Lactobacillus kimchii sp. nov., a new species from kimchi

The Role of Diet as a Modulator of the Inflammatory Process in the Neurological Diseases

Neurological diseases are recognized as major causes of disability and mortality worldwide. Due to the dynamic progress of diseases such as Alzheimer’s disease (AD), Parkinson’s Disease (PD), Schizophrenia, Depression, and Multiple Sclerosis (MD), scientists are mobilized to look for new and more effective methods of interventions. A growing body of evidence suggests that inflammatory processes and an imbalance in the composition and function of the gut microbiome, which play a critical role in the pathogenesis of various neurological diseases and dietary interventions, such as the Mediterranean diet the DASH diet, or the ketogenic diet can have beneficial effects on their course. The aim of this review was to take a closer look at the role of diet and its ingredients in modulating inflammation associated with the development and/or progression of central nervous system diseases. Presented data shows that consuming a diet abundant in fruits, vegetables, nuts, herbs, spices, and legumes that are sources of anti-inflammatory elements such as omega-3 fatty acids, polyphenols, vitamins, essential minerals, and probiotics while avoiding foods that promote inflammation, create a positive brain environment and is associated with a reduced risk of neurological diseases. Personalized nutritional interventions may constitute a non-invasive and effective strategy in combating neurological disorders.

Bacterial Communities in Lanna Phak-Gard-Dong (Pickled Mustard Green) from Three Different Ethnolinguistic Groups in Northern Thailand

The Lanna region, the main part of northern Thailand, is a place of ethnic diversity. In this study, we investigated phak-gard-dong (PGD), or pickled mustard green (Brassica juncea L. Czern.), for its beneficial bacteria content and to analyse the variations in bacterial compositions among the PGD of three different ethnolinguistic groups, the Karen, Lawa, and Shan. DNA was extracted from the PGD pickled brine, and 16S rRNA gene Illumina sequencing was performed. Metagenomic data were analysed and the results demonstrated that the dominant bacterial species were Weissella (54.2%, 65.0%, and 10.0%) and Lactobacillus (17.5%, 5.6%, and 79.1%) in the PGD of the Karen, Lawa, and Shan, respectively. Pediococcus was found only in the PGD of the Karen and Shan. Bacterial communities in PGD of the Lawa were distinctive from the other ethnic groups, both in the alpha and beta diversity, as well as the predicted functions of the bacterial communities. In addition, overall network analysis results were correlated to bacterial proportions in every ethnic PGD. We suggest that all ethnic PGDs have the potential to be a good source of beneficial bacteria, warranting its conservation and further development into health food products.

Microbial food: microorganisms repurposed for our food

Sustainable food production is a key to solve complicated and intertwined issues of overpopulation, climate change, environment and sustainability. Microorganisms, which have been routinely consumed as a part of fermented foods and more recently as probiotic dietary supplements, can be repurposed for our food to present a sustainable solution to current food production system. This paper begins with three snapshots of our future life with microbial foods. Next, the importance, possible forms, and raw materials (i.e. microorganisms and their carbon and energy sources) of microbial foods are discussed. In addition, the production strategies, further applications and current limitations of microbial foods are discussed.

Purification, Structural Characteristics, and Biological Activities of Exopolysaccharide Isolated From Leuconostoc mesenteroides SN-8

In this study, a novel exopolysaccharide (EPS) was extracted from Leuconostoc mesenteroides Shen Nong's (SN)-8 which can be obtained from Dajiang. After the purification step, EPS-8-2 was obtained with molecular weights of 1.46 × 105 Da. The structural characterization of EPS indicated that the EPS belonged to the class polysaccharide, mainly composed of glucan and also contained certain mannose residues that were found to be connected by α-1,6 glycosidic bonds. Moreover, the results demonstrated that EPS displayed a significant capacity to scavenge free radical to some extent, and this anti-oxidant potential was found to be concentration dependent. The results further revealed that EPS displayed a significant inhibitory potential on the growth of HepG2 cells by promoting apoptosis and induced cell cycle arrest in G1 and G2 phases. Overall, these results suggested that EPS can be explored as a possible anti-cancer agent.

Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches

Kimchi is a traditional Korean fermented food prepared via spontaneous fermentation by various microorganisms originating from vegetables such as kimchi cabbage, radishes, and garlic. Recent advances in meta-omics approaches that integrate metataxonomics, metagenomics, metatranscriptomics, and metabolomics have contributed to explaining and understanding food fermentation processes. Kimchi microbial communities are composed of majorly lactic acid bacteria such as Leuconostoc, Lactobacillus, and Weissella and fewer eukaryotic microorganisms and kimchi fermentation are accomplished by complex microbial metabolisms to produce diverse metabolites such as lactate, acetate, CO₂, ethanol, mannitol, amino acids, formate, malate, diacetyl, acetoin, and 2, 3-butanediol, which determine taste, quality, health benefit, and safety of fermented kimchi products. Therefore, in the future, kimchi researches should be systematically performed using the meta-omics approaches to understand complex microbial metabolisms during kimchi fermentation. KEY POINTS: • Spontaneous fermentation by raw material microbes gives kimchi its unique flavor. • The kimchi microbiome is altered by environmental factors and raw materials. • Through the multi-omics approaches, it is possible to accurately analyze the diversity and metabolic characteristics of kimchi microbiome and discover potential functionalities.

Lactobacillus suantsaicola sp. nov. and Lactobacillus suantsaiihabitans sp. nov., isolated from suan-tsai, a traditional fermented mustard green product of Taiwan

Four Gram-stain-positive strains, R7T, R11, R19T and R27, were isolated from suan-tsai, a traditional fermented mustard green product of Taiwan. Cells were rod-shaped, non-motile, non-haemolytic, asporogenous, facultatively anaerobic, heterofermentative, and did not exhibit catalase and oxidase activities. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences demonstrated that these novel strains were members of the genus Lactobacillus . 16S rRNA and the concatenated pheS and rpoA gene sequence similarities between strains R7T and R11, and strains R19T and R27 were very high (>99.8 % similarity), respectively. On the basis of 16S rRNA gene sequence similarities, the type strains of Lactobacillus paralimentarius (98.5 %), Lactobacillus kimchii (98.5 %), Lactobacillus alimentarius (98.1 %) and Lactobacillus bobalius (98.1 %) were the closest neighbours to strains R7T and R11, and the type strains of Lactobacillus brevis (98.9 %), Lactobacillus cerevisiae (98.4 %), Lactobacillus hammesii (98.4 %), Lactobacillus koreensis (98.4 %) and Lactobacillus yonginensis (98.0 %) were the closest neighbours to strains R19T and R27, respectively. The average nucleotide identity values of R7T and R19T with the closely related type strains were 78.9–80.1% and 75.7–80.5 %, respectively. The digital DNA–DNA hybridization values were 22.8–23.6% and 21.0–23.1 %, respectively. Phenotypic and genotypic test results demonstrated that these strains represent two novel species of the genus Lactobacillus , for which the name Lactobacillus suantsaicola sp. nov. (R7T=BCRC 81127T=NBRC 113530T) and Lactobacillus suantsaiihabitans sp. nov. (R19T=BCRC 81129T=NBRC 113532T) are proposed.

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

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

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex

The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences.

There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence.

IMPORTANCE The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences.

Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

Intake Trends of Red Meat, Alcohol, and Fruits and Vegetables as Cancer-Related Dietary Factors from 1998 to 2009

Objectives

Cancer is the leading cause of death worldwide, and cancer incidence and mortality have been increasing steadily in South Korea. This study aimed to examine the change in consumption of three cancer-related dietary factors—red meat, alcohol, and fruits/vegetables, and to evaluate consumption of these dietary factors among Koreans according to the criteria from the recommendations of the World Cancer Research Fund/American Institute of Cancer Research.

Methods

Consumption of red meat, alcoholic beverages, and fruits and vegetables was calculated from the 24-hour recall data of 36,486 individuals older than 20 years who were selected from the Korea National Health and Nutrition Examination Survey 1998–2009. The intake adequacy of these three factors was evaluated by the recommended criteria of the World Cancer Research Fund/American Institute of Cancer Research report.

Results

The mean red meat intake in the men in their 20s increased sharply (from 91.6 g to 111.3 g, p < 0.05). The mean alcohol intake increased continuously in men (from 10.3 g to 20.0 g, p < 0.05) and women (from 1.5 g to 3.5 g, p < 0.05). The mean fruit/vegetable intake decreased in the 21–29–year age group (from 349.4 g to 306.7 g in men; from 393.3 g to 292.5 g in women; p < 0.05). The percentage of individuals who did not meet the intake criteria for the three cancer-related dietary factors was especially high, and the percentage increased over 10 years in those in their 20s (p < 0.05).

Conclusion

We confirmed that intakes of red meat, alcoholic drink, and fruits and vegetables have moved toward a negative direction in both men and women in their 20s.

Comparative study on the epidemiological aspects of enterohemorrhagic Escherichia coli infections between Korea and Japan, 2006 to 2010

BACKGROUND/AIMS

To compare the epidemiological aspects of enterohemorrhagic Escherichia coli (EHEC) between Korea and Japan by analyzing the current state of EHEC infection outbreaks and related risk factors.

