Subspecies-level genome comparison of Lactobacillus delbrueckii

Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.

Short-length Homologous Region exhaustive Search algorithm (SHRS): A primer design algorithm for differentiating bacteria at the species, subspecies, or strain level based on a whole genome sequence

In fields such as the food industry, it is very important to identify target bacteria at the species level or lower for optimal product quality control. Bacteria identification at the subspecies or lower level requires time-consuming and high-cost analyses such as multi-locus sequence typing and amplified fragment length polymorphism analyses. Herein, we developed a primer design algorithm for precisely identifying bacteria based on a whole genome DNA sequence that is easy to apply. The algorithm designs primer sets that produce fragments from all input sequences and maximizes the differences in the amplicon size or amplicon sequence among input sequences. We demonstrate that the primer sets designed by the algorithm clearly classified six subspecies of Lactobacillus delbrueckii, and we observed that the resolution of the method is equal to that of a multi-locus sequence analysis. The algorithm allows the easy but precise identification of bacteria within a short time. (SHRS is available freely from PyPI under the MIT license.).

Genetic diversity of Lactobacillus delbrueckii isolated from raw milk in Hokkaido, Japan

Lactic acid bacteria (LAB) play important roles in acid production and flavor formation in fermented dairy products. Lactic acid bacteria strains with distinct characteristics confer unique features to products. Diverse LAB have been identified in raw milk and traditional fermented milk prepared from raw milk. However, little is known about LAB in raw milk in Japan. To preserve diverse LAB as potential starters or probiotics for future use, we have isolated and identified various kinds of LAB from raw milk produced in Japan. In this study, we focused on Lactobacillus delbrueckii, one of the most important species in the dairy industry. We identified L. delbrueckii subspecies isolated from raw milk in Hokkaido, Japan, by analyzing intraspecific diversity using 4 distinct methods, hsp60 cluster analysis, multilocus sequence analysis, core-genome analysis, and whole-genome analysis based on average nucleotide identity. The subspecies distribution and a new dominant subset of L. delbrueckii from raw milk in Japan were revealed. The discovery of new strains with different genotypes is important for understanding the geographic distribution and characteristics of the bacteria and further their use as a microbial resource with the potential to express unconventional flavors and functionalities. The strains identified in this study may have practical applications in the development of fermented dairy products.

Diversity of the type I-U CRISPR-Cas system in Bifidobacterium

The CRISPR-Cas system is widely distributed in prokaryotes and plays an important role in the adaptive immunity of bacteria and archaea. Bifidobacterium is an important component of the intestinal flora of humans and animals, and some species of this bacterium can be employed as food additives. However, the Bifidobacterium CRISPR-Cas system has not been fully elucidated to date. In this study, the genomes of 110 strains of Bifidobacterium were employed to research the diversity of the type I-U system. The 110 strains were divided into five groups according to the genes adjacent to the CRISPR locus, including group A, B, C, D and E. Strains in the intergroup had unique species classifications and MLST types. An evolutionary tree was constructed based on the conserved cas4/cas1 fusion gene. The results showed that group A had a different evolutionary branch compared with the other groups and had a relatively low spacer number. Notably, group B, C and E had exhibited ABC transporter regulators in the genes adjacent to the CRISPR locus. ABC transporters play important roles in the exocytosis of many antibiotics and are involved in horizontal gene transfer. This mechanism may have promoted the evolution of Bifidobacterium and the horizontal gene transfer of the type I-U system, which may have promoted the generation of system diversity. In summary, our results help to elucidate the role of the type I-U system in the evolution of Bifidobacterium.

Exploring the industrial potential of Lactobacillus delbrueckii ssp. bulgaricus by population genomics and genome-wide association study analysis

Lactobacillus delbrueckii ssp. bulgaricus is one of the most commonly used starter cultures for yogurt production. However, how its genetic background affects acid production capacity is unclear. This study investigated the industrial potential of L. delbrueckii ssp. bulgaricus using population genomics and GWAS analysis. To meet our goal, population genetics and functional genomics analyses were performed on 188 newly sequenced L. delbrueckii ssp. bulgaricus strains isolated from naturally fermented dairy products together with 19 genome sequences retrieved from the NCBI database. Four distinct clusters were identified, and they were correlated with the geographical sites where the samples were collected. The GWAS analysis about acidification fermentation results with sucrose-fortified reconstituted skim milk revealed a significant association between l-lactate dehydrogenase (lldD; Ldb2036) and the bacterial acid production rate. Our study has broadened the understanding of the population structure and genetic diversity of L. delbrueckii ssp. bulgaricus by identifying potential targets for further research, development, and use of lactic acid bacteria in the dairy industry.

