Identification of lactobacilli by pheS and rpoA gene sequence analyses

Lacticaseibacillus salsurivasis sp. nov. and Companilactobacillus muriivasis sp. nov., Isolated from Traditional Chinese Pickle

Three Gram-stain-positive bacterial strains were isolated from traditional Chinese pickle and characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain 74-4T was most closely related to the type strains of Lacticaseibacillus suibinensis and Lacticaseibacillus suilingensis, having 99.9% and 100% 16S rRNA gene sequence similarities, respectively, and that strains 419-1.2T and 262-4 were most closely related to the type strains of Companilactobacillus heilongjiangensis, Companilactobacillus nantensis, Companilactobacillus huachuanensis, and Companilactobacillus nuruki, having 98.5-99.7% 16S rRNA gene sequence similarities. The phylogenomic trees indicated that strain 74-4T was related to the type strains of L. suibinensis and L. suilingensis, and that strains 419-1.2T and 262-4 were related to the type strains of C. heilongjiangensis, C. nantensis, C. huachuanensis, and Companilactobacillus zhachilii. The ANI and dDDH values between strain 74-4T and type strains of phylogenetically related species were less than 92.7% and 49.9%, respectively. The ANI and dDDH values between strains 419-1.2T and 262-4 and type strains of phylogenetically related species were less than 93.4% and 51.7%, respectively. Based upon the data of polyphasic characterization obtained in the present study, two novel species, Lacticaseibacillus salsurivasis sp. nov. and Companilactobacillus muriivasis sp. nov., are proposed and the type strains are 74-4T (= JCM 35890T = CCTCC AB 2022414T) and 419-1.2T (= JCM 35891T = CCTCC AB 2022413T), respectively.

Genotypic and Phenotypic Characteristics of Lactic Acid Bacteria Associated with Forage Plants in the Native Grassland of Western Inner Mongolia and Their Application for Alfalfa Silage Fermentation

This study was conducted to investigate the genotypic and phenotypic characteristics of lactic acid bacteria (LAB) associated with forage plants in the native grassland of western Inner Mongolia and to evaluate their effects on alfalfa silage fermentation. Forage plants and their spontaneous fermentation silages were analysed using culture-based techniques for LAB isolation; the phenotypic properties and 16S rDNA and pheS or rpoA gene sequences of the isolates were evaluated; alfalfa was ensiled with four additive combinations: Lactiplantibacillus plantarum subsp. plantarum (GI19), Lact. plantarum subsp. plantarum and Pediococcus pentosaceus (GI19+GI51), GI19 and 20 g/kg fresh matter of sucrose (GI19+S), and GI19+GI51+S, for 60 d. A total of 73 strains belonging to 16 species were isolated. All isolates grew at 5-45 °C and in 3.0% NaCl, and most of them grew in 6.5% NaCl. Enterococcus faecalis and Lact. plantarum were 26.03% and 17.81% of the total isolates, respectively. All additives improved the silage quality, while GI19+S was more effective for alfalfa ensiling with a higher lactic acid content and lower pH, undesirable microorganism counts, and acetic acid and NH3-N contents than remnant additives. In conclusion, the LAB species were diverse, and most of them possessed good cryotolerance and osmotolerance; GI19+S was the optimal inoculant for alfalfa fermentation improvement.

Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential

Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.

Lactiplantibacillus paraxiangfangensis sp. nov., isolated from traditional Chinese pickle

Three Gram-stain-positive bacterial strains (designated 231-9T, 142-6 and 463-4) were isolated from traditional Chinese pickle, and were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strains 231-9T, 142-6 and 463-4 were phylogenetically related to the type strains of Lactiplantibacillus xiangfangensis, Lactiplantibacillus garii, Lactiplantibacillus carotarum, Lactiplantibacillus plajomi and Lactiplantibacillus modestisalitolerans, having 98.6-99.9 % 16S rRNA gene sequence similarities. Strains 231-9T, 142-6 and 463-4 were most closely related to the type strain of L. xiangfangensis, having 99.9 % 16S rRNA gene, 95.6 % pheS, 99.4 % rpoA and 98.2 % concatenated pheS and rpoA sequence similarities. Relatively low pheS (95.6 %) sequence similarity indicated that strain 231-9T should be further identified. Strain 231-9T shared 99.7-99.9 % average nucleotide identity (ANI) and 98.8-98.9 % digital DNA-DNA hybridization (dDDH) values with strains 142-6 and 463-4, indicating that they belonged to the same species. The ANI and dDDH values between strain 231-9T and L. xiangfangensis LMG 26013T were 92.4-92.9 and 49.6 %, respectively, less than the threshold for species demarcation (95-96% ANI and 70 % dDDH values, respectively), indicating that strains 231-9T, 142-6 and 463-4 represented a novel species within the genus Lactiplantibacillus. Acid production from d-ribose, d-adonitol, d-galactose and lactose, activity of β-galactosidase and β-glucosidase, Voges-Proskauer reaction, hydrolysis of hippurate, resistance to 5 µg ml-1 erythromycin, 100 µg ml-1 tetracycline hydrochloride, 50 µg ml-1 bacitracin, 300 µg ml-1 each of gentamicin sulphate, streptomycin sulphate and neomycin sulphate, tolerance to 6 % NaCl could distinguish strains 231-9T, 142-6 and 463-4 from L. xiangfangensis 3.1.1T. Based upon the data of polyphasic characterization obtained in the present study, a novel species, Lactiplantibacillus paraxiangfangensis sp. nov., is proposed and the type strain is 231-9T (=JCM 36258T=CCTCC AB 2023133T).

Leuconostoc mesenteroides and Liquorilactobacillus mali strains, isolated from Algerian food products, are producers of the postbiotic compounds dextran, oligosaccharides and mannitol

Six lactic acid bacteria (LAB) isolated from Algerian sheep's milk, traditional butter, date palm sap and barley, which produce dextran, mannitol, oligosaccharides and vitamin B2 have been characterized. They were identified as Leuconostoc mesenteroides (A4X, Z36P, B12 and O9) and Liquorilactobacillus mali (BR201 and FR123). Their exopolysaccharides synthesized from sucrose by dextransucrase (Dsr) were characterized as dextrans with (1,6)-D-glucopyranose units in the main backbone and branched at positions O-4, O-2 and/or O-3, with D-glucopyranose units in the side chain. A4X was the best dextran producer (4.5 g/L), while the other strains synthesized 2.1-2.7 g/L. Zymograms revealed that L. mali strains have a single Dsr with a molecular weight (Mw) of ~ 145 kDa, while the Lc. mesenteroides possess one or two enzymes with 170-211 kDa Mw. As far as we know, this is the first detection of L. mali Dsr. Analysis of metabolic fluxes from sucrose revealed that the six LAB produced mannitol (~ 12 g/L). The co-addition of maltose-sucrose resulted in the production of panose (up to 37.53 mM), an oligosaccharide known for its prebiotic effect. A4X, Z36P and B12 showed dextranase hydrolytic enzymatic activity and were able to produce another trisaccharide, maltotriose, which is the first instance of a dextranase activity encoded by Lc. mesenteroides strains. Furthermore, B12 and O9 grew in the absence of riboflavin (vitamin B2) and synthesized this vitamin, in a defined medium at the level of ~ 220 μg/L. Therefore, these LAB, especially Lc. mesenteroides B12, are good candidates for the development of new fermented food biofortified with functional compounds.