METHODS

We investigated the epidemiological aspects of EHEC infection cases between Korea and Japan from 2006 to 2010. The following factors were analyzed: national prevalence rate (PR), regional prevalence rate, epidemic aspects (i.e., Cases related to gender), male to female morbidity ratio, age, and seasonal distribution.

RESULTS

In total, there were 254 cases of EHEC with an average PR of 0.11 per 100,000 populations in Korea from 2006 to 2010. During the same period in Japan, there were 20,883 cases of EHEC with an average PR of 3.26 per 100,000 populations. The PR in Japan was significantly higher than that in Korea (p < 0.01). In both countries, more females than males had EHEC infections, with the highest incidence of infections (> 50%) observed for individuals younger than 9 years. EHEC is an emerging zoonosis and may be caused by consumption of raw or undercooked meat products from ruminants.

CONCLUSIONS

This study provides a quantitative analysis of the epidemiological aspects and risk factors of EHEC infections in Korea and Japan and will provide insight on effective future strategies to reduce these infections.

Immunomodulatory effects of kimchi in chinese healthy college students: a randomized controlled trial

This study examined the potential immunomodulatory effects of Kimchi, a traditional fermented Korean vegetable, in healthy Chinese college students. The four-week clinical-trial (randomized, open-label, prospective, controlled) was followed by a one week wash-out period. Healthy Chinese college students (over 20 years of age with a body mass index of 18.5-23.0 kg/m²) volunteered for this study. Forty-three students were randomly classified into two groups, Kimchi (n = 21, supplemented with 100 g of Kimchi per day) or non-Kimchi (n = 22, supplemented with 100 g of radish per day, control) groups. During the four-week intervention period, students were asked to maintain their usual diet and activity, and instructed not to take any medications, functional food products, or dietary supplements. Anthropometrics, nutritional intake, and blood immune parameters (lymphocyte subsets, cytokines, and immunoglobulins) were measured before and after the four weeks of intervention. Thirty-nine students (19 in the Kimchi group, 20 in the non-Kimchi group) finished the study. After the intervention, no significant changes were observed in lymphocyte subsets (T-cell, B-cell, NK cell), pro-inflammatory cytokines (IL-6, TNF-α), anti-inflammatory cytokines (IL-4 and IL-10), and immunoglobulins (Ig A, G, and M) between groups in either the Kimchi or non-Kimchi. These results suggest that the short-term consumption of Kimchi has no immunomodulatory effects in healthy Chinese college students.

Lactobacillus kimchiensis sp. nov., isolated from a fermented food

A novel bacterium was isolated from a traditional fermented food, kimchi. The morphology, physiology, biochemical properties and 16S rRNA gene sequence of strain L133T were studied. Strain L133T was Gram-reaction-positive, catalase-negative and homofermentative, with rod-shaped cells that formed cream colonies. Cells grew in the presence of 0–5 % (w/v) NaCl (optimum, 1–2 %), at pH 5.0–9.0 (optimum, pH 7.0–8.0) and at 15–37 °C (optimum, 25 °C). Comparative 16S rRNA gene and pheS sequence analysis of strain L133T indicated that the strain belonged to the genus Lactobacillus . The major fatty acids were identified as C18 : 1ω9c, C16 : 0 and C18 : 0, and the cell wall contained peptidoglycan of the l-Lys–d-Asp type. DNA–DNA relatedness values between strain L133T and related species were below 11±0.4 %. The DNA G+C content of strain L133T was 35.7 mol%. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain L133T and other species of the genus Lactobacillus . Based on these analyses, strain L133T is proposed to be a novel species of the genus Lactobacillus , named Lactobacillus kimchiensis. The type strain is L133T ( = KACC 15533T = JCM 17702T = DSM 24716T).

Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius

Characterization and identification of strain CW 1 ( = JCM 17161) isolated from corn silage were performed. Strain CW 1 was a Gram-positive, catalase-negative and homofermentative rod that produced the dl-form of lactic acid. This strain exhibited more than 99.6 % 16S rRNA gene sequence similarity and greater than 82 % DNA–DNA reassociation with type strains of Lactobacillus kimchii , L. bobalius and L. paralimentarius . To clarify the taxonomic positions of these type strains, phenotypic characterization, 16S rRNA gene sequencing, ribotyping and DNA–DNA relatedness were examined. The three type strains displayed different l-arabinose, lactose, melibiose, melezitose, raffinose and N-acetyl-β-glucosaminidase fermentation patterns. Phylogenetic analysis showed that L. paralimentarius is a closer neighbour of L. kimchii and L. bobalius , sharing 99.5–99.9 % 16S rRNA gene sequence similarity, which was confirmed by the high DNA–DNA relatedness (≥82 %) between L. paralimentarius JCM 10415T, L. bobalius JCM 16180T and L. kimchii JCM 10707T. Therefore, it is proposed that L. kimchii and L. bobalius should be reclassified as later synonyms of L. paralimentarius .

