Microbiology of fermented soy foods in Asia: Can we learn lessons for production of plant cheese analogues?

The food industry is facing the challenge of creating innovative, nutritious, and flavored plant-based products, due to consumer's increasing demand for the health and environmental sustainability. Fermentation as a unique and effective tool plays an important role in the innovation of food products. Traditional fermented soy foods are popular in many Asian and African countries as nutritious, digestible and flavorful daily staples or condiments. They are produced by specific microorganisms with the unique fermentation process in which microorganisms convert the ingredients of whole soybean or soybean curd to flavorful and functional molecules. This review provides an overview on traditional fermented food produced from soy, including douchi, natto, tempeh, and sufu as well as stinky tofu, including the background of these products, the manufacturing process, and the microbial diversity involved in fermentation procedures as well as flavor volatiles that were identified in the final products. The contribution of microbes to the quality of these five fermented soy foods is discussed, with the comparison to the role of cheese ripening microorganisms in cheese flavor formation. This communication aims to summarize the microbiology of fermented soy foods in Asia, evoking innovative ideas for the development of new plant-based fermented foods especially plant-based cheese analogues.

Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial isolates from stingless bees Tetragonula carbonaria and Austroplebeia australis

Four strains, SG5_A10T, SGEP1_A5T, SG4_D2T, and SG4_A1T, were isolated from the honey or homogenate of Australian stingless bee species Tetragonula carbonaria and Austroplebeia australis. Based on 16S rRNA gene phylogeny, core gene phylogenetics, whole genome analyses such as determination of amino acid identity (AAI), cAAI of conserved genes, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH), chemotaxonomic analyses, and the novel isolation sources and unique geography, we propose three new species and one genus with the names Apilactobacillus apisilvae sp. nov. (SG5_A10T = LMG 32133T = NBRC 114991T), Bombilactobacillus thymidiniphilus sp. nov. (SG4_A1T = LMG 32125T = NBRC 114984T), Bombilactobacillus folatiphilus sp. nov. (SG4_D2T = LMG 32126T = NBRC 115004T) and Nicolia spurrieriana sp. nov. (SGEP1_A5T = LMG 32134T = NBRC 114992T). Three out of the four strains were found to be fructophilic, where SG5_A10T and SGEP1_A5T belong to obligately fructophilic lactic acid bacteria, and SG4_D2T representing a new type denoted here as kinetically fructophilic. This study represents the first published lactic acid bacterial species associated with the unique niche of Australian stingless bees.

Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates

In Japan, during a screening of lactic acid bacteria in spent mushroom substrates, an unknown bacterium was isolated and could not be assigned to any known species. Strain YK48G^T is Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative. The isolate grew in 0-4 % (w/v) NaCl, at 15-37 °C (optimum, 30 °C) and at pH 4.0-8.0 (optimum, pH 6.0). The genomic DNA G+C content of strain YK48G^T was 42.5 mol%. Based on its 16S rRNA gene sequence, strain YK48G^T represented a member of the genus Lentilactobacillus and showed the highest pairwise similarity to Lentilactobacillus rapi DSM 19907^T (97.86 %). Phylogenetic analyses based on amino acid sequences of 466 shared protein-encoding genes also revealed that the strain was phylogenetically positioned in the genus Lentilactobacillus but did not suggest an affiliation with previously described species. The average nucleotide identity and digital DNA-DNA hybridization values between strain YK48G^T and the type strains of phylogenetically related species were 72.2-76.6% and 19.0-21.2 %, respectively, indicating that strain YK48G^T represents a novel species within the genus Lentilactobacillus. Phenotypic data further confirmed the differentiation of strain YK48G^T from other members of the genus Lentilactobacillus. According to the results of the polyphasic characterization presented in this study, strain YK48G^T represents a novel species of the genus Lentilactobacillus, for which the name Lentilactobacillus fungorum sp. nov. is proposed. The type strain is YK48G^T (=JCM 32598^T=DSM 107968^T).

Lentilactobacillus kosonis sp. nov., isolated from kôso, a Japanese sugar-vegetable fermented beverage

A novel lactic acid-producing, Gram-stain-positive, catalase-negative and rod-shaped strain, designated as strain C06_No.73^T, was isolated from a traditional Japanese fermented beverage called kôso. According to the results of phylogenetic analysis based on 16S rRNA gene sequences, strain C06_No.73^T belongs to the genus Lentilactobacillus. The closest type strain was Lentilactobacillus curieae CCTCC M 2011381^T, with a sequence identity of 98.1 %. The identity values with other strains were all below 97 %. The isolate propagated under the conditions of 18-39 °C (optimum, 27 °C for 48 h incubation) and pH 4.0-7.0 (optimum, pH 6.5). The G+C content of its genomic DNA was determined to be 37.9 mol%. The main fatty acids were C_16 : 0, C_18 : 1 ω7c, C_18 : 1 ω9c and C_19 : 0 cyclopropane 11,12. The major polar lipid was identified as phosphatidylglycerol. No isoprenoid quinone was detected. The predominant cell-wall amino acids were lysine, alanine, glutamic acid and aspartic acid. Neither meso-diaminopimelic acid nor ornithine were detected. On the basis of this polyphasic taxonomic study, the isolate is concluded to represent a novel species, for which the name Lentilactobacillus kosonis sp. nov. is proposed. The type strain is C06_No.73^T (=NBRC 111893^T=BCRC 81282^T).