In Vitro Hypoglycemic Activities of Lactobacilli and Bifidobacterium Strains from Healthy Children's Sources and Their Effect on Stimulating GLP-1 Secretion in STC-1 Cells

A long-term use of chemical drugs cannot cure type II diabetes mellitus (T2DM) and their numerous toxic side effects can be harmful to human health. In recent years, probiotics have emerged as a natural resource to replace chemical drugs in alleviating many human ailments. Healthy children's intestines have a lot of colonized Lactobacilli and Bifidobacterium, and these beneficial bacteria can help promote overall health. The objective of this study was to isolate potential antidiabetic probiotic strains from healthy children and evaluate their application prospects. Firstly, Lactobacillus and Bifidobacterium strains were isolated from healthy children's feces and identified by the pheS or clpC genes with their respective 16S rRNA genes. Then, hydrophobicity, artificial gastrointestinal fluid tolerance, α-Glucosidase and Dipeptidyl peptidase IV (DPP-IV) inhibitory activities of isolated strains were determined, and antioxidant activities and promoting secretion of GLP-1 in STC-1 cells of candidate strains were tested. Results showed that 6 strains of Lactobacillus and Bifidobacterium were obtained from the feces of healthy children aged 3 years, respectively, including Lacticaseibacillus paracasei L-21 and L-25, Levilactobacillus brevis L-16, Lentilactobacillus buchneri L-9, Lactiplantibacillus plantarum L-8 and L-3, Bifidobacterium bifidum 11-1 and B-84, Bifidobacterium longum subsp. longum 6-1, 6-2, B42 and B53. The hydrophobicity and auto-aggregation levels of all these strains were higher than 30% and 50%, respectively, and the decrease in the number of colonies of all strains in the artificial gastrointestinal fluid was less than 2 log CFU/mL. Strains L-3, L-8, L-9, L-21, 6-1, 11-1, B53 and B84 were selected based on their high α-glucosidase inhibitory activity and DPP-IV inhibitory activity, and results of the antioxidant capacity assay showed that the remaining strains all had intense comprehensive antioxidant activity. Additionally, Lacticaseibacillus paracasei L-21 and Bifidobacterium longum subsp. longum B-53 had the most substantial prompting effect on GLP-1 secretion in the STC-1 cell line. These results indicated that Lacticaseibacillus paracasei L-21 and Bifidobacterium longum subsp. longum B-53 could be used as a potential antidiabetic strain; thus, its application as a food supplement and drug ingredient could be recommended after in vivo mitigation of type II diabetes test.

Lactobacillus juensis sp. nov. and Lactobacillus rizhaonensis sp. nov., isolated from the gut of honeybee (Apis mellifera)

Four lactic acid bacteria, designated F690T, F697, F790T and F769-2, were isolated from the gut of honeybee (Apis mellifera). Results of 16S rRNA gene sequence analysis indicated that strains F690T and F697 were phylogenetically related to the type strains of Lactobacillus kimbladii, Lactobacillus laiwuensis, Lactobacillus kullabergensis and Lactobacillus huangpiensis, having 99.1-99.6 % 16S rRNA gene sequence similarities; and that strains F790T and F769-2 were most closely related to the type strain of Lactobacillus melliventris, having 99.2-99.3 % 16S rRNA gene sequence similarities. The phylogenies based on concatenated pheS, rpoA, gyrB, hsp60, recA, rpoB and tuf sequences and based on whole genome sequences were identical to that based on 16S rRNA gene sequences. Strains F690T and F697 exhibited the highest average nucleotide identity (ANI; 92.1-93.2 %), digital DNA-DNA hybridization (dDDH; 50-50.1 %) and average amino acid identity (AAI; 94.9-95.1 %) values with L. kimbladii Hma2NT. Strains F790T and F769-2 had the highest ANI (93.1-94 %), dDDH (54.4 %) and AAI (94.4-94.7 %) values with L. melliventris Hma8NT. Based upon the data obtained in the present study, two novel species, Lactobacillus juensis sp. nov. and Lactobacillus rizhaonensis sp. nov., are proposed and the type strains are F690T (=JCM 36259T=CCTCC AB 2023131T) and F790T (=JCM 36260T=CCTCC AB 2023132T), respectively.

Proposal to Reclassify Companilactobacillus futsaii subsp. chongqingensis as a Later Heterotypic Synonym of Companilactobacillus futsaii subsp. futsaii

Previous studies have shown that Lactobacillus futsaii (now Companilactobacillus futsaii) can be subdivided at the subspecies level. The main purpose of this study is to explore whether this is correct by using a polyphasic taxonomic approach. Lactobacillus futsaii subsp. chongqingii was proposed and effectively published in 2019. The names L. futsaii subsp. chongqingensis corrig. and Lactobacillus futsaii subsp. futsaii were not validated until March 2023. However, in the reclassification of the genus Lactobacillus by Zheng et al. in April 2020, L. futsaii was transferred to Companilactobacillus as Companilactobacillus futsaii. So Lactobacillus futsaii subsp. chongqingensis and Lactobacillus futsaii subsp. futsaii should be transferred to Companilactobacillus futsaii now. In the present study, the relationship between L. futsaii subsp. chongqingensis and L. futsaii subsp. futsaii was re-evaluated. The type strains of L. futsaii subsp. chongqingensis and L. futsaii subsp. futsaii shared identical pheS and rpoA sequences, high dDDH value, similar phenotypic characteristics and fatty acid compositions, indicating that they belonged to the same subspecies. Here, we propose to reclassify Lactobacillus futsaii subsp. chongqingensis and Lactobacillus futsaii subsp. futsaii as Companilactobacillus futsaii subsp. chongqingensis comb. nov. and Companilactobacillus futsaii subsp. futsaii comb. nov., respectively, and Companilactobacillus futsaii subsp. chongqingensis as a later heterotypic synonym of Companilactobacillus futsaii subsp. futsaii.

Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina

We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.

Lacticaseibacillus huelsenbergensis sp. nov., isolated from grass silage and corn silage

Two rod-shaped, facultative anaerobic, Gram-stain-positive lactic acid bacteria were isolated from corn silage and grass silage. They were characterized using a polyphasic approach and designated as HO 1656T and HO 0673. Analysis of 16S rRNA gene sequence of both strains indicated that they belong to the Lacticaseibacillus group. The most closely related species, Lacticaseibacillus casei DSM 20011T and Lacticaseibacillus zeae DSM 20178T, have digital DNA–DNA hybridization (dDDH) values of 63.9 and 53.4%, respectively, with the novel strains. In contrast, the dDDH value between strains HO 1656T and HO 0673 is 99.3 %, clearly showing that these two isolated strains belong to the same species. According to analysis of the housekeeping genes (dnaK, mutL and pheS), both strains form a distinct cluster within the Lacticaseibacillus group. Strains HO 0673 and HO 1656T could produce acid from d-arabinose, adonitol, ribose, rhamnose, dulcitol, sorbitol, turanose, l-fucose and l-arabitol, unlike their nearest phylogenetic neighbour L. casei DSM 20011T. The major cellular fatty acids of both strains are C16 : 0 and C18 : 1 ω9c. The G+C content of the genomic DNA of both strains is 48.0 mol%. Thus, strains HO 1656T and HO 0673 represent a novel species based on their chemotaxonomic, phenotypic and phylogenetic characteristics. The name Lacticaseibacillus huelsenbergensis sp. nov. is proposed with the type strain HO 1656T (=DSM 115425T=NCIMB 15466T).

