Characterization and correlation analysis of microbial flora and flavor profile of stinky acid, a Chinese traditional fermented condiment

To explore the microbial diversity and flavor profiles of stinky acid, we utilized high-throughput sequencing, culture-based techniques, and bionic E-sensory technologies. The results revealed a significant correlation between the acidity levels of stinky acid and the richness of its microbial community. Ten core bacterial genera and three core fungal genera exhibited ubiquity across all stinky acid samples. Through E-nose analysis, it was found that sulfides constituted the principal odor compounds responsible for stinky acid's distinct aroma. Further insights arose from the correlation analysis, indicating the potential contribution of Debaryomyces yeast to the sour taste profile. Meanwhile, three genera-Rhizopus and Thermoascus and Companilactobacillus-were identified as contributors to aromatic constituents. Interestingly, the findings indicated that Rhizopus and Thermoascus could reduce the intensity of the pungent odor of stinky acid. In summary, this investigation's outcomes offer new insights into the complex bacterial diversity of stinky acid.

Levilactobacillus yiduensis sp. nov., Isolated from Zha-chili in Yidu County, Hubei Province, China

The zha-chili isolate HBUAS62285^T is a facultative anaerobic strain. This bacterium was gram-positive, but it could not generate catalase, was not motile, did not form spores, had no flagella, and produced gamma-aminobutyric acid (GABA). Comparing of HBUAS62285^T with its related type strains Levilactobacillus suantsaiihabitans BCRC 81129^T, Levilactobacillus angrenensis M1530-1^T, Levilactobacillus cerevisiae DSM 100836^T, Levilactobacillus wangkuiensis 6-5(1)^T, Levilactobacillus lanxiensis 13B17^T, and Levilactobacillus mulengensis 112-3^T showed that the similarity of 16S rRNA gene sequence was less than 99.13%. Strain HBUAS62285^T has a G+C content of 50.57 mol%, an ANI value of less than 86.61%, an AAI value of less than 92.9%, and a dDDH value of less than 32.9% when compared to the aforementioned closely related strains. In the end, the most major fatty acids in cells were determined to be C_16:0, C_18:1 ω9c, C_19:1 cyclo ω9,10c, and summed feature 10. Overall, the results of the phenotypic, genomic, chemotaxonomic, and phylogenetic studies indicate that strains HBUAS62285^T and CD0817 constitute a new species within the genus Levilactobacillus, and the name Levilactobacillus yiduensis sp. nov. is proposed. The type strain is HBUAS62285^T (= JCM 35804^T = GDMCC 1.3507^T).

Rice varieties affect bacterial diversity, flavor, and metabolites of zha-chili

The structure and diversity of bacterial communities in spontaneously fermented zha-chili prepared using two different rice varieties (glutinous rice and indica rice) were investigated using high-throughput sequencing. Through metabolic pathway prediction, electronic senses and metabolite analysis, the relationships among the rice varieties used for preparation and the bacterial microbiota, flavor, and organic acid/amino acid metabolites in zha-chili were elucidated. We observed that the structure of bacterial communities in zha-chili samples differed significantly with the rice variety used during fermentation (p < 0.05), and that there was a greater abundance of bacterial species in zha-chili prepared using glutinous rice. Lactic acid bacteria were predominant in zha-chili, with an average relative abundance of 77.09%. The aroma of zha-chili was influenced by the raw material itself, while the characteristic tastes of zha-chili - including sourness, umami and richness - were significantly correlated with the bacterial microbiota. In addition, the abundance of lactic acid bacteria was positively correlated with the levels of organic acids and negatively correlated with the levels of amino acids. This also made the zha-chili prepared using glutinous rice sourer and imparted more umami taste to the zha-chili prepared using indica rice. Our observations provide a reference for the evaluation of zha-chili quality and could effectively guide the improvement of zha-chili products.

Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11^T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA-DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11^T belonged to the genus Companilactobacillus. The 16S rRNA gene sequence of strain NFFJ11^T exhibited high similarity to Companilactobacillus formosensis S215^T (99.66 %), Companilactobacillus farciminis Rv4 na^T (99.53 %), Companilactobacillus crustorum LMG 23699^T (99.19 %), Companilactobacillus futsaii YM 0097^T (99.06 %), Companilactobacillus zhachilii HBUAS52074^T (98.86 %) and Companilactobacillus heilongiiangensis S4-3^T (98.66 %). However, average nucleotide identity and in silico DNA-DNA hybridization values for these type strains were in the range of 79.90-92.93 % and 23.80-49.30 %, respectively, which offer evidence that strain NFFJ11^T belongs to a novel species of the genus Companilactobacillus. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11^T were C_18 : 1  ω9c (43.3 %), C_16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C_19 : 1  ω7c, C_19 : 1  ω6c and C_19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11^T represents a novel species belonging to the genus Companilactobacillus, for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11^T (= KACC 21771^T= JCM 34088^T).

Bacterial diversity and flavor profile of Zha-Chili, a traditional fermented food in China

Zha-chili is a traditional Chinese fermented food with special flavor, which is often used as an appetizer in condiments and an important energy source. The final quality of zha-chili is closely related to its microbial community structure. However, the differences of bacterial diversity in zha-chili from different regions and how bacterial species affect zha-chili fermentation process and flavor quality have not been reported. In this study, the bacterial diversity and flavor quality of zha-chili samples from different regions were analyzed using Illumina Miseq high-throughput sequencing, electronic nose and electronic tongue technology. Twenty-three bacterial phyla and 665 bacterial genera were identified in all zha-chili samples. Firmicutes, Proteobacteria and Actinobacteria were the dominant bacterial phyla in zha-chili samples, while Lactobacillus, Pseudomonas, Pediococcus, Weissella and Staphylococcus were the dominant bacterial genera. The bacterial community structure of zha-chili samples from different regions was significantly diverse (p < 0.05). The flavor of zha-chili samples also varied in different regions, and the discrepancy of taste was much greater than that of aroma. Moreover, there were significant correlations (p < 0.05) between 6 dominant bacterial genera and 8 flavor indicators (3 aroma indicators, 5 taste indicators). In addition, the results of microbiome phenotypes prediction by BugBase and bacterial functional potential prediction using PICRUSt showed that eight out of nine predicted phenotypic functions of zha-chili samples from different regions were significantly different (p < 0.05), bacterial metabolism was vigorous in the zha-chili samples, and Lactobacillus was the dominant bacterial genus involved in metabolism during fermentation.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium

A lactic acid bacterial strain, HBUAS57009T, isolated from traditionally fermented food (Zha-Chili) in China, was characterized to clarify its taxonomic status using a polyphasic approach. Strain HBUAS57009T was phylogenetically closely related to Lactobacillus koreensis DCY50T, Lactobacillus fujinensis 218-6T, Lactobacillus mulengensis 112-3T, Lactobacillus cerevisiae TUM BP 140423000-2250T, Lactobacillus tongjiangensis 218-10T and Lactobacillus yonginensis THK-V8T with sequence similarities of 98.6–99.3 %. The genome-to-genome distance and average nucleotide identity values between the genomes of strain HBUAS57009T and type strains of closely related Lactobacillus species were less than 32.0 and 86.0 %, respectively; this is below the threshold for species boundaries. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1  ω9c and iso-C19 : 0. The G+C content of the genomic DNA of strain HBUAS57009T was 47.8 mol%. Examination of the functional categories of the genome revealed that strain HBUAS57009T could perform both homolactic and heterolactic fermentation processes to produce lactic acid via complete glycolysis and the pentose phosphate pathway. The putative biosynthesis pathway of butane-2,3-diol and acetoin, two important flavour compounds in the food industry, were identified using kegg mapper analysis. Based on its genotypic and phenotypic features, strain HBUAS57009T (=GDMCC 1.1664T=KACC 21424T) is designated as the type strain of a novel species, for which the name Lactobacillus enshiensis sp. nov. is proposed.