesized vitamin B₂. The EPS produced by these strains were characterized as dextrans by physicochemical analysis, and the L. citreum polymer showed an unusually high degree of branching. Quantification of the riboflavin and the EPS productions showed that the W. cibaria strains produce the highest levels (585–685 μg/and 6.5–7.4 g/L, respectively). Therefore, these new LAB strains would be good candidates for the development of fermented foods bio-fortified with both dextrans and riboflavin. Moreover, this is the first report of riboflavin and dextran production by L. falkenbergense.

Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene

Leuconostoc spp. are environmental microorganisms commonly associated with fermented foods. Absence of antibiotic resistance (AR) in bacteria is a critical issue for global food safety. Herein, we updated the occurrence of AR genes in the Leuconostoc genus through in silico analyses of the genomes of 17 type strains. A total of 131 putative AR traits associated with the main clinically relevant antibiotics were detected. We found, for the first time, the lsaA gene in L. fallax ATCC 700006^T and L. pseudomesenteroides NCDO 768^T. Their amino acid sequences displayed high similarities (59.07% and 52.21%) with LsaA of Enterococcusfaecalis V583, involved in clindamycin (CLI) and quinupristin-dalfopristin (QUD) resistance. This trait has different distribution patterns in Leuconostoc nontype strains-i.e., L. pseudomesenteroides, L. lactis and L. falkenbergense isolates from fermented vegetables, cheeses, and starters. To better explore the role of lsaA, MIC for CLI and QUD were assessed in ATCC 700006^T and NCDO 768^T; both strains were resistant towards CLI, potentially linking lsaA to their resistant phenotype. Contrarily, NCDO 768^T was sensitive towards QUD; however, expression of lsaA increased in presence of this antibiotic, indicating an active involvement of this trait and thus suggesting a revision of the QUD thresholds for this species.