Resolution of inter/intraspecies variation in Weissella group requires multigene analysis and functional characterization

Weissella confusa and Weissella cibaria strains isolated from the human- gut are considered as potential probiotics, but remain under-explored owing to their ambiguous taxonomic assignment. The present study assesses the taxonomic resolution of 11 strains belonging to W. confusa and W. cibaria species and highlights the inter- and intraspecies variations using an array of phenetic and molecular methods. Remarkable genomic variability among the strains was observed by phylogenetic analysis using concatenated housekeeping genes (pheS, gyrB, and dnaA) along with 16S rRNA gene sequence, suggesting intraspecies variations; which is also supported by the phenetic data. Analysis showed that 16S rRNA gene sequence alone could not resolve the variation, and among the tested marker genes, signals from pheS gene provide better taxonomic resolution. The biochemical and antibiotic susceptibility tests also showed considerable variations among the isolates. Additionally, 'quick' identification using mass spectroscopy-based matrix-assisted laser desorption/ionization-time of flight mass spectra was accurate up to genus only, and not species level, for the Weissella group. The study highlights need for inclusion of functional, phenetic, and multigene phylogenetic analysis in addition to 16S rRNA gene-based identification for the Weissella group, to provide better resolution in taxonomic assignments, which is often a prerequisite for the selection of potential strains with biotechnological applications.

Levilactobacillus humaensis sp. nov. and Lapidilactobacillus luobeiensis sp. nov., isolated from traditional Chinese pickle

Two Gram-stain-positive bacterial strains, designated 213-9(3)^T and 30-1(2)^T, were isolated from traditional Chinese pickle, and were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain 213-9(3)^T was most closely related to Levilactobacillus paucivorans TMW 1.1424^T, Levilactobacillus huananensis 151-2B^T and Levilactobacillus lindianensis 220-4^T, having 99.7-99.9 % 16S rRNA gene sequence similarities; strain 30-1(2)^T was most closely related to Lapidilactobacillus achengensis 247-4^T, with 99.4 % 16S rRNA gene sequence similarity. Strain 213-9(3)^T shared the highest pheS (93.9 %), rpoA (99.3 %) and concatenated pheS and rpoA (97.5 %) sequence similarities to L. paucivorans TMW 1.1424^T. Strain 30-1(2)^T had the highest pheS (82.4 %), rpoA (95.5 %) and concatenated pheS and rpoA (91.2 %) sequence similarities to L. achengensis 247-4^T. The phylogenetic relationships based on concatenated pheS and rpoA sequences and whole genome sequences were identical to those based on 16S rRNA gene sequences. Strain 213-9(3)^T exhibited the highest average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values (92.7 and 48.8 %, respectively) to L. paucivorans DSM 22467^T. Strain 30-1(2)^T had the highest ANI (84.4 %) and dDDH (32.8 %) values with L. achengensis 247-4^T. Acid production from d-galactose, d-glucose, d-mannose, N-acetyl-β-glucosaminidase, arbutin, salicin, cellobiose, maltose, gentiobiose, d-tagatose and gluconate, hydrolysis of aesculin, and activity of cystine arylamidase could differentiate strain 213-9(3)^T from L. paucivorans DSM 22467^T. Acid production from l-arabinose, d-ribose, d-xylose and d-galactose, and activity of alkaline phosphatase, esterase (C4), α-mannosidase and α-fucosidase could differentiate strain 30-1(2)^T from L. achengensis 247-4^T. Based upon the data obtained in the present study, two novel species, Levilactobacillus humaensis sp. nov. and Lapidilactobacillus luobeiensis sp. nov., are proposed and the type strains are 213-9(3)^T (=CCM 9241^T=CCTCC AB 2022115^T=JCM 35554^T) and 30-1(2)^T (=CCM 9240^T=CCTCC AB 2022114^T=JCM 35553^T), respectively.

Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump

A lactic acid bacteria isolated from pig faeces was characterized using a polyphasic approach. Cells of the strain were Gram-stain-positive, rod-shaped and facultative anaerobic. Phylogenetic analysis of 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus; however, the similarity to other homologues within the genus was <98 %. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus absianus and Lacticaseibacillus daqingensis. The main fatty acids of the strain is the C_18 : 1ω9c and C_16 : 0. The G+C content of the genomic DNA was 62.8 mol %. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lac21^T (=KCTC 21185=JCM 34953) represents a novel species. The name Lacticaseibacillus kribbianus sp. nov. is proposed.

A novel species of lactic acid bacteria, Ligilactobacillus pabuli sp. nov., isolated from alfalfa silage

In this study, we isolated a novel strain of lactic acid bacteria, AF129T, from alfalfa silage prepared locally in Morioka, Iwate, Japan. Polyphasic taxonomy was used to characterize the bacterial strain. The bacterium was rod-shaped, Gram-stain-positive, non-spore-forming and catalase-negative. The strain grew at various temperatures (15–40°C) and pH levels (4.0–8.0). The optimum growth conditions were a temperature of 30°C and a pH of 6.0. AF129T exhibited growth at salt (NaCl) concentrations of up to 6.5 % (w/v). The G+C content of the strain’s genomic DNA was 41.5 %. The major fatty acids were C16 : 0, C18 : 1ω9c, C19 : 0cyclo ω8c and summed feature 8. 16S rRNA gene sequencing revealed that AF129T represents a member of the genus Ligilactobacillus and it has higher sequence similarities with Ligilactobacillus pobuzihii (98.4 %), Ligilactobacillus acidipiscis (97.5 %) and Ligilactobacillus salitolerans (97.4 %). The digital DNA–DNA hybridization values for AF129T and phylogenetically related species of the genus Ligilactobacillus ranged from 19.8% to 24.1%. The average nucleotide identity of the strain with its closely related taxa was lower than the threshold (95 %–96 %) used for species differentiation. In the light of the above-mentioned physiological, genotypic, chemotaxonomic and phylogenetic evidence, we confirm that AF129T represents a member of the genus Ligilactobacillus and constitutes a novel species; we propose the name Ligilactobacillus pabuli sp. nov. for this species. The type strain is AF129T =MAFF 518002T =JCM 34518T=BCRC 81335T.

PMA-qPCR method for the selective quantitation of viable lactic acid bacteria in fermented milk

The number of viable lactic acid bacteria (LAB) is a key indicator of the quality of fermented milk. Currently, the combination of propidium monoazide (PMA) and qPCR has been applied in the quantification of viable bacteria in various matrices. In this research, the PMA-qPCR method was used to detect the number of viable bacteria of each LAB species in fermented milk. By analyzing pheS gene and 16S rRNA gene sequence similarities in five species of LAB, namely Lactobacillus delbrueckii subsp. bulgaricus, Lactiplantibacillus plantarum, Streptococcus thermophilus, Lactobacillus helveticus, and Lactococcus lactis subsp. lactis, the pheS gene resolved species identities better and was thus selected to design specific primers and probes. The pheS gene was cloned into the pUC19 vector and used to construct a standard curve for absolute quantification. Standard curves for quantification were constructed for each LAB species for serial dilutions between 1011 and 106 CFU/mL, with R2 &gt; 0.99. The number of viable bacteria in the fermented milk detected by PMA-qPCR was significantly lower than that of qPCR (P &lt; 0.05), indicating that PMA inhibited the amplification of DNA from dead cells. This was corroborated by the results from bacterial staining and plate count experiments. The proposed PMA-qPCR method provided rapid qualitative and quantitative determination of the number of viable bacteria for each LAB species in fermented milk within 3 h.

Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways

(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.

