Isolation of endosulfan sulfate-degrading Rhodococcus koreensis strain S1-1 from endosulfan contaminated soil and identification of a novel metabolite, endosulfan diol monosulfate.

An aerobic endosulfan sulfate-degrading bacterium, Rhodococcus koreensis strain S1-1, was isolated from soil to which endosulfan had been applied annually for more than 10 years until 2008. The strain isolated in this work reduced the concentration of endosulfan sulfate (2) from 12.25 µM to 2.11 µM during 14 d at 30 °C. Using ultra performance liquid chromatography-electrospray ionization-mass spectroscopy (UPLC-ESI-MS), a new highly water-soluble metabolite possessing six chlorine atoms was found to be endosulfan diol monosulfate (6), derived from 2 by hydrolysis of the cyclic sulfate ester ring. The structure of 6 was elucidated by chemical synthesis of the candidate derivatives and by HR-MS and UPLC-MS analyses. Therefore, it was suggested that the strain S1-1 has a new metabolic pathway of 2. In addition, 6 was expected to be less toxic among the metabolites of 1 because of its higher water-solubility.

Characterization of flagellins isolated from a highly motile strain of Lactobacillus agilis.

BACKGROUND: Most lactic acid bacteria are non-motile but some of them are flagellated and exhibit motility. So far, motile lactobacilli have rarely been studied, and characteristics of their flagellins are poorly understood. In this study, a highly motile strain of Lactobacillus agilis was recruited for transcriptional analysis and characterization of its flagellins. RESULTS: Unlike another motile lactic acid bacteria of intestinal isolate, Lactobacillus ruminis, flagellar filaments of the L. agilis strain probably consist of two homologous but distinct flagellins. Glycosylation of the flagellar filaments and their resistance to heat, acid and SDS were also observed. The immunological activity of the flagellins was evaluated through the stimulation of Caco-2 cells. The results show that TLR5-stimulating activity of the protein is attenuated, likely due to an incomplete TLR5-recognition site. CONCLUSIONS: The flagella filaments of L. agilis BKN88 consist of two homologous glycosylated flagellins, which likely have an incomplete TLR5-recognition site. The characteristics of the flagellin are presumably a consequence of adaptation as a commensal microbe in the gastrointestinal tract.

Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.

BACKGROUND: Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus, based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp. RESULTS: Fructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position. CONCLUSION: The present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.

Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade.

Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin­Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.

Alicyclobacillus dauci sp. nov., a slightly thermophilic, acidophilic bacterium isolated from a spoiled mixed vegetable and fruit juice product.

A novel, moderately thermophilic, acidophilic, Gram-variable, rod-shaped, endospore-forming bacterium was isolated from a spoiled mixed vegetable and fruit juice product that had the off-flavour of guaiacol. The bacterium, strain 4F(T), grew aerobically at 20-50 °C (optimum 40 °C) and pH 3.0-6.0 (optimum pH 4.0) and produced acid from glycerol, d-galactose and d-glucose. It contained menaquinone-7 (MK-7) as the major isoprenoid quinone and the DNA G+C content was 49.6 mol%. The predominant cellular fatty acids of strain 4F(T) were ω-alicyclic (ω-cyclohexane fatty acids), which are characteristic of the genus Alicyclobacillus. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the Alicyclobacillus cluster, and is related most closely to the type strains of Alicyclobacillus acidoterrestris (97.4 % similarity) and Alicyclobacillus fastidiosus (97.3 %). Strain 4F(T) produced guaiacol from vanillic acid. It can be distinguished from related species by its acid production type and guaiacol production. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness values, it can be concluded that the strain represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus dauci sp. nov. is proposed; the type strain is 4F(T) ( = DSM 28700(T) = NBRC 108949(T) = NRIC 0938(T)).

Lactobacillus furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles.

Two strains of lactic acid bacteria, Nu27(T) and Nu29, were isolated from Nukadoko, rice bran paste for Japanese pickles. The isolates were Gram-stain-positive, rod-shaped, catalase-negative, non-motile and facultatively anaerobic lactic acid bacteria. The isolates showed identical 16S rRNA gene sequences. The closest relatives to strain Nu27(T) based on 16S rRNA gene sequence similarities were Lactobacillus versmoldensis KU-3(T) (98.9% 16S rRNA gene sequence similarity), Lactobacillus nodensis iz4b(T) (96.3%) and Lactobacillus tucceti CECT 5290(T) (97.2%). DNA-DNA relatedness values revealed genotype separation of the two isolates from the above three species. Based on the physiological, biochemical and genotypic characteristics provided, the isolates represent a novel species of the genus Lactobacillus, for which name is Lactobacillus furfuricola proposed. The type strain is Nu 27(T) ( = JCM 18764(T) = NRIC 0900(T) = DSM 27174(T)).

