Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau

BACKGROUND

The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits.

METHODS

This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform.

RESULTS

The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality.

CONCLUSIONS

The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role.

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.

Pangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum

BACKGROUND

Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods.

METHODS

We selected as diverse a set of strains as possible in terms of sources, previous genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed.

RESULTS

Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. The distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence.

CONCLUSION

Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution and lifestyle of L. gelidum and L. gasicomitatum in foods have not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.

Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower

A Fructobacillus strain was isolated from the flower of a nodding thistle (Carduus nutans) collected in Bavaria, Germany. The strain is Gram-positive, rod-shaped, non-motile, non-sporulating, catalase- and oxidase-negative, and facultatively anaerobic. Growth can be detected at 10-37 °C and pH 4 to 9. The genome size is about 1.56 Mbp and the G+C content is 43.76 mol%. Assignment to the genus Fructobacillus was done by average nucleotide identity (ANI), 16S rRNA gene sequence and multilocus sequence analyses. Calculations of ANI and digital DNA-DNA hybridization values indicate a novel species with Fructobacillus tropaeoli DSM 23246^T (93.58% ANI and 57.9 % dDDH) being its closest relative. Therefore, a new species named Fructobacillus cardui sp. nov. with TMW 2.2452^T (=DSM 113480^T=CECT 30515^T) as type strain is proposed.

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.

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).

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.

The Altitude of Coffee Cultivation Causes Shifts in the Microbial Community Assembly and Biochemical Compounds in Natural Induced Anaerobic Fermentations

Coffee harvested in the Caparaó region (Minas Gerais, Brazil) is associated with high-quality coffee beans resulting in high-quality beverages. We characterize, microbiologically and chemically, fermented coffees from different altitudes through target NGS, chromatography, and conventional chemical assays. The genera Gluconobacter and Weissella were dominant in coffee’s fruits from altitudes 800 and 1,000 m. Among the Eukaryotic community, yeasts were the most dominant in all altitudes. The most dominant fungal genus was Cystofilobasidium, which inhabits cold environments and resists low temperatures. The content of acetic acid was higher at altitudes 1,200 and 1,400 m. Lactic acid and the genus Leuconostoc (Pearson: 0.93) were positively correlated. The relative concentration of volatile alcohols, especially of 2-heptanol, was high at all altitudes. Bacteria population was higher in coffees from 800 m, while at 1,000 m, fungi richness was favored. The altitude is an important variable that caused shifts in the microbial community and biochemical compounds content, even in coffees belonging to the same variety and cultivated in the same region under SIAF (self-induced anaerobic fermentation) conditions. Coffee from lower altitudes has higher volatile alcohols content, while high altitudes have esters, aldehydes, and total phenolics contents.

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

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

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).

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.

Weissella sagaensis sp. nov., isolated from traditional Chinese yogurt

Three Gram-stain-positive bacterial strains, designated X0750^T, X0278 and X0401, isolated from traditional yogurt in Tibet Autonomous Region, PR China, were characterized by a polyphasic approach, including sequence analyses of the 16S rRNA gene and three housekeeping genes (pheS, rpoA and recA), determination of average nucleotide identity (ANI) and average amino acid identity (AAI), in silico DNA-DNA hybridization (isDDH), fatty acid methyl ester (FAME) analysis and phenotypic characterization. Strain X0750^T was phylogenetically related to the type strains of Weissella hellenica, Weissella bombi, Weissella paramesenteroides, Weissella jogaejeotgali, Weissella thailandensis, Weissella oryzae, Weissella cibaria and Weissella confusa, having 94.4-100 % 16S rRNA gene sequence similarities, 76.7-90.0 % pheS gene sequence similarities, 88.9-99.4 % rpoA gene sequence similarities and 77.6-92.8 % recA gene sequence similarities, respectively. ANI, isDDH and AAI values between strain X0750^T and type strains of phylogenetically related species were less than 90.4, 40.9 and 92.8 % respectively, confirming that strain X0750^T represents a novel species within the genus Weissella. Based upon the data obtained in the present study, a novel species, Weissella sagaensis sp. nov., is proposed and the type strain is X0750^T(=NCIMB 15192^T=CCM 8924^T=LMG 31184^T=CCTCC AB 2018403^T).