Controlled fermentation of kimchi using naturally occurring antimicrobial agents

Kimchi is a traditional Korean fermented food. Since it ferments continuously during distribution and storage, the extension of shelf life by preventing over-acidification is a major concern in the kimchi industry. One of the most frequently attempted ways to delay fermentation is to add naturally occurring antimicrobial agents. Many researchers have investigated ways to delay over-acidification by adding minor ingredients, fruits or fruit seed extracts, extracts of medicinal herbs, culinary herbs and spices, and other miscellaneous substances to kimchi. The addition of naturally occurring antimicrobial agents may enhance the acceptability of kimchi to consumers over a longer period of time but may also have a disadvantage in that it may cause changes in sensory quality, especially if added in large amounts. To avoid undesirable sensory changes, application of hurdle technologies (i.e., multifactor preservative systems) which involve using combinations of low amounts of various naturally occurring antimicrobial agents as ingredients should be explored with the goal of controlling fermentation. If synergistic or additive antimicrobial effects can be achieved using small amounts of a combination of natural agents, changes in sensory qualities will be minimized, thereby prolonging shelf life. Research findings summarized in this review provide a basis for developing effective hurdle technologies using naturally occurring antimicrobial agents to extend shelf life of kimchi and perhaps other types of traditional fermented foods.

Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi

A Gram-staining-positive, non-motile and non-spore-forming lactic acid bacterium, designated strain M2(T), was isolated from fermented brown algae (Undaria pinnatifida) kimchi in South Korea. Cells of the isolate were facultatively anaerobic ovoids and showed catalase- and oxidase-negative reactions. Growth of strain M2(T) was observed at 4-35 °C and at pH 5.0-9.0. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M2(T) belonged to the genus Leuconostoc and was most closely related to Leuconostoc inhae IH003(T), Leuconostoc kimchii IH25(T), Leuconostoc gasicomitatum LMG 18811(T), Leuconostoc gelidum DSM 5578(T), Leuconostoc palmae TMW2.694(T) and Leuconostoc holzapfelii BFE 7000(T) with 98.9 %, 98.8 %, 98.8 %, 98.7 %, 98.5 % and 98.2 % sequence similarity, respectively. DNA-DNA hybridization values between strain M2(T) and Leuconostoc inhae KACC 12281(T), Leuconostoc kimchii IH25(T), Leuconostoc gelidum KACC 12256(T), Leuconostoc gasicomitatum KACC 13854(T), Leuconostoc palmae DSM 21144(T) and Leuconostoc holzapfelii DSM 21478(T) were 13.8±3.2 %, 14.3±3.4 %, 9.9±1.0 %, 13.2±0.8 %, 22.4±4.9 % and 16.2±4.6 %, respectively, which allowed differentiation of strain M2(T) from the closely related species of the genus Leuconostoc. On the basis of phenotypic and molecular properties, strain M2(T) represents a novel species in the genus Leuconostoc, for which the name Leuconostoc miyukkimchii sp. nov. is proposed. The type strain is M2(T) ( = KACC 15353(T)  = JCM 17445(T)).

Lactobacillus kimchicus sp. nov., a β-glucosidase-producing bacterium isolated from kimchi

A Gram-reaction-positive, non-spore-forming, rod-shaped, non-motile, β-glucosidase-producing bacterium, designated DCY51T, was isolated from kimchi, a Korean fermented vegetable food. 16S rRNA gene sequence analysis revealed that strain DCY51T belonged to the genus Lactobacillus and exhibited highest 16S rRNA gene sequence similarity with Lactobacillus paracollinoides AB 74 (96.9 %), L. similis JCM 2765T (96.9 %), L. collinoides JCM 1123T (96.7 %) and L. hilgardii DSM 20176T (95.5 %). Subsequently, pheS sequence analysis confirmed that strain DCY51T formed a distinct lineage within the Lactobacillus plantarum group. The major polar lipid of strain DCY51T was phosphatidylethanolamine and minor amounts of phosphatidylglycerol and diphosphatidylglycerol were found. Phenotypic characteristics and DNA–DNA relatedness indicated that strain DCY51T was clearly distinguished from other type strains of species of the genus Lactobacillus. A novel species, Lactobacillus kimchicus sp. nov., is proposed, with type strain DCY51T ( = KCTC 12976T  = JCM 15530T).