Fructophilic characteristics of Fructobacillus spp. may be due to the absence of an alcohol/acetaldehyde dehydrogenase gene (adhE).

Fructophilic strains of Leuconostoc spp. have recently been reclassified to a new genus, i.e., Fructobacillus. Members of the genus are differentiated from Leuconostoc spp. by their preference for fructose on growth, requirement of an electron acceptor for glucose metabolism, and the inability to produce ethanol from the fermentation of glucose. In the present study, enzyme activities and genes involved in ethanol production were studied, since this is the key pathway for NAD(+)/NADH cycling in heterofermentative lactic acid bacteria. Fructobacillus spp. has a weak alcohol dehydrogenase activity and has no acetaldehyde dehydrogenase activity, whereas both enzymes are active in Leuconostoc mesenteroides. The bifunctional alcohol/acetaldehyde dehydrogenase gene, adhE, was described in Leuconostoc spp., but not in Fructobacillus spp. These results suggested that, due to the deficiency of the adhE gene, the normal pathway for ethanol production is absent in Fructobacillus spp. This leads to a shortage of NAD(+), and the requirement for an electron acceptor in glucose metabolism. Fructophilic characteristics, as observed for Fructobacillus spp., are thus due to the absence of the adhE gene, and a phenotype that most likely evolved as a result of regressive evolution.

Characterization of a Lactobacillus gasseri JCM 1131T lipoteichoic acid with a novel glycolipid anchor structure.

We determined the chemical structure of lipoteichoic acid (LTA) from Lactobacillus gasseri JCM 1131(T). The repeating unit was comprised of glycerolphosphate and 2-alanylglycerolphosphate. The glycolipid anchor was tetrahexosylglycerol with two or three acyl groups. To our knowledge, this is the first demonstration of a tetrahexose structure in an LTA glycolipid anchor.

An increased number of CD4+CD25+ cells induced by an oral administration of Lactobacillus plantarum NRIC0380 are involved in antiallergic activity.

BACKGROUND: Our previous study showed that an oral administration of Lactobacillus plantarum NRIC0380 inhibited immunoglobulin E (IgE) production in a murine model, and that orally administered NRIC0380 induced CD4+CD25+ Foxp3+ T, i.e. regulatory T (Treg), cells in the spleen and Peyer's patch of mice. Although it has been reported that Treg cells might suppress the allergic symptoms, the involvement of the cells in the antiallergic activity of lactic acid bacteria has not been clearly demonstrated. We therefore examined in detail the antiallergic activity of Treg cells obtained from mice that had been fed NRIC0380. METHODS: Treg cells were obtained from mice that had been fed NRIC0380. The T cell-suppressive effect of the cells was analyzed by coculturing the cells with splenocytes of ß-lactoglobulin-immunized mice and ß-lactoglobulin. The effects of the Treg cells on the IgE production and cutaneous anaphylaxis reaction were then analyzed by transferring the cells into another mouse. RESULTS: The Treg cells obtained from the mice that had been fed NRIC0380 showed similar T cell-suppressive activity to those cells obtained from the control mice. The Treg cells obtained from the mice fed NRIC0380 significantly inhibited the IgE production and active cutaneous anaphylaxis reaction when transferred into another mouse that was subsequently immunized with the antigen. Furthermore, the Treg cells also significantly suppressed the passive cutaneous anaphylaxis reaction when cotransferred with the IgE antibody into another mouse. CONCLUSIONS: The induction of Treg cells by the oral administration of NRIC0380 would be involved in the antiallergic activity of NRIC0380.

Induction of ALDH activity in intestinal dendritic cells by Lactobacillus plantarum NRIC0380.