Phylogenetic Analyses of pheS, dnaA and atpA Genes for Identification of Weissella confusa and Weissella cibaria Isolated from a South African Sugarcane Processing Factory

A previous study reported on the isolation of 430 polysaccharide (gum)-producing bacteria from a South African sugarcane processing factory and the identification of isolates by comparative 16S rRNA gene sequencing. A large number of isolates (202) belonged to the genus Weissella and clustered with reference strains of Weissella cibaria and Weissella confusa. In this study, we identified 147 strains as W. cibaria and 55 as W. confusa based on phylogenetic analyses of pheS and dnaA gene sequences of representative isolates. We also included atpA gene sequence analysis of Weissella isolates as potential future phylogenetic marker to differentiate amongst strains of W. cibaria and W. confusa.

Mapping the dominant microbial species diversity at expiration date of raw meat and processed meats from equine origin, an underexplored meat ecosystem, in the Belgian retail

Although equine meats and their derived smoked or fermented products are popular in some regions of the world, they only form a minor fraction of the global meat consumption. The latter may explain why their associated bacterial communities have not received much attention. In the present study, 69 different samples of equine meats and meat products were investigated. The samples consisted of raw meat from horses (17 samples) and zebra (7), as well as non-fermented but smoked (24) and fermented (21) horse meat products. After purchase, all samples were stored at 4 °C and analysed at expiration date. Besides an estimation of the total microbial counts, specific attention was paid to the identification of lactic acid bacteria (LAB) and catalase-positive cocci, in particular the group of coagulase-negative staphylococci (CNS), involved, due to their technological relevance in view of the elaboration of meat products. Samples that were loosely wrapped in butcher paper instead of vacuum- or modified-atmosphere packages were also screened for pseudomonads and enterobacterial species. In total, 1567 bacterial isolates were collected, subjected to (GTG)₅-PCR fingerprinting of genomic DNA, and identified by multiple gene sequencing (based on the 16S rRNA, pheS, rpoA, rpoB, and/or tuf genes). Overall, the bacterial species diversity consisted mostly of LAB but was contingent on the type of product. Raw meat was dominated by Carnobacterium divergens, Lactobacillus sakei, Lactococcus piscium, and Leuconostoc gelidum, with zebra meat being particularly rich in lactococci. Smoked and fermented horse meat products contained mostly Lb. sakei and, to a lesser degree, Lactobacillus curvatus. In addition, several catalase-positive cocci (mostly Staphylococcus equorum), Anoxybacillus sp., Brevibacterium sp., Brochothrix thermosphacta, and the enterobacterial species Hafnia alvei were found.

Komagataeibacter cocois sp. nov., a novel cellulose-producing strain isolated from coconut milk

Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7^T, isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter. DNA-DNA correlation or average nucleotide identity analysis was performed between WE7^T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7^T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7^T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7^T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7^T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7^T (=CGMCC 1.15338^T=JCM 31140^T).

Identification and Classification for the Lactobacillus casei Group

Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.

Analysis of Leuconostoc citreum strains using multilocus sequence typing

The objective of this study was to perform genetic diversity analysis of 13 strains isolated from South Korean foods by multilocus sequence typing (MLST). For typing, seven housekeeping loci (atpA, dnaA, dnaK, gyrB, pheS, pyrG, and rpoA) were selected, amplified and analyzed. Fifty-one polymorphic sites varying from 1 to 22 in each species were identified. Thirteen sequence types were generated with allele numbers ranged from 2 to 10. The overall relationship between strains was assessed by unweighted pair group method with arithmetic mean dendrogram and minimum spanning tree. In addition, combined spits tree analysis revealed intragenic recombination. No clear relationship was observed between the isolation sources and strains. The developed MLST scheme enhanced our knowledge of the population diversity of Leu. citreum strains and will be used further for the selection of industrially important strain.

Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing

In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail

Sliced cooked poultry products are susceptible to bacterial spoilage, notwithstanding their storage under modified-atmosphere packaging (MAP) in the cold chain. Although the prevailing bacterial communities are known to be mostly consisting of lactic acid bacteria (LAB), more information is needed about the potential variation in species diversity within national markets. In the present study, a total of 42 different samples of sliced cooked poultry products were collected in the Belgian retail and their bacterial communities were analysed at expiration date. A total of 629 isolates from four different culture media, including plate count agar for the total microbiota and de Man-Rogosa-Sharpe (MRS), modified MRS, and M17 agar as three selective agar media for LAB, were subjected to (GTG)₅-PCR fingerprinting and identification by gene sequencing. Overall, Carnobacterium, Lactobacillus, and Leuconostoc were the dominant genera. Within each genus, the most encountered isolates were Carnobacterium divergens, Lactobacillus sakei, and Leuconostoc carnosum. When comparing samples from chicken origin with samples from turkey-derived products, a higher dominance of Carnobacteria spp. was found in the latter group. Also, an association between the dominance of lactobacilli and the presence of added plant material and lactate salts was found.

Lactobacillus panisapium sp. nov., from honeybee Apis cerana bee bread

A novel facultatively anaerobic, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative bacterium of the genus Lactobacillus, designated strain Bb 2-3^T, was isolated from bee bread of Apis cerana collected from a hive in Kunming, China. The strain was regular rod-shaped. Optimal growth occurred at 37 °C, pH 6.5 with 5.0 g l⁻¹ NaCl. The predominant fatty acids were C_18 : 1ω9c, C_16 : 0 and C_19 : 0 iso. Respiratory quinones were not detected. Seven glycolipids, three lipids, phosphatidylglycerol and diphosphatidylglycerol were detected. The peptidoglycan type A4α l-Lys-d-Asp was determined. Strain Bb 2-3^T was closely related to Lactobacillus bombicola DSM 28793^T, Lactobacillus apis LMG 26964^T and Lactobacillus helsingborgensis DSM 26265^T, with 97.8, 97.6 and 97.0 % 16S rRNA gene sequence similarity, respectively. A comparison of two housekeeping genes, rpoA and pheS, revealed that strain Bb 2-3^T was well separated from the reference strains of species of the genus Lactobacillus. The average nucleotide identity between strain Bb 2-3^T and the type strains of closely related species was lower than the 95–96 % threshold value for delineation of genomic prokaryotic species. The G+C content of the genomic DNA of strain Bb 2-3^T was 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain Bb 2-3^T is proposed to represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus panisapium sp. nov. The type strain is Bb 2-3^T (=DSM 102188^T=ACCC 19955^T).

Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features

The genome of Leuconostoc suionicum DSM 20241^T (=ATCC 9135^T = LMG 8159^T = NCIMB 6992^T) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative properties and metabolites of strain DSM 20241^T during fermentation. The genome of L. suionicum DSM 20241^T consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb) with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs. Analysis of the metabolic pathways of L. suionicum DSM 20241^T revealed that strain DSM 20241^T performs heterolactic acid fermentation and can metabolize diverse organic compounds including glucose, fructose, galactose, cellobiose, mannose, sucrose, trehalose, arbutin, salcin, xylose, arabinose and ribose.

A proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences

The type strains of four subspecies of Leuconostocmesenteroides, L. mesenteroidessubsp. mesenteroides, L. mesenteroidessubsp. cremoris, L. mesenteroidessubsp. dextranicum and L. mesenteroidessubsp. suionicum, and strain DRC1506T, used as a starter culture for commercial kimchi production in Korea, were phylogenetically analyzed on the basis of their complete genome sequences. Although the type strains of the four L. mesenteroides subspecies and strain DRC1506T shared very high 16S rRNA gene sequence similarities (>99.72 %), the results of analysis of average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH) and core-genome-based relatedness indicated that they could form five different phylogenetic lineages. The type strains of L. mesenteroidessubsp. mesenteroides, L. mesenteroidessubsp. cremoris and L. mesenteroidessubsp. dextranicum and DRC1506T shared higher ANI and in silico DDH values than the thresholds (95-96 % and 70 %, respectively) generally accepted for different species delineation, whereas the type strain of L. mesenteroidessubsp. suionicum (DSM 20241T) shared lower ANI (<94.1 %) and in silico DDH values (<57.0 %) with the other four L. mesenteroides lineage strains, indicating that DSM 20241T couldn be reclassified as representing a different species. Here, we report that DRC1506T represents a novel subspecies within the species Leuconostoc mesenteroides, for which the name Leuconostoc mesenteroidessubsp. jonggajibkimchii subsp. nov. is proposed. The type strain is DRC1506T (=KCCM 43249T=JCM 31787T). In addition, L. mesenteroidessubsp. suionicum is also reclassified as Leuconostoc suionicum. sp. nov. (type strain DSM 20241T=ATCC 9135T=LMG 8159T=NCIMB 6992T).

Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut

Spectra of five isolates (LMG 28358^T, LMG 29879^T, LMG 29880^T, LMG 28359^T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359^T and R-53705 which also grouped in the same MALDI-TOF MS cluster, while different DNA fingerprints were obtained for the other isolates. Comparative 16S rRNA gene sequence analysis of the four different strains identified Gilliamella apicola NCIMB 14804^T as nearest neighbour species. Average nucleotide identity values of draft genome sequences of the four isolates and of G. apicola NCIMB 14804^T were below the 96% threshold value for species delineation and all four strains and G. apicola NCIMB 14804^T were phenotypically distinct. Together, the draft genome sequences and phylogenetic and phenotypic data indicate that the four strains represent four novel Gilliamella species for which we propose the names Gilliamella intestini sp. nov., with LMG 28358^T as the type strain, Gilliamella bombicola sp. nov., with LMG 28359^T as the type strain, Gilliamella bombi sp. nov., with LMG 29879^T as the type strain and Gilliamella mensalis sp. nov., with LMG 29880^T as the type strain.

Diversity of the dominant bacterial species on sliced cooked pork products at expiration date in the Belgian retail

Pork-based cooked products, such as cooked hams, are economically valuable foods that are vulnerable to bacterial spoilage, even when applying cooling and modified atmosphere packaging (MAP). Besides a common presence of Brochothrix thermosphacta, their microbiota are usually dominated by lactic acid bacteria (LAB). Yet, the exact LAB species diversity can differ considerably among products. In this study, 42 sliced cooked pork samples were acquired from three different Belgian supermarkets to map their bacterial heterogeneity. The community compositions of the dominant bacterial species were established by analysing a total of 702 isolates from selective agar media by (GTG)₅-PCR fingerprinting followed by gene sequencing. Most of the isolates belonged to the genera Carnobacterium, Lactobacillus, and Leuconostoc, with Leuconostoc carnosum and Leuconostoc gelidum subsp. gelidum being the most dominant members. The diversity of the dominant bacterial species varied when comparing samples from different production facilities and, in some cases, even within the same product types. Although LAB consistently dominated the microbiota of sliced cooked pork products in the Belgian market, results indicated that bacterial diversity needs to be addressed on the level of product composition and batch variation. Dedicated studies will be needed to substantiate potential links between such variability and microbial composition. For instance, the fact that higher levels of lactobacilli were associated with the presence of potassium lactate (E326) may be suggestive of selective pressure but needs to be validated, as this finding referred to a single product only.

Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages

Leuconostoc gelidum subsp. gasicomitatum is a predominant lactic acid bacterium (LAB) in spoilage microbial communities of different kinds of modified-atmosphere packaged (MAP) food products. So far, only one genome sequence of a poultry-originating type strain of this bacterium (LMG 18811(T)) has been available. In the current study, we present the completely sequenced and functionally annotated genome of strain KG16-1 isolated from a vegetable-based product. In addition, six other vegetable-associated strains were sequenced to study possible "niche" specificity suggested by recent multilocus sequence typing. The genome of strain KG16-1 consisted of one circular chromosome and three plasmids, which together contained 2,035 CDSs. The chromosome carried at least three prophage regions and one of the plasmids encoded a galactan degradation cluster, which might provide a survival advantage in plant-related environments. The genome comparison with LMG 18811(T) and six other vegetable strains suggests no major differences between the meat- and vegetable-associated strains that would explain their "niche" specificity. Finally, the comparison with the genomes of other leuconostocs highlights the distribution of functionally interesting genes across the L. gelidum strains and the genus Leuconostoc.

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages

Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups ("phylotypes") may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.

Apibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota

Isolates LMG 28357T (=R-53146T) and LMG 28623 were obtained from gut samples of Bombus lapidarius bumblebees caught in Ghent, Belgium. They had identical 16S rRNA gene sequences which were 95.7 % identical to that of Apibacter adventoris wkB301T, a member of the family Flavobacteriaceae. Both isolates had highly similar matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and randomly amplified polymorphic DNA (RAPD) profiles. A draft genome sequence was obtained for strain LMG 28357T (Gold ID Gp0108260); its DNA G+C content was 30.4%, which is within the range reported for members of the family Flavobacteriaceae (27 to 56 mol%) and which is similar to that of the type strain of A. adventoris (29.0 mol%). Whole-cell fatty acid methyl ester analysis of strain LMG 28357T revealed many branched-chain fatty acids, a typical characteristic of bacteria of the family Flavobacteriaceae and a profile that was similar to that reported for A. adventoris wkB301T. MK6 was the major respiratory quinone, again conforming to bacteria of the family Flavobacteriaceae. The isolates LMG 28357T and LMG 28623 could be distinguished from A. adventoris strains through their oxidase activity. On the basis of phylogenetic, genotypic and phenotypic data, we propose to classify both isolates as representatives of a novel species of the genus Apibacter, Apibacter mensalis sp. nov., with LMG 28357T (=DSM 100903T=R-53146T) as the type strain.

Antibiotic Susceptibility Profiles of Dairy Leuconostoc, Analysis of the Genetic Basis of Atypical Resistances and Transfer of Genes In Vitro and in a Food Matrix

In spite of a global concern on the transfer of antibiotic resistances (AR) via the food chain, limited information exists on this issue in species of Leuconostoc and Weissella, adjunct cultures used as aroma producers in fermented foods. In this work, the minimum inhibitory concentration was determined for 16 antibiotics in 34 strains of dairy origin, belonging to Leuconostoc mesenteroides (18), Leuconostoc citreum (11), Leuconostoc lactis (2), Weissella hellenica (2), and Leuconostoc carnosum (1). Atypical resistances were found for kanamycin (17 strains), tetracycline and chloramphenicol (two strains each), and erythromycin, clindamycin, virginiamycin, ciprofloxacin, and rifampicin (one strain each). Surprisingly, L. mesenteroides subsp. mesenteroides LbE16, showed resistance to four antibiotics, kanamycin, streptomycin, tetracycline and virginiamycin. PCR analysis identified tet(S) as responsible for tetracycline resistance in LbE16, but no gene was detected in a second tetracycline-resistant strain, L. mesenteroides subsp. cremoris LbT16. In Leuconostoc mesenteroides subsp. dextranicum LbE15, erythromycin and clindamycin resistant, an erm(B) gene was amplified. Hybridization experiments proved erm(B) and tet(S) to be associated to a plasmid of ≈35 kbp and to the chromosome of LbE15 and LbE16, respectively. The complete genome sequence of LbE15 and LbE16 was used to get further insights on the makeup and genetic organization of AR genes. Genome analysis confirmed the presence and location of erm(B) and tet(S), but genes providing tetracycline resistance in LbT16 were again not identified. In the genome of the multi-resistant strain LbE16, genes that might be involved in aminoglycoside (aadE, aphA-3, sat4) and virginiamycin [vat(E)] resistance were further found. The erm(B) gene but not tet(S) was transferred from Leuconostoc to Enterococcus faecalis both under laboratory conditions and in cheese. This study contributes to the characterization of AR in the Leuconostoc-Weissella group, provides evidence of the genetic basis of atypical resistances, and demonstrates the inter-species transfer of erythromycin resistance.