Multilocus Sequence Typing of Leuconostoc mesenteroides Strains From the Qinghai-Tibet Plateau

Leuconostoc mesenteroides strains were a type of epiphytic bacterium widely used in fermented foods and products in the biochemical and pharmaceutical industries but data on its presence in foods from Qinghai-Tibet Plateau in China was scarce. In this study, molecular analysis based on multilocus sequence typing (MLST) with eight housekeeping genes (pyrG, groeL, rpoB, recA, uvrC, murC, carB, and pheS) was carried out on 45 L. mesenteroides strains isolated from different plants and dairy products from Qinghai-Tibet Plateau in China. The objective of this study was to perform genetic diversity analysis and explore the relationship between strains and isolate samples or separate regions. A total of 25 sequence types (STs) were identified with a diversity of up to 55.6%, which were grouped into one clonal complexes (CCs), 3 doublets and 17 singletons by eBURST. The results of minimum spanning tree and clustering analysis indicated these L. mesenteroides strains from the Qinghai-Tibet Plateau were relatively weakly related to the isolated region. However, there was a close relationship between the genotypes of L. mesenteroides strains and the type of the isolated sample, which was consistent with the results of API 50CH. The MLST scheme presented in this study provides a shareable and comparable sequence database and enhances our knowledge of the population diversity of L. mesenteroides strains which will be further used for the selection of industrial strains.

Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain

Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation of L. acidophilus strains. In this study, a whole-genome sequence-based analysis was carried out to establish high-resolution strain typing of 41 L. acidophilus strains (including commercial isolates and reference strains) using the cano-wgMLST_BacCompare analytics platform; consequently, a strain-specific discrimination method for the probiotic strain LA1063 was developed. Using a core-genome multilocus sequence-typing (cgMLST) scheme based on 1390 highly conserved genes, 41 strains could be assigned to 34 sequence types. Subsequently, we screened a set of 92 loci with a discriminatory power equal to that of the 1390 loci cgMLST scheme. A strain-specific polymerase chain reaction combined with a multiplex minisequencing method was developed based on four (phoU, secY, tilS, and uvrA_1) out of 21 loci, which could be discriminated between LA1063 and other L. acidophilus strains using the cgMLST data. We confirmed that the strain-specific single-nucleotide polymorphisms method could be used to quickly and accurately identify the L. acidophilus probiotic strain LA1063 in commercial products.

Mining Lactobacillus and Bifidobacterium for organisms with long-term gut colonization potential

Probiotics administered orally endure one of two fates: some merely pass through, but others colonize the gut permanently. Although probiotics that can stably engraft in the gut are believed to exert beneficial effects on the host in terms of increasing the efficiency of metabolic activity and enabling durable modulation of the indigenous microbiota, the strains of long-term gut colonizers are poorly delineated. This review summarizes the gut colonization modes of Lactobacillus and Bifidobacterium in the context of their natural niches and engraftment metadata in an attempt to identify organisms with long-term gut colonization potential. Advances in colonization evaluation methods are identified, and the effects of dietary components and metabolic interactions among ingested strains on bacterial colonization are discussed.

Genomic Characterization of Lactobacillus delbrueckii TUA4408L and Evaluation of the Antiviral Activities of its Extracellular Polysaccharides in Porcine Intestinal Epithelial Cells

In lactic acid bacteria, the synthesis of exopolysaccharides (EPS) has been associated with some favorable technological properties as well as health-promoting benefits. Research works have shown the potential of EPS produced by lactobacilli to differentially modulate immune responses. However, most studies were performed in immune cells and few works have concentrated in the immunomodulatory activities of EPS in non-immune cells such as intestinal epithelial cells. In addition, the cellular and molecular mechanisms involved in the immunoregulatory effects of EPS have not been studied in detail. In this work, we have performed a genomic characterization of Lactobacillus delbrueckii subsp. delbrueckii TUA4408L and evaluated the immunomodulatory and antiviral properties of its acidic (APS) and neutral (NPS) EPS in porcine intestinal epithelial (PIE) cells. Whole genome sequencing allowed the analysis of the general features of L. delbrueckii TUA4408L genome as well as the characterization of its EPS genes. A typical EPS gene cluster was found in the TUA4408L genome consisting in five highly conserved genes epsA-E, and a variable region, which includes the genes for the polymerase wzy, the flippase wzx, and seven glycosyltransferases. In addition, we demonstrated here for the first time that L. delbrueckii TUA4408L and its EPS are able to improve the resistance of PIE cells against rotavirus infection by reducing viral replication and regulating inflammatory response. Moreover, studies in PIE cells demonstrated that the TUA4408L strain and its EPS differentially modulate the antiviral innate immune response triggered by the activation of Toll-like receptor 3 (TLR3). L. delbrueckii TUA4408L and its EPS are capable of increasing the activation of interferon regulatory factor (IRF)-3 and nuclear factor κB (NF-κB) signaling pathways leading to an improved expression of the antiviral factors interferon (IFN)-β, Myxovirus resistance gene A (MxA) and RNaseL.