Lactic acid bacteria have been reported to have various immune-regulating activities. We also found in the previous study that the oral administration of heat-killed Lactobacillus plantarum NRIC0380 induced CD4(+)CD25(+)Foxp3(+) cells (Treg cells). We examine in this present study the influence of NRIC0380 on the function of intestinal dendritic cells (DCs) in vitro and in vivo. The aldehyde dehydrogenase (ALDH) activity was significantly induced in DCs obtained from the mesenteric lymph node (MLN) by culturing with NRIC0380. The oral administration of NRIC0380 also significantly increased ALDH-positive DCs in MLN. NRIC0380 significantly enhanced the production of TGF-ß from MLN cells in vitro. These effects were not apparent in cells from the Peyer's patch (PP) and spleen (SPL). NRIC0380 also significantly enhanced the expression of B7-H1 on DCs of all organs in vitro. The effects of NRIC0380 on DCs, especially those located in MLN, might be involved in its function to induce Treg cells.

Determination of strain-specific wall teichoic acid structures in Lactobacillus plantarum reveals diverse α-D-glucosyl substitutions and high structural uniformity of the repeating units.

The structural diversity of wall teichoic acid (WTA) was investigated using biochemical and NMR analyses among 19 strains of Lactobacillus plantarum, of which seven were previously established to contain a glycerol-type backbone, whereas the remaining 12 strains possess ribitol-containing WTA. Despite the fact that the WTAs consisted of identical components, namely phosphoric acid, alditol (glycerol or ribitol) and glucose, comparative analysis of the (1)H and (13)C NMR spectra indicated the presence of six different structures, based on the observed differences in the anomeric signals of glucose residues. To determine the six WTA structures, their repeating units were prepared by alkaline hydrolysis, followed by fractionation on HPLC, and analysis by NMR spectroscopy using synthetic molecules as a reference. The structures of the six isolates were established as 1-α-D-glucosyl-sn-glycerol 3-phosphate, 1-α-D-kojibiosyl-sn-glycerol 3-phosphate, 1-α-D-nigerosyl-sn-glycerol 3-phosphate, 4-α-D-kojibiosylribitol 1-phosphate and 1,5-linked di-(2,4-di-α-D-glucosylribitol) phosphate. The backbone structures appeared to be 3,6'-linked poly(1-α-D-glucosyl-sn-glycerol phosphate) for the glycerol-type WTA and 1,5-linked poly(ribitol phosphate) for the ribitol-containing WTA. Moreover, in the analysis of the alkaline hydrolysates on HPLC, only single structures of repeating units were released from each WTA, indicating the high structural uniformity of the WTA in each strain. Notably, analyses of lipoteichoic acid isolated from representative strains harbouring the six different WTAs revealed the universal presence of a 1,3-linked poly(glycerol phosphate) chain, substituted at C-2 of the glycerol residues with glucose residues. These findings provide fundamental information on WTA structural variability in Lb. plantarum, which seems likely to play a pivotal role in the physiology of this bacterial species.

Characterization and emended description of Lactobacillus kunkeei as a fructophilic lactic acid bacterium.

Lactobacillus kunkeei is an inhabitant of fructose-rich niches and is a potential member of the fructophilic lactic acid bacteria. In the present study, the phylogenetic and biochemical characteristics of the type strain and eight isolates of L. kunkeei, originating from wine, flowers and honey, were studied. The nine isolates, including the type strain, formed a well-defined phylogenetic subcluster based on the analysis of 16S rRNA gene sequences. The subcluster was not closely related to other subclusters in the Lactobacillus phylogenetic group. Biochemically, the eight new isolates showed typical fructophilic characteristics. The eight isolates grew poorly on glucose, but grew well on fructose. Good growth on glucose was only recorded in the presence of electron acceptors. The type strain of L. kunkeei differed from the other isolates only on the basis of poor growth on fructose. Although they belong to a group of obligately heterofermentative lactic acid bacteria, all nine isolates, including the type strain, produced almost equimolar amounts of lactic acid and acetic acid and very little ethanol from glucose. Eight of the isolates can thus be regarded as typical 'obligately' fructophilic lactic acid bacteria. Although the type strain of L. kunkeei was phenotypically slightly different from the other isolates, it possessed several important fructophilic characteristics. On the basis of the evidence gathered in this study, the type strain of L. kunkeei is recognized as a member of the 'obligately' fructophilic lactic acid bacteria.

Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching.

BACKGROUND: Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. RESULTS: Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. CONCLUSIONS: The study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality.

Lactobacillus plantarum NRIC1832 enhances IL-10 production from CD4⁺ T cells in vitro.