What's Inside That Seed We Brew? A New Approach To Mining the Coffee Microbiome

Coffee is a critically important agricultural commodity for many tropical states and is a beverage enjoyed by millions of people worldwide. Recent concerns over the sustainability of coffee production have prompted investigations of the coffee microbiome as a tool to improve crop health and bean quality. This review synthesizes literature informing our knowledge of the coffee microbiome, with an emphasis on applications of fruit- and seed-associated microbes in coffee production and processing. A comprehensive inventory of microbial species cited in association with coffee fruits and seeds is presented as reference tool for researchers investigating coffee-microbe associations. It concludes with a discussion of the approaches and techniques that provide a path forward to improve our understanding of the coffee microbiome and its utility, as a whole and as individual components, to help ensure the future sustainability of coffee production.

Leuconostoc rapi sp. nov., isolated from sous-vide-cooked rutabaga

A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676T, was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676T from all established species of the genus Leuconostoc. Strain LMG 27676T ( = R-50029T = MHB 277T = DSM 27776T) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.

Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi

Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.

A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia

BACKGROUND

Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China.

RESULTS

Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates.

CONCLUSIONS

Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.

The microbial diversity of traditional spontaneously fermented lambic beer

Lambic sour beers are the products of a spontaneous fermentation that lasts for one to three years before bottling. The present study determined the microbiota involved in the fermentation of lambic beers by sampling two fermentation batches during two years in the most traditional lambic brewery of Belgium, using culture-dependent and culture-independent methods. From 14 samples per fermentation, over 2000 bacterial and yeast isolates were obtained and identified. Although minor variations in the microbiota between casks and batches and a considerable species diversity were found, a characteristic microbial succession was identified. This succession started with a dominance of Enterobacteriaceae in the first month, which were replaced at 2 months by Pediococcus damnosus and Saccharomyces spp., the latter being replaced by Dekkera bruxellensis at 6 months fermentation duration.

Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum

In the present study we investigated the taxonomic status of 20 lactic acid bacteria (LAB) originating from packaged meat. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Leuconostoc with Leuconostoc gelidum, Leuconostoc inhae and Leuconostoc gasicomitatum as the closest phylogenetic relatives. The novel strains shared more than 70 % DNA-DNA relatedness with type and reference strains of both L. gelidum and L. gasicomitatum. The DNA-DNA relatedness values between L. gelidum type and reference strains and L. gasicomitatum type and reference strains were also above 70 %, showing that all these strains belonged to the same species. Sequence analyses of concatenated atpA, pheS, and rpoA genes demonstrated that the novel strains as well as type and reference strains of L. gelidum and L. gasicomitatum are phylogenetically closely related, but form three clearly separated subgroups. Numerical analysis of HindIII ribopatterns and phenotypic tests supported this subdivision. Based on the data presented in this study, we propose to reclassify Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov. (type strain, LMG 18811(T) = DSM 15947(T)). The novel strains isolated in the present study represent a novel subspecies, for which the name Leuconostoc gelidum subsp. aenigmaticum subsp. nov. is proposed, with POUF4d(T) ( = LMG 27840(T) = DSM 19375(T)) as the type strain. The proposal of these two novel subspecies automatically creates the subspecies Leuconostoc gelidum subsp. gelidum subsp. nov. (type strain, NCFB 2775(T) = DSM 5578(T)). An emended description of Leuconostoc gelidum is also provided.