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

Background

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events.

Results

We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20′800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species’ level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class “genetic information processing” is conserved in the core-genome but that “signaling and cellular processes” is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation.

Conclusions

Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus’ evolution is directed by the environment and HGT.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4601-5) contains supplementary material, which is available to authorized users.

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.

Multilocus Genetic Characterization of Lactobacillus fermentum Isolated from Ready-to-Eat Canned Food

The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.

The Lactobacillus rhamnosus and Lactobacillus fermentum strains from human biotopes characterized with MLST and toxin-antitoxin gene polymorphism

The diversity of Lb. rhamnosus and Lb. fermentum strains isolated from feces, saliva, and the vaginal cavity of 18-22-year-old healthy women residing in central regions of the Russian Federation has been characterized. The results obtained using multilocus sequence typing were identical to those obtained with the analysis of genetic and genomic polymorphism in TA systems. Different as well as identical Lb. rhamnosus and Lb. fermentum sequence types (ST) were isolated from various parts of the body of the same person. Identical ST were also isolated from different women, suggesting that such strains belong to a common pool of strains circulating among the population members. Our results demonstrate that TAs are suitable for characterizing intra-specific diversity of Lb. rhamnosus and Lb. fermentum strains. The advantage of using polymorphisms in TA systems for genotyping is based on the weak number of genes used, and consequently, less time is required for the analysis.

DFAST and DAGA: web-based integrated genome annotation tools and resources

Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.

Multilocus sequence typing of Lactobacillus casei isolates from naturally fermented foods in China and Mongolia

Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from homemade fermented foods, including naturally fermented dairy products, acidic gruel, and Sichuan pickles from 38 different regions in China and Mongolia. The MLST scheme was developed based on the analysis of 10 selected housekeeping genes (carB, clpX, dnaA, groEL, murE, pyrG, pheS, recA, rpoC, and uvrC). All 229 isolates could be allocated to 171 unique sequence types, including 25 clonal complexes and 71 singletons. The high index of association value (1.3524) and standardized index of association value (0.1503) indicate the formation of an underlying clonal population by all the isolates. However, split-decomposition, relative frequency of occurrence of recombination and mutation, and relative effect of recombination and mutation in the diversification values confirm that recombination may have occurred, and were more frequent than mutation during the evolution of Lb. casei. Results from Structure analyses (version 2.3; http://pritch.bsd.uchicago.edu/structure.html) demonstrated that there were 5 lineages in the Lb. casei isolates, and the overall relatedness built by minimum spanning tree showed no clear relationship between the clonal complexes with either the isolation sources or sampling locations of the isolates. Our newly developed MLST scheme of Lb. casei was an easy and valuable tool that, together with the construction of an MLST database, will contribute to further detailed studies on the evolution and population genetics of Lb. casei from various niches.

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.

Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods

Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2–CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1–L6, with various homologous recombination rates. Although L2–L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.

Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources

BACKGROUND

Lactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. In the present study, the genetic diversity and population structure within 186 L. plantarum isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These isolates had originated from different sources and geographic regions: 179 isolates were from our own culture collection and originated from China and Mongolia and seven isolates were type or reference isolates from other collections.

RESULTS

The results showed that 179 isolates and seven reference isolates could be assigned to 73 different sequence types (STs), forming ten clonal complexes (CCs) and 23 singletons. There were 158 polymorphic sites detected in total, and the nucleotide diversity per site varied from 0.00401 in clpX to 0.03220 in groEL. The minimum spanning tree analyses suggested that the evolution of L. plantarum isolates have little relationship with ecological sources have similar nucleotide diversity. Phylogenetic trees and structure indicated that there were six lineages in the L. plantarum isolates used in our study. Split-decomposition and ClonalFrame analysis indicated that recombination had occurred throughout the population of L. plantarum, but it occurred at a low frequency in these eight loci.