Apilactobacillus zhangqiuensis sp. nov. and Apilactobacillus xinyiensis sp. nov., isolated from the gut of honeybee (Apis mellifera)

Three Gram-stain-positive bacterial strains (designated F502-1T, F575-4T and F582-1) were isolated from the gut of honeybee (Apis mellifera). These strains were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain F502-1T was phylogenetically related to the type strains of Apilactobacillus kunkeei , Apilactobacillus nanyangensis and Apilactobacillus apinorum , having 98.7–99.9 % 16S rRNA gene sequence similarities, 84.6–92.5 % pheS sequence similarities and 95.2–99.0 % rpoA sequence similarities, and that strains F575-4T and F582-1 were closely related to the type strain of Apilactobacillus ozensis , having 99.7 and 99.4 % 16S rRNA gene sequence similarities, respectively. Strains F575-4T and F582-1 had less than 88.7 % pheS and 96.4 % rpoA sequence similarities to strain F502-1T and type strains of all Apilactobacillus species. The average nucleotide identity and digital DNA–DNA hybridization values between strains F502-1T, F575-4T, F582-1 and type strains of all Apilactobacillus species were less than 91.3 and 43.5 %, respectively, confirming that they represent two novel species within the genus Apilactobacillus . Based upon the data obtained in the present study, two novel species, Apilactobacillus zhangqiuensis sp. nov. and Apilactobacillus xinyiensis sp. nov., are proposed and the type strains are F502-1T (=JCM 34500T=CCTCC AB 2021026T) and F575-4T (=JCM 34501T=CCTCC AB 2021028T), respectively.

Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product

Two lactic acid bacterial strains (IMAU80584T and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to Lentilactobacillus rapi . However, phylogenetic tree analyses of two housekeeping genes, rpoA (encoding RNA polymerase alpha subunit) and pheS (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from L. rapi DSM 19907T, forming an infra-specific subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between IMAU80584T and L. rapi DSM 19907T were 93.1 and 52.8 %, respectively. Strains IMAU80584T and IMAU92037 are distinguished from L. rapi DSM 19907T because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584T was 42.3 mol%. The major cellular fatty acids were C16 : 0, C18 : 1  ω9t and summed feature 5 (C18 : 0 ante and/or C18 : 2  ω6c and/or C18 : 2  ω9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584T and IMAU92037 could be considered as a novel subspecies in the species L. rapi with the proposed name Lentilactobacillus rapi subsp. dabitei subsp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).

Mechanism of high D-aspartate production in the lactic acid bacterium Latilactobacillus sp. strain WDN19

D-Aspartate (D-Asp) is a useful compound for a semisynthetic antibiotic and has potentially beneficial effects on humans. Several lactic acid bacteria (LAB) species produce D-Asp as a component of cell wall peptidoglycan. We previously isolated a LAB strain (named strain WDN19) that can extracellularly produce a large amount of D-Asp. Here, we show the factors that contribute to high D-Asp production ability. Strain WDN19 was most closely related to Latilactobacillus curvatus. The D-Asp production ability of strain WDN19 in a rich medium was 13.7-fold higher than that of L. curvatus DSM 20019. A major part of D-Asp was synthesized from L-Asp contained in the medium by aspartate racemase (RacD). During their cultivation, the RacD activity in strain WDN19 was higher than in strain DSM 20019, especially much higher in the early exponential growth phase because of the higher racD transcription and the higher activity of RacD itself of strain WDN19. In a synthetic medium, the extracellular production of D,L-Asp was observed in strain WDN19 but not in strain DSM 20019. The addition of L-asparagine (L-Asn) to the medium increased and gave D,L-Asp production in strains WDN19 and DSM 20019, respectively, suggesting L-Asp synthesis by L-asparaginase (AsnA). The L-Asn uptake ability of the strains was similar, but the AsnA activity in the middle exponential and early stationary growth phases and intracellular D,L-Asp was much higher in strain WDN19. In their genome sequences, only an aspartate aminotransferase gene was found among L-Asp-metabolizing enzymes, except for RacD, but was disrupted in strain WDN19 by transposon insertion. These observations indicated that the high D-Asp production ability of strain WDN19 was mainly based on high RacD and AnsA activities and L-Asp supply. KEY POINTS: • Strain WDN19 was suggested to be a strain of Latilactobacillus curvatus. • Extracellular high d-Asp production ability was not a common feature of L. curvatus. • High d-Asp production was due to high RacD and AnsA activities and l-Asp supply.

Companilactobacillus salsicarnum Zheng et al. 2020 is a later heterotypic synonym of Companilactobacillus mishanensis (Wei and Gu 2019) Zheng et al. 2020

Lactobacillus mishanensis was isolated from Chinese traditional pickle, and validly published in October 2019. Lactobacillus salsicarnum was isolated from salami products in Germany, and effectively described in November 2019. In the reclassification of the genus Lactobacillus by Zheng et al. in April 2020, L. mishanensis was transferred to Companilactobacillus as Companilactobacillus mishanensis comb. nov., and Companilactobacillus salsicarnum was proposed as a novel species. In the present study, the relationship between C. mishanensis and C. salsicarnum was evaluated. The type strains of C. mishanensis and C. salsicarnum shared 100 % 16S rRNA gene sequence similarity, 100 % pheS sequence similarity, 99.9 % rpoA sequence similarity, a 99.9 % average nucleotide identity value and a 99.5 % digital DNA–DNA hybridization value, indicating that they represent the same species. On the basis of the results presented here, we propose C. salsicarnum [Zheng et al. 2020] as a later heterotypic synonym of C. mishanensis (Wei and Gu 2019) [Zheng et al. 2020].

Lactobacillus huangpiensis sp. nov. and Lactobacillus laiwuensis sp. nov., isolated from the gut of honeybee (Apis mellifera)

Four Gram-stain-positive bacterial strains were isolated from the gut of honeybee (Apis mellifera) in China. These strains were characterized using a polyphasic taxonomic approach. The data demonstrated that three of the four strains represented two novel species of the genus Lactobacillus , strains F306-1T and F551-2T were designated as the type strains. Results of 16S rRNA gene sequence analysis indicated that strains F306-1T, F447 and F551-2T were phylogenetically related to the type strains of Lactobacillus kimbladii and Lactobacillus kullabergensis , having 99.1–99.7 % 16S rRNA gene sequence (about 1400 bp) similarities. The phylogenetic tree based on concatenated pheS, rpoA, gyrB, hsp60, recA, rpoB and tuf sequences (4114 bp) and the phylogenomic tree based on whole genome sequences indicated that strains F306-1T and F447 were most closely related to L. kullabergensis Biut2NT, and strain F551-2T was most closely related to L. kimbladii Hma2NT. Strains F306-1T and F447 shared 99.9 % average nucleotide identity (ANI), 99.7 % digital DNA–DNA hybridization (dDDH) and 99.9 % average amino acid identity (AAI) values, indicating that they belong to the same species. Strain F306-1T exhibited the highest ANI (94.4 %), dDDH (56.7 %) and AAI (94.7 %) values to L. kullabergensis Biut2NT. Strain F551-2T had the highest ANI (94.0 %), dDDH (54.3 %) and AAI (95.8 %) values with L. kimbladii Hma2NT. Acid production from amygdalin, maltose, starch, gentiobiose and turanose, activity of esterase (C4) and α-glucosidase, growth with 3 % NaCl at 37 °C under strict anaerobic condition (on mMRS agar plates), and growth with 1–6% NaCl at 37 °C under aerobic condition (on mMRS agar plates supplemented with 0.05 % cysteine or with 1 % cysteine and 2 % fructose) could differentiate strains F306-1T and F447 from L. kullabergensis DSM 26262T. Acid production from d-glucose, arbutin and gentiobiose, growth with 3 % NaCl at 37 °C under strict anaerobic condition (on mMRS agar plates), and growth at 45 °C under strict anaerobic condition (on mMRS agar plates) could differentiate strain F551-2T from L. kimbladii DSM 26263T. Based upon the data obtained in the present study, two novel species, Lactobacillus huangpiensis sp. nov. and Lactobacillus laiwuensis sp. nov., are proposed and the type strains are F306-1T (=LMG 32144T=JCM 34361T=CCTCC AB 2020300T) and F551-2T (=JCM 34502T=CCTCC AB 2021027T), respectively.

Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Thirteen Gram-positive, catalase-positive, rod-shaped single colonies were obtained after culturing a strawberry leaf on de Man–Rogosa–Sharpe agar. Based on 16S rRNA gene and rpoA gene sequence similarities, ranging between 99.0–100% and 96.5–100%, respectively, the 13 isolates were found to be closely related to each other. Two of the independent isolates, AMBP162^T and AMBP252, were whole-genome sequenced, and showed to be undistinguishable with an average nucleotide identity (ANI) value of 100 %. Compared to the reference genomes for all species in the family Lactobacillaceae, the AMBP162^T genome was most similar to the reference strain of Latilactobacillus curvatus with ANI of only 89.5 %, indicating they were a different species. Based on genotypic and phenotypic data, a novel Latilactobacillus species, Latilactobacillus fragifolii sp. nov., with the type strain AMBP162^T (=LMG 32285^T=CECT 30357^T) is proposed.

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).

Isolation, identification, and impact on intestinal barrier integrity of Lactiplantibacillus plantarum from fresh tea leaves (Camellia sinensis)

Lactic acid bacteria (LAB) are safe microorganisms that have been used in the processing of fermented food for centuries. The aim of this study was to isolate Lactobacillus from fresh tea leaves and examine the impact of an isolated strain on intestinal barrier integrity. First, the presence of Lactobacillus strains was investigated in fresh tea leaves from Kagoshima, Japan. Strains were isolated by growing on De Man, Rogosa and Sharpe (MRS) agar medium containing sodium carbonate, followed by the identification of one strain by polymerase chain reaction (PCR) and pheS sequence analysis, with the strain identified as Lactiplantibacillus plantarum and named L. plantarum LOC1. Second, the impact of strain LOC1 in its heat-inactivated form on intestinal barrier integrity was investigated. Strain LOC1, but not L. plantarum ATCC 14917^T or L. plantarum ATCC 8014, significantly suppressed dextran sulfate sodium (DSS)-induced decreases in transepithelial electrical resistance values of Caco-2:HT29-MTX 100:0 and 90:10 co-cultures. Moreover, in Caco-2:HT29-MTX co-cultures (90:10 and 75:25), levels of occludin mRNA were significantly increased by strain LOC1 compared with untreated co-cultures, and strain LOC1 had higher mRNA levels of MUC2 and MUC4 mucins than L. plantarum ATCC 14917^T and L. plantarum YT9. These results indicate that L. plantarum LOC1 may be used as a safe probiotic with beneficial effects on the intestinal barrier, suggesting that fresh tea leaves could be utilized as a safe source for isolating probiotics.

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.

Health-Promoting Properties of Lacticaseibacillus paracasei: A Focus on Kefir Isolates and Exopolysaccharide-Producing Strains

Among artisanal fermented beverages, kefir (fermented milk drink) and water kefir (fermented nondairy beverage) are of special interest because their grains can be considered natural reservoirs of safe and potentially probiotic strains. In the last years, several reports on Lacticaseibacillus paracasei (formerly Lactobacillus paracasei) isolated from both artisanal fermented beverages were published focusing on their health-promoting properties. Although this is not the predominant species in kefir or water kefir, it may contribute to the health benefits associated to the consumption of the fermented beverage. Since the classification of L. paracasei has been a difficult task, the selection of an adequate method for identification, which is essential to avoid mislabeling in products, publications, and some publicly available DNA sequences, is discussed in the present work. The last findings in health promoting properties of L. paracasei and the bioactive compounds are described and compared to strains isolated from kefir, providing a special focus on exopolysaccharides as effector molecules. The knowledge of the state of the art of Lacticaseibacillus paracasei from kefir and water kefir can help to understand the contribution of these microorganisms to the health benefits of artisanal beverages as well as to discover new probiotic strains for applications in food industry.

Proposal of Lactococcus garvieae subsp. bovis Varsha and Nampoothiri 2016 as a later heterotypic synonym of Lactococcus formosensis Chen et al. 2014 and Lactococcus formosensis subsp. bovis comb. nov

Currently, Lactococcus garvieae contains two subspecies: L. garvieae subsp. bovis and L. garvieae subsp. garvieae. In a study by Varsha and Nampoothiri, high pheS (99.7 %) and rpoA (99.6 %) sequence similarities indicated that L. garvieae subsp. bovis and Lactococcus formosensis probably have a close taxonomic relationship; low pheS (92.2 %) and rpoA (97.8 %) sequence similarities and relatively low DNA-DNA hybridization value (75.8 %) indicated that L. garvieae subsp. bovis and L. garvieae subsp. garvieae probably represent two different species. In the present study, the taxonomic relationships between L. garvieae subsp. bovis, L. garvieae subsp. garvieae and L. formosensis were re-examined based on sequence analyses of 16S rRNA, pheS, recA, rpoA and rpoB genes, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) values, average amino acid identity (AAI), fatty acid methyl ester analysis and phenotypic characterization. L. garvieae subsp. bovis LMG 30663^T exhibited 97.3 % ANI, 78.3 % dDDH and 96.4 % AAI values to L. formosensis NBRC 109475^T, higher than the threshold for species demarcation (95-96, 70 and 95-96 %, respectively), indicating that L. garvieae subsp. bovis LMG 30663^T and L. formosensis NBRC 109475^T belong to the same species. L. garvieae subsp. bovis LMG 30663^T had 91.2 % ANI, 43.3 % dDDH and 92.9-93.0% AAI values with the type strain of L. garvieae subsp. garvieae, indicating that they represent two different species. Because L. formosensis has been proposed and validated before L. garvieae subsp. bovis, L. garvieae subsp. bovis is transferred to L. formosensis as L. formosensis subsp. bovis comb. nov. The type strain of L. formosensis subsp. bovis is BSN307^T (=DSM 100577^T=MCC 2824^T=KCTC 21083^T=LMG 30663^T). The type strain of L. formosensis subsp. formosensis is 516^T (=NBRC 109475^T=BCRC 80576^T).

Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., isolated from traditional Chinese pickle and the gut of honeybee (Apis mellifera)

Thirteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and the gut of honeybee (Apis mellifera). These strains were characterized using a polyphasic taxonomic approach. The data demonstrated that 12 of the 13 strains represented eight novel species belonging to the genera Apilactobacillus, Secundilactobacillus, Levilactobacillus and Lacticaseibacillus; strains HN36-1^T, 887-11^T, F79-211-2^T, 866-3^T, 6-5(1)^T, 13B17^T, 117-1^T and ZW152^T were designated as the type strains. Based upon the data of polyphasic characterization obtained in the present study, eight novel species, Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., are proposed and the type strains are HN36-1^T (=JCM 33867^T=CCTCC AB 2019385^T), 887-11^T (=NCIMB 15201^T=CCM 8950^T=JCM 33864^T=CCTCC AB 2018396^T), F79-211-2^T (=NCIMB 15254^T=JCM 33866^T=CCTCC AB 2019384^T), 866-3^T (=JCM 33863^T=CCTCC AB 2019383^T), 6-5(1)^T (=NCIMB 15229^T=CCM 8977^T=JCM 33564^T=CCTCC AB 2019168^T), 13B17^T (=NCIMB 15230^T=CCM 8979^T=JCM 33565^T=CCTCC AB 2019167^T), 117-1^T (=NCIMB 15232^T=CCM 8980^T=JCM 33567^T) and ZW152^T (=JCM 34363^T=CCTCC AB 2020299^T=LMG 32143^T=CCM 9110^T), respectively.