The anti-inflammatory effect of lactic acid bacteria (LAB) has been reported in several models for autoimmune diseases. It was considered in those studies that IL-10 induced by LAB might have been involved in such anti-inflammatory activity. We therefore examined the IL-10-inducing activity of LAB in detail by using an in vitro culture system of DO11.10 splenocytes. Most strains of LAB tested in this study increased IL-10 production. A further study using one of the tested strains with potent immune-regulatory activity, Lactobacillus plantarum NRIC1832, showed that the enhanced IL-10 was mainly produced by T cells. However, this enhancement required several types of cells other than T cells. NRIC1832 enhanced IL-10 production after short-term exposure to T cells, but this effect diminished after long-term exposure, indicating that the enhancement of IL-10 production by NRIC1832 was temporary, in contrast to the enhancement of IFN-γ production which was still apparent after long-term exposure.

Isolation and identification of dieldrin-degrading Pseudonocardia sp. strain KSF27 using a soil-charcoal perfusion method with aldrin trans-diol as a structural analog of dieldrin.

We isolated a novel aerobic dieldrin-degrading bacterium from an enrichment culture in a soil-charcoal perfusion system. Enrichment culture using a soil-charcoal perfusion system was an effective way to obtain microorganisms that degrade recalcitrant compounds. The soil-charcoal perfusion was performed using aldrin trans-diol, which was a metabolite of dieldrin. Aldrin trans-diol had higher bioavailability (2.5 mg/l) than dieldrin (0.1-0.25 mg/l), therefore it is possible for microorganisms to utilize it as a substrate in soil. After 100 days of circulation and three exchanges of the medium, the enriched charcoal was harvested and a bacterium isolated. The isolate was designated as strain KSF27 and was found to be closely related to Pseudonocardia spp. as determined by 16S rRNA sequencing analysis. Strain KSF27 degraded aldrin trans-diol by 0.05 µmol/l from an initial concentration of 25.5 µmol/l. The metabolite of aldrin trans-diol was detected by HPLC/MS and determined to be aldrindicarboxylic acid based on retention time and the MS fragment. Moreover, strain KSF27 degraded dieldrin from 14.06 µmol/l to 2.01 µmol/l over a 10-day incubation at 30°C. This strain degraded dieldrin and other persistent organochlorine pesticides, such as α-endosulfan, ß-endosulfan, endosulfan sulfate, heptachlor, heptachlor epoxide and chlordecone.

Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers.

Five strains (Ryu1-2(T), Gon2-9, Ryu4-3, Nog8-1 and Aza1-1) of lactic acid bacteria were isolated from flowers in mountainous areas in Japan, Oze National Park, Iizuna mountain and the Nikko area. The five isolates were found to share almost identical (99.6-100 % similar) 16S rRNA gene sequences and were therefore deemed to belong to the same species. These isolates exhibited low levels of 16S rRNA gene sequence similarity to known lactic acid bacteria; the closest recognized relatives to strain Ryu1-2(T) were the type strains of Lactobacillus hilgardii (92.8 % similarity), Lactobacillus kefiri (92.7 %), Lactobacillus composti (92.6 %) and Lactobacillus buchneri (92.4 %). Comparative analyses of rpoA and pheS gene sequences demonstrated that the novel isolates did not show significant relationships to other Lactobacillus species. The strains were Gram-stain-positive, catalase-negative and homofermentative. The isolates utilized a narrow range of carbohydrates as sources of carbon and energy, including glucose and fructose. On the basis of phenotypic characteristics and phylogenetic data, these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus floricola sp. nov. is proposed. The type strain is Ryu1-2(T) ( = NRIC 0774(T)  = JCM 16512(T)  = DSM 23037(T)).

Fructobacillus tropaeoli sp. nov., a fructophilic lactic acid bacterium isolated from a flower.

A fructophilic lactic acid bacterium, designated strain F214-1(T), was isolated from a flower of Tropaeolum majus in South Africa. Based on phylogenetic analysis of 16S rRNA gene sequences, the strain formed a subcluster with Fructobacillus ficulneus and Fructobacillus pseudoficulneus and, based on recA gene sequences, the strain formed a subcluster with F. ficulneus. DNA-DNA hybridization studies showed that strain F214-1(T) was phylogenetically distinct from its closest relatives. Acid was produced from the fermentation of d-glucose, d-fructose and d-mannitol only. d-Fructose was the preferred sole carbon and energy source and was fermented more rapidly than d-glucose. Growth of the strain on d-glucose under anaerobic conditions was very weak but external electron acceptors such as oxygen and pyruvate enhanced growth on d-glucose. Lactic acid and acetic acid were produced from d-glucose in equimolar amounts. Ethanol was produced at very low levels, despite the strain's obligately heterofermentative metabolism. Based on these data, strain F214-1(T) represents a novel species of fructophilic bacteria in the genus Fructobacillus, for which the name Fructobacillus tropaeoli sp. nov. is proposed. The type strain is F214-1(T) ( = JCM 16675(T)  = DSM 23246(T)).