CONCLUSION

We deduced that L. plantarum isolates from the same ecological niches have similar genetic diversity and population structure. The MLST scheme presented in this study provides abundant sequence data for L. plantarum and enabled global comparisons of isolates associated with various environmental origins to be made. This will further advance our understanding of the microbial ecology of this industrially important LAB.

Multilocus sequence typing of Streptococcus thermophilus from naturally fermented dairy foods in China and Mongolia

Background

Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a multilocus sequence typing (MLST) scheme for this important food bacterium. Sequences of 10 housekeeping genes (carB, clpX, dnaA, murC, murE, pepN, pepX, pyrG, recA, and rpoB) were obtained for 239 S. thermophilus strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China.

Methods

All 10 genes of S. thermophilus were sequenced, aligned, and defined sequence types (STs) using the BioNumerics Software. The nucleotide diversity was calculated by START v2.0. The population structure, phylogenetic relationships and the role of recombination were inferred using ClonalFrame v1.2, SplitsTree 4.0 and Structure v2.3.

Results

The 239 S. thermophilus isolates and 18 reference strains could be assigned into 119 different STs, which could be further separated into 16 clonal complexes (CCs) and 38 singletons. Among the 10 loci, a total of 132 polymorphic sites were detected. The standardized index of association (I_A^S = 0.0916), split-decomposition and ρ/θ (relative frequency of occurrence of recombination and mutation) and r/m value (relative impact of recombination and mutation in the diversification) confirms that recombination may have occurred, but it occurred at a low frequency in these 10 loci. Phylogenetic trees indicated that there were five lineages in the S. thermophilus isolates used in our study. MSTree and ClonalFrame tree analyses suggest that the evolution of S. thermophilus isolates have little relationship with geographic locality, but revealed no association with the types of fermented dairy product. Phylogenetic analysis of 36 whole genome strains (18 S. thermophilus, 2 S. vestibularis and 16 S. salivarius strains) indicated that our MLST scheme could clearly separate three closely related species within the salivarius group and is suitable for analyzing the population structure of the other two species in the salivarius group.

Conclusions

Our newly developed MLST scheme improved the understanding on the genetic diversity and population structure of the S. thermophilus, as well as provided useful information for further studies on the genotyping and evolutionary research for S. thermophilus strains with global diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0551-0) contains supplementary material, which is available to authorized users.

Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

Lactobacillus rhamnosus is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of L. rhamnosus in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65 L. rhamnosus strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of L. rhamnosus strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of L. rhamnosus GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters: l-rhamnose, cellobiose, l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate with l-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species L. rhamnosus and explores the relationships between specific carbohydrate utilization capacities and genotype and/or niche adaptation of this species.

The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST)

Background

Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC).

Results

MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (I_A^S) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type.

Conclusions

The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0447-z) contains supplementary material, which is available to authorized users.

Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets

The species Bifidobacterium longum is currently divided into three subspecies, B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. This classification was based on an assessment of accumulated information on the species' phenotypic and genotypic features. The three subspecies of B. longum were investigated using genotypic identification [amplified-fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST)]. By using the AFLP and the MLSA methods, we allocated 25 strains of B. longum into three major clusters corresponding to the three subspecies; the cluster comprising the strains of B. longum subsp. suis was further divided into two subclusters differentiable by the ability to produce urease. By using the MLST method, the 25 strains of B. longum were divided into eight groups: four major groups corresponding to the results obtained by AFLP and MLSA, plus four minor disparate groups. The results of AFLP, MLSA and MLST analyses were consistent and revealed a novel subspeciation of B. longum, which comprised three known subspecies and a novel subspecies of urease-negative B. longum, for which the name B. longum subsp. suillum subsp. nov. is proposed, with type strain Su 851(T)=DSM 28597(T)=JCM 19995(T).