Adaptability of lactic acid bacteria and yeasts to sourdoughs prepared from cereals, pseudocereals and cassava and use of competitive strains as starters

The adaptability of lactic acid bacteria (LAB) and yeasts to sourdoughs prepared from cereals, pseudocereals and cassava was investigated using PCR-DGGE and bacteriological culture combined with rRNA gene sequence analysis. Sourdoughs were prepared either from flours of the cereals wheat, rye, oat, barley, rice, maize, and millet, or from the pseudocereals amaranth, quinoa, and buckwheat, or from cassava, using a starter consisting of various species of LAB and yeasts. Doughs were propagated until a stable microbiota was established. The dominant LAB and yeast species were Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus paralimentarius, Lactobacillus plantarum, Lactobacillus pontis, Lactobacillus spicheri, Issatchenkia orientalis and Saccharomyces cerevisiae. The proportion of the species within the microbiota varied. L. paralimentarius dominated in the pseudocereal sourdoughs, L. fermentum, L. plantarum and L. spicheri in the cassava sourdough, and L. fermentum, L. helveticus and L. pontis in the cereal sourdoughs. S. cerevisiae constituted the dominating yeast, except for quinoa sourdough, where I. orientalis also reached similar counts, and buckwheat and oat sourdoughs, where no yeasts could be detected. To assess the usefulness of competitive LAB and yeasts as starters, the fermentations were repeated using flours from rice, maize, millet and the pseudocereals, and by starting the dough fermentation with selected dominant strains. At the end of fermentation, most of starter strains belonged to the dominating microbiota. For the rice, millet and quinoa sourdoughs the species composition was similar to that of the prior fermentation, whereas in the other sourdoughs, the composition differed.

Lactobacillus tucceti sp. nov., a new lactic acid bacterium isolated from sausage

Following the application of several molecular techniques strain R 19c, isolated from sausage by Reuter in 1970 and deposited at the DSMZ as Lactobacillus sp., has been identified as pertaining to a new species. It showed singular ISR-DdeI and ISR-HaeIII profiles that allowed its differentiation from 68 lactic acid bacteria reference strains analyzed. Phylogenetic analysis based on 16S rRNA gene sequences places this strain in the genus Lactobacillus within the Lactobacillus alimentarius group. Species L. versmoldensis is the closest phylogenetic neighbor with 96.3% sequence similarity. DNA-DNA hybridization experiments confirmed the independent status at species level of this strain. Species-specific primers for PCR detection of this new species have been developed. Phenotypically it can be distinguished from the closest relative L. versmoldensis by several traits such as the peptidoglycan type (L-Lys-Gly-D-Asp), acid production from L-rhamnose, D-mannitol and L-fucose and its inability to ferment d-galactose, d-melibiose and d-sucrose. The name Lactobacillus tucceti sp. nov. is proposed with strain R 19c(T) (=DSM 20183(T)= CECT 5920(T)) as the type strain.

Diversity of a stable enrichment culture which is useful for silage inoculant and its succession in alfalfa silage

Alfalfa is a kind of forage that is difficult to ensile for good quality. Therefore, inoculants are always used to enhance the preservation of alfalfa silage. Through continuous restricted subcultivation, a lactic acid bacteria community (Al2) was selected from well-fermented alfalfa silage, which sharply decreased the pH level and produced a large amount of lactic acid. The adding of Al2 to alfalfa at ensiling resulted in a more rapid drop in pH and higher levels of lactic acid, and it also reduced the ammonia-nitrogen content significantly (P < 0.01). Plate isolation, denaturing gradient gel electrophoresis (DGGE) and the construction of a 16S rRNA gene clone library were used to identify the composition diversity of the Al2 community; seven strains were detected in the community, the predominant strain belonging to Lactobacillus plantarum. Samples of alfalfa silages of duration 0, 2, 5, 10, 20 and 30 days were studied with DGGE analysis. The DGGE band patterns of Al2-treated and non inoculated were rather different, and the components of Al2 were the dominant bacteria in Al2-treated silages, especially L. plantarum, while Pediococcus pentosaceaus was predominant in naturally fermented alfalfa silage.