Probiotic Lactobacilli in Fermented Dairy Products: Selective Detection, Enumeration and Identification Scheme

A selection of 36 commercial probiotic fermented dairy products from UK and Europe markets were evaluated for the numbers, types, and viability of Lactobacillus strains against the stated information on their packages. A comparative study was carried out on selectivity of MRS-Clindamycin, MRS-Sorbitol, and MRS-IM Maltose, to select the right medium for enumeration of probiotic Lactobacillus. Based on selectivity of medium for recovery of the targeted lactobacilli, and also simplicity of preparation, MRS-Clindamycin was chosen as the best medium for enumeration of probiotic Lactobacillus in fermented milks. The results of enumeration of lactobacilli showed that 22 out of a total 36 tested products contained more than 10⁶ colony-forming units/g at the end of their shelf life, which comply with the recommended minimum therapeutic level for probiotics. Rep-PCR using primer GTG-5 was applied for initial discrimination of isolated strains, and isolates, which presented different band profile, were placed in different groups. The isolated Lactobacillus spp. were identified mainly as Lactobacillus acidophilus, Lactobacillus casei, and Lactobacillus paracasei by analysis of partial sequences of the 16S ribosomal RNA and rpoA genes.

The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314^T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding

Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.

Lacticaseibacillus absianus sp. nov., isolated from the cecum of a mini-pig

A rod-shaped, facultative anaerobic, Gram-stain-positive bacteria, isolated from the cecum of a mini-pig, was designated as strain YH-lac23^T. Analysis of 16S rRNA gene sequences revealed that the strain was closely related to Lacticaseibacillus daqingensis JCM 33273^T (97.9 %), Lacticaseibacillus porcinae KCTC 21027^T (96.2 %) and Lacticaseibacillus manihotivorans KCTC 21010^T (95.7 %). Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster with L. daqingensis. The average nucleotide identity value for YH-lac23^T and its most closely related strain (L. daqingensis) is 80.7 %. The main fatty acids are C_18 : 1ω9c and C_16 : 0. The cell wall contains the peptidoglycan of meso-diaminopimelic acid. The G+C content of the genomic DNA is 59.8 mol%. In view of the chemotaxonomic, phenotypic and phylogenetic properties, YH-lac23^T (=KCTC 25006=JCM 33998) represents a novel taxon. The name Lacticaseibacillus absianus sp. nov. is proposed.

Decoding the Capability of Lactobacillus plantarum W1 Isolated from Soybean Whey in Producing an Exopolysaccharide

This study aims at producing exopolysaccharides (EPS) from a lactic acid bacterial strain. The soybean whey-isolated Lactobacillus plantarum W1 (EPS-W1), which belongs to genus Lactobacillus, is identified using the phenylalanyl-tRNA sequencing method. Of all the examined strains, R-49778 (as numbered by BCCM/LMG Bacteria Collection, Ghent University, Belgium) showed the highest capability of producing exopolysaccharides. Structural characterization revealed a novel exopolysaccharide consisting of repeating units of →6)-d-Glcp-(1→; →3)-d-Manp-(1→; →3)-d-Glcp-(1→ and a branch of →6)-d-Manp-(1→; →2)-d-Glcp-(1→. This discovery opens up avenues for the production of EPS for food industries, functional foods, and biomedical applications.

Optimization of culture conditions for gamma-aminobutyric acid production by newly identified Pediococcus pentosaceus MN12 isolated from 'mam nem', a fermented fish sauce

This study was aimed to identify and optimize the culture conditions for gamma-aminobutyric acid (GABA) production by a lactic acid bacterium strain isolated from mam nem, a fermented fish sauce. Among the six isolates obtained from mam nem, the MN12 had the most potent GABA-producing capability. The strain was then identified to be Pedioccocus pentosaceus by employing MALDI-TOF-MS and phenylalanyl-tRNA synthase sequencing methods. The initial cell density of 5.10⁶ CFU/mL, monosodium glutamate concentration of 60 mM, initial pH of 7, temperature of 45°C and cultivation time of 72 h were found to be the optimal culture conditions for highest production of GABA, reaching 27.9 ± 0.42 mM, by this strain. The cultivation conditions for GABA production by P. pentosaceus MN12 have been successfully optimized, providing a foundation for the development of fermented foods enriched with GABA.

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.

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

In the present study, the taxonomic positions of five strains (C, 17-2, LMG 10779^T, LMG 18969 and LMG 11483) of Leuconostoc pseudomesenteroides were re-evaluated by a polyphasic approach, including the analyses of 16S rRNA, pheS and rpoA gene sequences, cellular fatty acids, average nucleotide and amino acid identities (ANI and AAI), digital DNA-DNA hybridization (dDDH), and phenotypic features. Based on rpoA sequence analysis, the five strains and L. pseudomesenteroides LMG 11482^T were divided into two groups: strains C, LMG 10779^T and LMG 18969; strains 17-2, LMG 11483 and LMG 11482^T. Each of the two groups had almost identical rpoA sequences. The rpoA sequence similarity between strain LMG 10779^T and L. pseudomesenteroides LMG 11482^T was 95.6 %. Strains LMG 11483 and 17-2 had 98.1 and 97.2 % ANI values, 83.5 and 73.2 % dDDH values, and a 97.0 % AAI value with L. pseudomesenteroides LMG 11482^T, greater than the threshold for species demarcation, indicating that strains LMG 11483 and 17-2 belong to L. pseudomesenteroides. Strains LMG 18969 and C shared 97.1 and 98.2 % ANI values, 73.4 and 83.2 % dDDH values, and 96.9 and 96.6 % AAI values with strain LMG 10779^T, greater than the threshold for species demarcation, indicating that strains LMG 10779^T, LMG 18969 and C represent the same species. The ANI, dDDH and AAI values between strain LMG 10779^T and the type strains of phylogenetically related species were 75.2-92.5, 20.0-48.2 and 75.3-93.9 %, respectively, below the thresholds for species demarcation, indicating that strain LMG 10779^T represents a novel species within the genus Leuconostoc. On the basis of the results presented here, (i) strains 17-2 and LMG 11483 belong to L. pseudomesenteroides, and (ii) strains LMG 10779^T, LMG 18969 and C are considered to represent a novel species within the genus Leuconostoc, for which the name Leuconostoc falkenbergense sp. nov. is proposed with the type strain LMG 10779^T (=CCUG 27119^T).

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.