Enterococcus xiangfangensis sp. nov., isolated from Chinese pickle

A Gram-stain-positive bacterial strain, 11097(T), was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized using a polyphasic approach, including 16S rRNA gene sequence analysis, phenylalanyl-tRNA synthase (pheS) gene sequence analysis, RNA polymerase α subunit (rpoA) gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 11097(T) was phylogenetically related to Enterococcus devriesei, E. pseudoavium, E. viikkiensis, E. avium, E. malodoratus, E. gilvus and E. raffinosus. Strain 11097(T) had 99.1-99.9% 16S rRNA gene sequence similarities, 78.2-83.2% pheS gene sequence similarities and 93.8-96.6% rpoA gene sequence similarities with type strains of phylogenetically related species. Based upon polyphasic characterization data obtained in the present study, a novel species of the genus Enterococcus, Enterococcus xiangfangensis sp. nov., is proposed with the type strain 11097(T) ( = LMG 27495(T) = NCIMB 14834(T)).

Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough

Three Gram-stain-positive bacterial strains, 11050T, 7-19T and 11102T, were isolated from traditional pickle and sourdough in Heilongjiang Province, China. These bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 11050T belonged to the Lactobacillus plantarum species group and shared 98.0–98.4 % 16S rRNA gene sequence similarities and 84.7–88.9 % dnaK gene sequence similarities with type strains of Lactobacillus plantarum subsp. plantarum , Lactobacillus plantarum subsp. argentoratensis , Lactobacillus pentosus , Lactobacillus paraplantarum , Lactobacillus fabifermentans and Lactobacillus xiangfangensis and had 75.9–80.7 % pheS gene sequence similarities and 90.7–92.5 % rpoA gene sequence similarities with Lactobacillus plantarum subsp. plantarum LMG 6907T, Lactobacillus plantarum subsp. argentoratensis LMG 9205, Lactobacillus pentosus LMG 10755T, Lactobacillus paraplantarum LMG 16673T, Lactobacillus fabifermentans LMG 24284T and Lactobacillus xiangfangensis 3.1.1T, respectively. Strain 7-19T was phylogenetically related to Lactobacillus thailandensis , Lactobacillus pantheris and Lactobacillus sharpeae , having 94.1–96.7 % 16S rRNA gene sequence similarities, 71.5–82.3 % pheS gene sequence similarities and 71.2–83.4 % rpoA gene sequence similarities with type strains of Lactobacillus thailandensis , Lactobacillus pantheris and Lactobacillus sharpeae , respectively. Strain 11102T was phylogenetically related to Lactobacillus oligofermentans , Lactobacillus suebicus , Lactobacillus vaccinostercus and Lactobacillus hokkaidonensis . Strain 11102T had 99.2 % 16S rRNA gene sequence similarity, 81.3 % pheS gene sequence similarity and 96.1 % rpoA gene sequence similarity with Lactobacillus oligofermentans LMG 22743T, respectively. Strain 11102T shared 96.0–96.8 % 16S rRNA gene sequence similarities, 73.3–81.0 % pheS gene sequence similarities and 74.6–76.9 % rpoA gene sequence similarities with type strains of Lactobacillus suebicus , Lactobacillus vaccinostercus and Lactobacillus hokkaidonensis , respectively. Based upon the data from polyphasic characterization obtained in the present study, three novel species, Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., are proposed and the type strains are 11050T ( = LMG 27194T = CCUG 62991T), 7-19T ( = LMG 27191T = NCIMB 14832T = CCUG 62990T) and 11102T ( = LMG 27192T = NCIMB 14833T), respectively.