Lactobacillus nantensis sp. nov., isolated from French wheat sourdough

A polyphasic taxonomic study of the bacterial flora isolated from traditional French wheat sourdough, using phenotypic characterization and phylogenetic as well as genetic methods, revealed a consistent group of isolates that could not be assigned to any recognized species. These results were confirmed by randomly amplified polymorphic DNA and amplified fragment length polymorphism fingerprinting analyses. Cells were Gram-positive, homofermentative rods. Comparative 16S rRNA gene sequence analysis of the representative strain LP33T indicated that these strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives Lactobacillus farciminis, Lactobacillus alimentarius, Lactobacillus paralimentarius and Lactobacillus mindensis. DNA–DNA reassociation experiments with the three phylogenetically closest Lactobacillus species confirmed that LP33T (=DSM 16982T=CIP 108546T=TMW 1.1265T) represents the type strain of a novel species, for which the name Lactobacillus nantensis sp. nov. is proposed.

Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis

Kimchi is a traditional Korean food fermented from a variety of vegetables. We elucidated the microbial community structure of five commercially produced kimchis made from Chinese cabbage by examining culture-independent 16S rRNA gene clone libraries. Most of the clones (347 out of 348) belonged to lactic acid bacteria and included several species of the genera Lactobacillus, Leuconostoc and Weissella. Weissella koreensis was found in all the samples and predominated in three of them (42.6-82%). Leuconostoc gelidum, Leuconostoc gasicomitatum and Lactobacillus sakei were common in the remaining kimchi clone libraries (>34%). The composition of bacterial phylotypes in kimchi varied between samples. Our approach revealed different community structures from those reported in previous culture-dependent studies based on phenotypic identification methods. The culture-independent method used here proved to be efficient and accurate and showed that the bacterial communities in kimchi differ from those in other fermented vegetable foods.

Bacterial population in traditional sourdough evaluated by molecular methods

AIMS

To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches.

METHODS AND RESULTS

Forty-five LAB isolates were identified both by phenotypic and molecular methods. The restriction fragment length polymorphism and 16S ribosomal DNA gene sequencing gave evidence of a variety of species with the dominance of Lactobacillus sanfranciscensis and Lactobacillus pentosus, in all sourdoughs tested. Culture-independent method, such as denaturing gradient gel electrophoresis (DGGE) of the V6-V8 regions of the 16S rDNA, was applied for microbial community fingerprint. The DGGE profiles revealed the dominance of L. sanfranciscensis species. In addition, Lactobacillus-specific primers were used to amplify the V1-V3 regions of the 16S rDNA. DGGE profiles flourished the dominance of L. sanfranciscensis and Lactobacillus fermentum in the traditional sourdoughs, and revealed that the closely related species Lactobacillus kimchii and Lactobacillus alimentarius were not discriminated.

CONCLUSIONS

Lactobacillus-specific PCR-DGGE analysis is a rapid tool for rapid detection of Lactobacillus species in artisanal sourdough.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reports a characterization of Lactobacillus isolates from artisanal sourdoughs and highlights the value of DGGE approach to detect uncultivable Lactobacillus species.

Klebsiella singaporensis sp. nov., a novel isomaltulose-producing bacterium

Cells of strain LX3(T), isolated from soil, were Gram-negative, facultatively anaerobic, non-motile, capsulated and non-endospore-forming straight rods, able to grow at 10 degrees C, unable to produce gas from lactose at 45 degrees C and unable to produce indole. The isolate converted sucrose to isomaltulose and did not produce detectable glucose by-products. The G+C content of the DNA was 56.4 mol%. Furthermore, comparison of 16S rRNA and rpoB gene sequences showed that the isolate clearly belongs to the genus Klebsiella. The closest phylogenetic relative was Klebsiella pneumoniae, there being 99.3 and 97.5 % similarity in 16S rRNA and rpoB gene sequences, respectively. DNA-DNA hybridization analysis demonstrated a very low level of relatedness to other members of the genus Klebsiella, indicating that the isolated strain and other species in the genus Klebsiella were not related at the species level. The isolate could be differentiated from other previously described members of the genus Klebsiella on the basis of phenotypic differences and 16S rRNA and rpoB gene sequence divergence, together with DNA-DNA reassociation data. Therefore, it is proposed that strain LX3(T) (=DSM 16265(T)=JCM 12419(T)) should be classified as the type strain of a novel species of genus Klebsiella, Klebsiella singaporensis sp. nov.