Genotypic and phenotypic diversity among Lactobacillus plantarum and Lactobacillus pentosus isolated from industrial scale cucumber fermentations

The Lactobacillus plantarum and Lactobacillus pentosus genotypes existing in industrial-scale cucumber fermentations were defined using rep-PCR-(GTG)5. The ability of each genotype to ferment cucumbers under various conditions was evaluated. Rep-PCR-(GTG)5 was the technique capable of illustrating the most intraspecies discrimination compared to the sequencing of housekeeping genes (recA, dnaK, pheS and rpoA), MLST and RAPD with primers LP1, OPL5, M14 and COC. Ten genotypic clusters were defined for the 199 L. pentosus tested and three for the 17 L. plantarum clones. The ability of the 216 clones genotyped and 37 additional cucumber fermentation isolates, of the same species, to rapidly decrease the pH of cucumber juice medium under various combinations of sodium chloride (0 or 6%), initial pH (4.0 or 5.2) and temperatures (15 or 30 °C) was determined using a fractional factorial screening design. A reduced fermentation ability was observed for the L. plantarum strains as compared to L. pentosus, except for clone 3.2.8, which had a ropy phenotype and aligned to genotypic cluster A. L. pentosus strains belonging to three genotypic clusters (B, D and J) were more efficient in cucumber juice fermentation as compared to most L. plantarum strains. This research identified three genetically diverse L. pentosus strains and one L. plantarum as candidates for starter cultures for commercial cucumber fermentations.

Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli

The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.

Co-Fermentation of Food Waste and Municipal Sludge from the Saudi Arabian Environment to Improve Lactic Acid Production by Lactobacillus rhamnosus AW3 Isolated from Date Processing Waste

Food waste and municipal sludge were used as the substrates for the biosynthesis of lactic acid in a batch fermentor. The probiotic bacterial strain Lactobacillus rhamnosus AW3 isolated from date processing waste was used to produce lactic acid in a batch fermentor. Co-fermentation enhanced the biosynthesis of lactic acid and decreased substrate inhibition more than mono-substrate fermentation. A maximum yield of 28.4 ± 0.87 g/L of lactic acid was obtained through co-fermentation of food waste and municipal sludge at an optimized ratio of 2:0.5. Lactic acid production was improved by the supplementation of fructose, peptone, and sodium dihydrogen phosphate at pH 5.5 after 48 h fermentation. This production was approximately three-fold higher than that during mono-fermentation of food waste. The tested bacterial strains were obtained from the Microbial Type Culture Collection (MTCC). Lactic acid showed potent antimicrobial activity against pathogenic organisms, such as Bacillus subtilis MTCC 5981 (14 mm), Staphylococcus aureus MTCC 737 (20 mm), Pseudomonas aeruginosa MTCC 424 (24 mm), Enterobacter aerogenes MTCC111 (19 mm), Escherichia coli MTCC 443 (18 mm), Penicillium chrysogenum MTCC 5108 (19 mm), and Aspergillus niger MTCC 282 (19 mm). The antimicrobial properties of lactic acid have significant potential to inhibit the growth of pathogenic bacteria and fungi and improve probiotic properties. The lactic acid extracted from L. rhamnosus AW3 decreased the pH value of soil (p < 0.01) and increased the availability of soil phosphorus (p < 0.01). These findings demonstrate the bioconversion of food waste and municipal sludge into lactic acid, and the recycling of food wastes in urban areas to enhance soil nutrients.

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species

The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.

Complete Genome and Comparative Genome Analysis of Lactobacillus reuteri YSJL-12, a Potential Probiotics Strain Isolated From Healthy Sow Fresh Feces

Lactobacillus reuteri YSJL-12 was isolated from healthy sow fresh feces and used as probiotics additives previously. To investigate the genetic basis on probiotic potential and identify the genes in the strain, the complete genome of YSJL-12 was sequenced. Then comparative genome analysis on 9 strains of Lactobacillus reuteri was performed. The genome of YSJL-12 consisted of a circular 2,084,748 bp chromosome and 2 circular plasmids (51,906 and 15,134 bp). From among the 2065 protein-coding sequences (CDSs), the genes resistant to the environmental stress were identified. The function of COG (Clusters of Orthologous Group) protein genes was predicted, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were analyzed. The comparative genome analysis indicated that the pan-genome contained a core genome of 1257 orthologous gene clusters, an accessory genome of 1064 orthologous gene clusters, and 1148 strain-specific genes, and the antibacterial mechanism among Lactobacillus reuteri strains might be different. The phylogenetic analysis and genomic collinearity revealed that the phylogenetic relationship among 9 strains of Lactobacillus reuteri was connected with host species and showed host specificity. The research could help us to better predict genes function and understand genetic basis on adapting to host gut in Lactobacillus reuteri YSJL-12.

Novel Exopolysaccharide Produced from Fermented Bamboo Shoot-Isolated Lactobacillus Fermentum

This study aimed at providing a route towards the production of a novel exopolysaccharide (EPS) from fermented bamboo shoot-isolated Lactobacillus fermentum. A lactic acid bacteria strain, with high EPS production ability, was isolated from fermented bamboo shoots. This strain, R-49757, was identified in the BCCM/LMG Bacteria Collection, Ghent University, Belgium by the phenylalanyl-tRNA synthetase gene sequencing method, and it was named Lb. fermentum MC3. The molecular mass of the EPS measured via gel permeation chromatography was found to be 9.85 × 10⁴ Da. Moreover, the monosaccharide composition in the EPS was analyzed by gas chromatography–mass spectrometry. Consequently, the EPS was discovered to be a heteropolysaccharide with the appearance of two main sugars—D-glucose and D-mannose—in the backbone. The results of one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance spectroscopy analyses prove the repeating unit of this polysaccharide to be [→6)-β-D-Glcp-(1→3)-β-D-Manp-(1→6)-β-D-Glcp-(1→]_n, which appears to be a new EPS. The obtained results open up an avenue for the production of novel EPSs for biomedical applications.

Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera)

Lactobacillus kosoi Chiou et al. 2018 and Lactobacillus micheneri McFrederick et al. 2018 are closely related, and they share 100 % 16S rRNA gene sequence similarity, 99.6 % pheS gene sequence similarity, 100 % rpoA gene sequence similarity, 97.3 % average nucleotide identity (ANI) value and 76.6 % in silico DNA-DNA hybridization (isDDH) value, indicating that they represent the same species. Fatty acid methyl esters (FAME) analysis and phenotypic characterization also indicated that L. kosoi and L. micheneri are very similar. We propose L. kosoi Chiou et al. 2018 as a later heterotypic synonym of L. micheneri McFrederick et al. 2018. The taxonomic position of Lactobacillus plantarum subsp. argentoratensis in the L. plantarum group was re-examined using a polyphasic approach, including sequence analyses of 16S rRNA, pheS, rpoA and recA genes, average nucleotide identity analysis, in silico DNA-DNA hybridization, fatty acid methyl ester analysis and phenotypic characterization. Results of 16S rRNA gene sequence analysis indicated that L. plantarum subsp. argentoratensis was closely related to L. plantarum subsp. plantarum, L. pentosus and L. paraplantarum in the L. plantarum group, sharing 99.6-99.7 % 16S rRNA gene sequence similarities. Results of pheS, rpoA and recA gene sequence analyses indicated that L. plantarum subsp. argentoratensis was most closely related to L. plantarum subsp. plantarum, having 91.8 % pheS gene sequence similarity, 98.9 % rpoA gene sequence similarity and 93.1 % recA gene sequence similarity. L. plantarum subsp. argentoratensis DSM 16365^T shared 95.6 % ANI value and 62.9 % isDDH value with L. plantarum subsp. plantarum ATCC 14917^T. The low isDDH value confirmed that L. plantarum subsp. argentoratensis and L. plantarum subsp. plantarum represent two different species, rather than two different subspecies in the L. plantarum group. On the basis of the data from polyphasic characterization obtained in the present study and in previous studies, L. plantarum subsp. argentoratensis is elevated to the species level and represents a novel species of the genus Lactobacillus, for which the name Lactobacillus argentoratensis sp. nov. is proposed and the type strain is DKO 22^T (=CIP 108320^T=DSM 16365^T=JCM 16169^T). Two novel Gram-stain-positive bacterial strains, designated 1206-1^T and F027-1-2, were isolated from traditional pickle in Heilongjiang Province, PR China, and from the intestinal tract of a honey bee (Apis mellifera) in Hubei Province, PR China, respectively. The two bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, average nucleotide identity analysis, in silico DNA-DNA hybridization analysis and an analysis of phenotypic features. The results of 16S rRNA gene sequence analysis indicated that strains 1206-1^T and F027-1-2 were distantly related to Lactobacillus sharpeae, Lactobacillus hulanensis, Lactobacillus songhuajiangensis, Lactobacillus pantheris, Lactobacillus thailandensis, Lactobacillus camelliae, Lactobacillus jixianensis, Lactobacillus nasuensis, Lactobacillus baoqingensis, Lactobacillus manihotivorans and Lactobacillus porcinae. Strain 1206-1^T exhibited 94.2-96.4 % 16S rRNA gene sequence similarities, 69.5-83.3 % pheS gene sequence similarities and 73.1-90.3 % rpoA gene sequence similarities to type strains of phylogenetically related species. ANI and isDDH values between strain 1206-1^T and the type strains of phylogenetically related species were 52.7-73.7 % and 21.1-30.1 %, respectively. On the basis of the data obtained in the present study, a novel species, Lactobacillus zhaodongensis sp. nov. is proposed and the type strain is 1206-1^T (=CCM 8981^T=CCTCC AB 2019200^T=LMG 31620^T).