Pediococcus pentosaceus Sn26 inhibits IgE production and the occurrence of ovalbumin-induced allergic diarrhea in mice.

We investigated the anti-allergic effect of a new strain (Pediococcus pentosaceus Sn26, the Sn26 strain) among 59 strains isolated from Japanese fermented vegetable pickles, the Sunki pickle. The Sn26 strain increased Th1 type cytokine (IL-12 and IFN-gamma) production of Peyer's patch (PP) cells in BALB/c mice, improved the Th1/Th2 balance, and inhibited IgE production of splenocytes of ovalbumin (OVA)-induced allergic diarrheic mice. Next we demonstrated, by neutralizing IL-12 and IFN-gamma, that the Sn26 strain first induced IL-12, that IL-12 induced IFN-gamma, and that decreases in IL-4 and IgE production followed. Furthermore, oral administration of the Sn26 strain decreased serum OVA-specific IgE levels and ameliorated the appearance of diarrhea in OVA-induced allergic diarrheic mice. Based on these results, it was assumed that oral administration of the Sn26 strain ameliorated type-1 allergies through improvement of the Th1/Th2 balance and decreases in IgE production.

Comparison of components and synthesis genes of cell wall teichoic acid among Lactobacillus plantarum strains.

The contents, components, and synthesis genes of cell wall teichoic acid (WTA) in 18 strains of Lactobacillus plantarum were compared. The WTA of each strain was classified by its components as being either the glycerol- or the ribitol-type. The different strains in the WTA type showed marked differences also in two gene regions, tagD1-tagF2 and lp_1816-tagB2, as for the presence or absence, nucleotide sequences, and transcriptional activities. Our results clearly showed that the tagD1-tagF2 and lp_1816-tagB2 regions contained the synthesis genes of the WTA backbone of L. plantarum. We verified that the genes in the tagD1-tagF2 region were involved in the synthesis of the glycerol-type backbone. Furthermore, we propose that the genes in the lp_1816-tagB2 region were tarI, tarJ, tarK, and tarL, which are involved in the synthesis of the ribitol-type backbone.

Characterisation of the bacterial community structures of sunki, a traditional unsalted pickle of fermented turnip leaves.

The bacterial community structure in 29 naturally fermented samples of sunki, an unsalted lactic-fermented pickle in Japan, was determined by 16S rRNA gene-targeted metagenomic analysis. The data revealed that genus Lactobacillus was dominant in all samples and various bacterial species, related to Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus buchneri, Lactobacillus fermentum, Lactobacillus reuteri, Lactobacillus crispatus, Lactobacillus intestinalis, and Lactobacillus gasseri, showed a range of dominance depending on the samples. Comparative analysis of the bacterial composition by principal coordinate analysis and hierarchical clustering classified the varied bacterial composition of the 29 samples into three types of bacterial community structure. These types comprised lactobacilli belonging to different phylogenetic groups: type A had a certain ratio of Lactobacillus fermentum (70.3-22.1%, average 41.2%) in combination with several species belonging to Lactobacillus delbrueckii-phylogenetic group, type B comprised remarkably high levels of species Lactobacillus delbrueckii (average 89.5%), and type C had combinations of species belonging to Lactobacillus plantarum- and Lactobacillus buchneri-phylogenetic groups. Interestingly, these types differed in the compositional profiles of water-soluble and volatile compounds, and statistically significant differences were observed in the levels of acetic acid, succinic acid, ethanol, ethyl acetate, glutamic acid, γ-aminobutyric acid, and isovaleraldehyde. Furthermore, metabolomic analysis revealed a correlation of Lactobacillus fermentum dominance with pH value and lactic and acetic acid levels, with high R values of 0.643, -0.642, and 0.528, respectively. The data reported in this study showed the characteristics of the bacterial composition in the unsalted sunki pickle and its potential relationship with the compositional profile.