Polyphasic study of wine Lactobacillus strains: taxonomic implications

One hundred and seventy-eight lactobacilli isolated from wine were characterized by a polyphasic approach. Strains were phenotypically identified at genus and species level by classical tests including the analysis of cell morphology, homo/heterofermentative character, sugar fermentation patterns, growth at different temperatures and the optical nature of the isomer of lactic acid produced from glucose. Molecular techniques such as random amplification of polymorphic DNA (RAPD), amplified 16S rDNA restriction analysis (16S-ARDRA), PFGE-RFLP and ribotyping were used to characterize strains, and their potential for identification and/or typing was evaluated. The information obtained with these techniques was processed with the BioNumerics software in order to analyse relationships existing between isolated strains and various reference species of the genus. Then, taxonomic dendrograms were obtained, and this information allowed the proposal of molecular procedures suitable for the identification and typing of these wine micro-organisms. The techniques useful for both identification and typing were RAPD and ribotyping, while 16S-ARDRA was only useful for identification and PFGE-RFLP only for typing purposes. The wine strains were identified as Lactobacillus brevis (19 strains), Lactobacillus collinoides (2 strains), Lactobacillus hilgardii (71 strains), Lactobacillus paracasei (13 strains), Lactobacillus pentosus (2 strains), Lactobacillus plantarum (34 strains) and Lactobacillus mali (10 strains).

The Depletion of Sodium Nitrite by Lactic Acid Bacteria Isolated from Kimchi

Nitrites, whether added or naturally occurring in foods, are potential carcinogens, and controlling their concentrations is important for maintaining a safe food supply. In this study we investigated the depletion of sodium nitrite (150 microg/mL) during the fermentation in Lactobacilli MRS broth at 5, 10, 15, 20, 25, 30, and 36 degrees C by lactic acid bacteria (LAB-A, -B, -C, and -D) isolated from kimchi and Leuconostoc mesenteroides strain KCTC3100. The four species of lactic acid bacteria isolated from kimchi were identified as L. mesenteroides, and all produced depletion of less than 20% of sodium nitrite after 10 days of incubation at 5 degrees C. There was less than 40% depletion after 9 days at 10 degrees C, 86.4-92.8% after 7 days at 15 degrees C, 81.4-87.8% after 4 days and more than 90.0% after 5 days at 20 degrees C, 76.3-85.7% after 3 days and more than 90.0% after 5 days at 25 degrees C, and more than 90.0% after 2 days at 30 and 36 degrees C. The depletion by LAB isolates was similar or higher than that by L. mesenteroides strain KCTC3100, and in particular, the LAB-D strain showed the highest depletion effect of all the strains tested, up to 15 degrees C. From these results, the strains isolated from kimchi were very effective for the depletion of sodium nitrite at high temperature, and all sodium nitrite was depleted at the initial period of incubation (1-2 days) at 30 and 36 degrees C. But as the temperature was lowered, the depletion effect of sodium nitrite was decreased in all the strains tested from kimchi. This illustrates that the depletion of nitrite by each strain is subject to the influence of temperatures.

Lactobacillus versmoldensis sp. nov., isolated from raw fermented sausage

Lactobacillus versmoldensis sp. nov. (KU-3T) was isolated from raw fermented sausages. The new species was present in high numbers, and frequently dominated the lactic acid bacteria (LAB) populations of the products. 16S rDNA sequence data revealed that the isolates are closely related to the species Lactobacillus kimchii DSM 13961T, Lactobacillus paralimentarius DSM 13238T, Lactobacillus alimentarius DSM 20249T and Lactobacillus farciminis DSM 20184T. DNA-DNA reassociation data, however, clearly distinguished the new isolates from these species; they showed a low degree of DNA relatedness with the type strains of this group of phylogenetically closely related lactobacilli. These results warrant separate species status for strain KU-3T, for which the name Lactobacillus versmoldensis sp. nov. is proposed. The type strain is KU-3T (=DSM 14857T =NCCB 100034T =ATCC BAA-478T).

Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov

Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

The biodiversity of lactic acid bacteria in Greek traditional wheat sourdoughs is reflected in both composition and metabolite formation

Lactic acid bacteria (LAB) were isolated from Greek traditional wheat sourdoughs manufactured without the addition of baker's yeast. Application of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total cell protein, randomly amplified polymorphic DNA-PCR, DNA-DNA hybridization, and 16S ribosomal DNA sequence analysis, in combination with physiological traits such as fructose fermentation and mannitol production, allowed us to classify the isolated bacteria into the species Lactobacillus sanfranciscensis, Lactobacillus brevis, Lactobacillus paralimentarius, and Weissella cibaria. This consortium seems to be unique for the Greek traditional wheat sourdoughs studied. Strains of the species W. cibaria have not been isolated from sourdoughs previously. No Lactobacillus pontis or Lactobacillus panis strains were found. An L. brevis-like isolate (ACA-DC 3411 t1) could not be identified properly and might be a new sourdough LAB species. In addition, fermentation capabilities associated with the LAB detected have been studied. During laboratory fermentations, all heterofermentative sourdough LAB strains produced lactic acid, acetic acid, and ethanol. Mannitol was produced from fructose that served as an additional electron acceptor. In addition to glucose, almost all of the LAB isolates fermented maltose, while fructose as the sole carbohydrate source was fermented by all sourdough LAB tested except L. sanfranciscensis. Two of the L. paralimentarius isolates tested did not ferment maltose; all strains were homofermentative. In the presence of both maltose and fructose in the medium, induction of hexokinase activity occurred in all sourdough LAB species mentioned above, explaining why no glucose accumulation was found extracellularly. No maltose phosphorylase activity was found either. These data produced a variable fermentation coefficient and a unique sourdough metabolite composition.