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov

Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.

Phylogenetic analysis of Leuconostoc and Lactobacillus species isolated from sugarcane processing streams

High levels of gums such as dextran, produced by Leuconostoc and Lactobacillus spp., have a severe impact on factory throughput and sugar quality. This study aimed to determine the phylogenetic relationships between gum‐producing Leuconostoc and Lactobacillus bacteria which were isolated from various locations in a sugarcane processing factory at times when low‐ and high‐dextran raw sugar, respectively, were produced. Phylogenetic analysis of 16S rRNA gene sequences grouped 81 isolates with the type strains of Leuconostoc mesenteroides (subspp. mesenteroides, dextranicum, and cremoris), Leuconostoc pseudomesenteroides, Leuconostoc lactis, and Leuconostoc citreum, respectively. Forty‐three isolates clustered with the type strain of Lactobacillus fermentum. The phylogenetic relatedness of the isolates was determined by sequencing and analysis of the housekeeping genes rpoA and dnaA for Leuconostoc spp. and the pheS and tuf genes for the Lactobacillus spp. The rpoA gene proved discriminatory for the phylogenetic resolution of all of the isolated Leuconostoc spp. and the dnaA housekeeping gene was shown to be effective for isolates clustering with the type strains of Leuc. mesenteroides and Leuc. citreum. None of the loci examined permitted differentiation at the subspecies level of Leuc. mesenteroides. Single‐locus analysis, as well as the concatenation of the pheS and tuf housekeeping gene sequences, yielded identical phylogenies for the Lactobacillus isolates corresponding to L. fermentum.

Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Taxonomic relationships between Lactobacillus casei , Lactobacillus paracasei and Lactobacillus zeae have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains L. casei ATCC 393T and L. zeae ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that L. casei could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the L. zeae strains, and supported an emended the description of the name of Lactobacillus zeae (ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.

Lactobacillus hegangensis sp. nov., Lactobacillus suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and Lactobacillus angrenensis sp. nov., isolated from Chinese traditional pickle and yogurt

Fourteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and yogurt. The strains were characterized using a polyphasic taxonomic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, determination of average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and an analysis of phenotypic features. The data demonstrated that the 14 strains represented ten novel species belonging to the genus Lactobacillus , strains 73-4T, 247-3T, 143-4(a)T, 33-1T, 143-6T, 247-4T, 17-4T, 143-1T, 735-2T and M1530-1T were designated as the type strains. Strains 73-4T and 247-3T were phylogenetically related to the type strains of Lactobacillus camelliae and Lactobacillus jixianensis , having 97.0–98.9 % 16S rRNA gene sequence similarities, 83.9–87.2 % pheS gene sequence similarities and 86.8–93.3 % rpoA gene sequence similarities. Strains 143-4(a)T and 33-1T were phylogenetically related to the type strains of Lactobacillus rhamnosus , Lactobacillus paracasei and Lactobacillus casei , having 93.6–96.5 % 16S rRNA gene sequence similarities, 73.9–77.2 % pheS gene sequence similarities and 76.1–77.6 % rpoA gene sequence similarities. Strains 143-6T, 247-4T, 17-4T and 143-1T were phylogenetically related to the type strains of Lactobacillus concavus , Lactobacillus dextrinicus and Lactobacillus bayanensis , exhibiting 95.5–99.9 % 16S rRNA gene sequence similarities, 76.5–83.1 % pheS gene sequence similarities and 83.6–98.3 % rpoA gene sequence similarities. Strain 735-2T was phylogenetically related to the type strains of Lactobacillus zhaoyuanensis , Lactobacillus jiayinensis and Lactobacillus coryniformis , having 98.2–99.1 % 16S rRNA gene sequence similarities, 82.8–84.1 % pheS gene sequence similarities and 93.0–93.9 % rpoA gene sequence similarities. Strain M1530-1T was phylogenetically related to the type strains of Lactobacillus suantsaiihabitans and Lactobacillus brevis , having 99.5 and 99.0 % 16S rRNA gene sequence similarities, 90.3 and 81.7 % pheS gene sequence similarities and 97.7 and 91.1 % rpoA gene sequence similarities. The ANI and isDDH values between strains 73-4T, 247-3T, 143-4(a)T, 33-1T, 143-6T, 247-4T, 17-4T, 143-1T, 735-2T, M1530-1T and type strains of phylogenetically related species were less than 86.8 % and 33.9 % respectively, confirming that they represent ten novel species within the genus Lactobacillus . Based upon the data of polyphasic characterization obtained in the present study, ten novel species, Lactobacillus hegangensis sp. nov., Lactobacillus suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and Lactobacillus angrenensis sp. nov., are proposed and the type strains are 73-4T (=NCIMB 15177T=CCM 8912T=CCTCC AB 2018407T), 247-3T (=NCIMB 15176T=JCM 33275T), 143-4(a)T (=NCIMB 15173T=CCM 8948T=JCM 33273T=CCTCC AB 2018390T), 33-1T (=NCIMB 15169T=CCM 8947T=JCM 33272T=CCTCC AB 2018405T), 143-6T (=NCIMB 15162T=CCM 8951T=JCM 33274T=CCTCC AB 2018411T), 247-4T (=NCIMB 15155T=CCM 8897T=LMG 31059T=CCTCC AB 2018410T), 17-4T (=NCIMB 15161T=CCM 8946T=JCM 33271T=CCTCC AB 2018406T), 143-1T (=NCIMB 15157T=CCM 8937T=CCTCC AB 2018409T), 735-2T (=NCIMB 15190T=CCM 8925T=LMG 31186T) and M1530-1T (=NCIMB 15150T=CCM 8893T=LMG 31046T=CCTCC AB 2018402T), respectively.