High-level expression of a β-mannanase (manB) in Pichia pastoris GS115 for mannose production with Penicillium brevicompactum fermentation pretreatment of soybean meal

An endo-1,4-β-mannanase gene (manB) from a Bacillus pumilus Nsic-2 grown in a stinky tofu emulsion was cloned and expressed in Pichia pastoris GS115. After characterized, the endo-1,4-β-mannanase (manB) show maximum activity at pH 6.0 and 50 °C with LBG as substrate and perform high stability at a range of pH 6-8. After applying for a shake flask fermentation, the specific activity of manB reached 3462 U/mg. To produce mannose, the soybean meal (SBM) was pretreated by biological fermentation for 11 days with Penicillium brevicompactum, and then hydrolyzed by manB. As a result, mannose yield reached 3.58 g per 1 kg SBM which indicated that 0.358% SBM was converted into mannose after hydrolyzation, and mean a total 20% mannan of SBM converting into mannose, while the control group demonstrated only 1.78% conversion. An effective β-mannanase for the bioconversion of mannan-rich biomasses and an efficient method to produce mannose with soybean meal were introduced.

Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach

The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.

Lentilactobacillus kribbianus sp. nov., isolated from the small intestine of a mini pig

A Gram-stain-positive, facultative anaerobic, rod-shaped bacteria isolated from the small intestine of a mini pig was designated as strain YH-lac9^T. 16S rRNA gene sequence analysis revealed that the strain belongs to the genus Lentilactobacillus and is closely related to Lentilactobacillus senioris JCM 17472^T, Lentilactobacillus rapi JCM 15042^T and Lentilactobacillus diolivorans JCM 13927^T, with 97.6, 96.2 and 95.7 % sequence similarity, respectively. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster with L. senioris, supporting the results of 16S rRNA gene sequences analysis. The average nucleotide identity value for YH-lac9^T and the most closely related strain is 74.1 %. The main fatty acids are C_18 : 1ω9c, summed feature 7, C_16 : 0 and summed feature 8. The G+C content of the genomic DNA is 37.8 mol%. In view of its chemotaxonomic, phenotypic and phylogenetic properties, YH-lac9^T (=KCTC 25005=JCM 33997) represents a novel taxon. The name Lentilactobacillus kribbianus sp. nov. is proposed.

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).

Taxono-genomics description of 'Lactobacillus raoultii sp. nov.', strain Marseille-P4006T, a new Lactobacillus species isolated from the female genital tract of a patient with bacterial vaginosis

Strain Marseille-P4006^T, a Gram-stain-positive, rod-shaped, non-sporulating, facultatively anaerobic bacterium, was isolated from the vaginal swab of a 45-year-old woman with recurrent bacterial vaginosis. We studied its phenotypic characteristics and sequenced its whole genome. The major fatty acids were C_16:0 (48%), C_19:1n9 (14%) and C_18:0 (11%). The 3 070 142-bp-long genome contains 2855 protein-coding genes and 68 RNAs. Strain Marseille-P4006^T exhibited 98.1% 16S rRNA similarity with Lactobacillus farraginis, the closest species phylogenetically. Thus, strain Marseille-P4006 is distinct enough to represent a new species for which we propose the name Lactobacillus raoultii sp. nov. The type strain is Marseille-P4006^T.

Characterisation of mango flavoured curd powder developed using spray drying technique

This research communication describes the production of flavoured (Mango) curd powder. The mango flavoured curd powder was developed in two different temperatures (150 °C and 170 °C) in various ratios with one control curd sample. The final powder was obtained in high quality which can be used directly or as an ingredient. The percentage of lactic acid in the developed powder showed the healthy amount of probiotic present in it. The physical properties and probiotic growth of the mango flavoured curd powder, developed by spray drying technique, have been evaluated in this article. Various properties were analysed, including moisture content, water activity, dispersibility, bulk and tapped density, porosity, particle morphology, colour analysis, pH, functional group identification using FTIR, identification of the pure culture and % of lactic acid for 3 different Curd and Mango ratios (1:0·5, 1:1, 0·5:1), respectively with one control curd sample. The lactobacillus strain found in this newly developed flavoured powder was Lactobacillus curieae. Lactic acid percentage showed the powder to contain appropriate and healthy amount of probiotic and significant flavour. Future studies are focused on storage studies of the produced powder.

Genome Sequence of Lactobacillus curieae CCTCC M 2011381T, a Novel Producer of Gamma-aminobutyric Acid

Lactobacillus curieae CCTCC M 2011381(T) is a novel species of the genus Lactobacillus and a gamma-aminobutyric acid producer that was isolated from stinky tofu brine. Here, we present a 2.19-Mb assembly of its genome, which may provide further insights into the molecular mechanisms underlying its beneficial properties.