Genotypic and phenotypic characterization of garlic-fermenting lactic acid bacteria isolated from som-fak, a Thai low-salt fermented fish product

AIMS

To evaluate the importance of garlic for fermentation of a Thai fish product, and to differentiate among garlic-/inulin-fermenting lactic acid bacteria (LAB) at strain level.

METHODS AND RESULTS

Som-fak was prepared by fermentation of a mixture of fish, salt, rice, sucrose and garlic. pH decreased to 4.5 in 2 days, but omitting garlic resulted in a lack of acidification. LAB were predominant and approximately one third of 234 isolated strains fermented garlic and inulin (the carbohydrate reserve in garlic). These strains were identified as Lactobacillus pentosus and Lact. plantarum. Randomly Amplified Polymorphic DNA (RAPD) analysis revealed one major RAPD type (29 strains) isolated from all stages of fermentation.

CONCLUSION

Garlic was essential for acidification of som-fak and garlic-fermenting strains constituted a significant, homogeneous part of the LAB flora.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study indicates the role of fructans (garlic/inulin) as carbohydrate sources for LAB. Fructan fermenters may have several biotechnological applications, for example, as probiotics.

Fermentation and microflora of plaa-som, a thai fermented fish product prepared with different salt concentrations

Plaa-som is a Thai fermented fish product prepared from snakehead fish, salt, palm syrup and sometimes roasted rice. We studied the effects of different salt concentrations on decrease in pH and on microflora composition during fermentation. Two low-salt batches were prepared, containing 6% and 7% salt (w/w) as well as two high-salt batches, containing 9% and 11% salt. pH decreased rapidly from 6 to 4.5 in low-salt batches, whereas in high-salt batches, a slow or no decrease in pH was found. Lactic acid bacteria (LAB) and yeasts were isolated as the dominant microorganisms during fermentation. LAB counts increased to 10(8)-10(9) cfu g(-1) and yeast counts to 10(7)-5 x 10(7) cfu g(-1) in all batches, except in the 11% salt batch, where counts were 1-2 log lower. Phenotypic tests, ITS-PCR, carbohydrate fermentations and 16S rRNA gene sequencing identified LAB isolates as Pediococcus pentosaceus, Lactobacillus alimentarius/farciminis, Weisella confusa, L. plantarum and Lactococcus garviae. The latter species was only isolated from high-salt batches. Phenotypic characteristics, ITS-PCR and carbohydrate assimilation identified 95% of the yeasts as Zygosaccharomyces rouxii. It is concluded that the fermentation of plaa-som is delayed by a salt-level of 9% due to an inhibition of LAB growth. The growth of Z. rouxii has no influence on the fermentation rate, but may contribute positively to the flavour development of the product.

Molecular typing techniques to characterize the development of a lactic acid bacteria community on vacuum-packaged beef

The development of a community of lactic acid bacteria from vacuum-packaged beef was investigated during a 6-week storage trial at 2 degrees C. The lactic acid bacteria population was monitored by using molecular techniques to identify a random sample of isolates at biweekly intervals during the storage trial. The polymerase chain reaction and a randomly amplified polymorphic DNA technique were used to identify and distinguish populations of lactic acid bacteria that developed during the storage trial. At week 0, the population of lactic acid bacteria was 3.5 log cfu/120 cm2 and by week 6, the population reached a maximum of 7.6 log cfu/120 cm2. A sampling from the week 0 population indicated a mixed community of Lactobacillus curvatus, Lactobacillus sakei and Leuconostoc spp. However, the sampling from week 6 indicated the population composition had changed to one where a single Leuconostoc strain predominated. This strain demonstrated antagonism towards the growth of other lactic acid bacteria isolated during the study. Additionally, the strain inhibited the growth of foodborne pathogens Escherichia coli O157:H7 and Listeria monocytogenes. DNA sequence data from the 16S rRNA gene suggested that the isolate may be a Leuconostoc gelidum strain.