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins

To investigate the influences of host genotype and environment on Bifidobacterium longum subsp. longum inhabiting human intestines at the strain level, six pairs of twins, divided into two groups (children and adults), were recruited. Each group consisted of two monozygotic (MZ) twin pairs and one dizygotic (DZ) twin pair. Child twins had been living together from birth, while adult twins had been living separately for 5 to 10 years. A total of 345 B. longum subsp. longum isolates obtained from 60 fecal samples from these twins were analyzed by multilocus sequence typing (MLST), and 35 sequence types (STs) were finally acquired. Comparison of strains within and between the twin pairs showed that no strains with identical STs were observed between unrelated individuals or within adult DZ twin pairs. Eight STs were found to be monophyletic, existing within MZ twins and child DZ twins. The similarity of strain types within child cotwins was significantly higher than that within adult cotwins, which indicated that environment was one of the important determinants in B. longum subsp. longum strain types inhabiting human intestines. However, although these differences between MZ and DZ twins were observed, it is still difficult to reach an exact conclusion about the impact of host genotype. This is mainly because of the limited number of subjects tested in the present study and the lack of strain types tracing in the same twin pairs from birth until adulthood.

Lactobacillus ruminis strains cluster according to their mammalian gut source

BACKGROUND

Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics.

RESULTS

We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780(T). Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis.

CONCLUSIONS

We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour.

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.

Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action

Background

Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus are lactic acid producing bacteria that are largely used in dairy industries, notably in cheese-making and yogurt production. An earlier in-depth study of the first completely sequenced ssp. bulgaricus genome revealed the characteristics of a genome in an active phase of rapid evolution, in what appears to be an adaptation to the milk environment. Here we examine for the first time if the same conclusions apply to the ssp. lactis, and discuss intra- and inter-subspecies genomic diversity in the context of evolutionary adaptation.

Results

Both L. delbrueckii ssp. show the signs of reductive evolution through the elimination of superfluous genes, thereby limiting their carbohydrate metabolic capacities and amino acid biosynthesis potential. In the ssp. lactis this reductive evolution has gone less far than in the ssp. bulgaricus. Consequently, the ssp. lactis retained more extended carbohydrate metabolizing capabilities than the ssp. bulgaricus but, due to high intra-subspecies diversity, very few carbohydrate substrates, if any, allow a reliable distinction of the two ssp. We further show that one of the most important traits, lactose fermentation, of one of the economically most important dairy bacteria, L. delbruecki ssp. bulgaricus, relies on horizontally acquired rather than deep ancestral genes. In this sense this bacterium may thus be regarded as a natural GMO avant la lettre.

Conclusions

The dairy lactic acid producing bacteria L. delbrueckii ssp. lactis and ssp. bulgaricus appear to represent different points on the same evolutionary track of adaptation to the milk environment through the loss of superfluous functions and the acquisition of functions that allow an optimized utilization of milk resources, where the ssp. bulgaricus has progressed further away from the common ancestor.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-407) contains supplementary material, which is available to authorized users.

Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera

Minimal standards for the description of new cultivable strains that represent novel genera and species belonging to the genera Bifidobacterium , Lactobacillus and related genera are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision): the description of novel species should be based on phenotypic, genotypic and ecological characteristics to ensure a rich polyphasic characterization. Concerning genotypic characterization, in addition to DNA G+C content (mol%) data, the description should be based on DNA–DNA hybridization (DDH), 16S rRNA gene sequence similarities and at least two housekeeping gene (e.g. hsp60 and recA) sequence similarities. DDH might not be needed if the 16S rRNA gene sequence similarity to the closest known species is lower than 97 %. This proposal has been endorsed by members of the Subcommittee on the Taxonomy of Bifidobacterium , Lactobacillus and related organisms of the International Committee on the Systematics of Prokaryotes.

Development of a multilocus sequence typing scheme for Streptococcus gallolyticus

Streptococcus gallolyticus is often found as a member of the normal gut microflora in various animals. However, it has been reported to cause mastitis in cattle, septicaemia in pigeons, and meningitis, septicaemia and endocarditis in humans. However, little is known about the epidemiology and crucial virulence factors of S. gallolyticus. To help address these issues, we developed a multilocus sequence typing (MLST) scheme for S. gallolyticus. Seven housekeeping gene fragments were sequenced from each of 58 S. gallolyticus isolates collected from diverse origins and sources. The MLST scheme had good discriminatory ability. The 63 strains, including the 5 whole genome sequenced strains examined, resolved into 57 sequence types (STs), with 52 STs represented by only a single strain. With respect to the identification of S. gallolyticus subspecies (i.e. S. gallolyticus subsp. gallolyticus, S. gallolyticus subsp. pasteurianus and S. gallolyticus subsp. macedonicus), the results of biochemical tests and DNA-DNA hybridization were in high concordance with those of the MLST scheme. The MLST scheme developed in this study may be a useful tool capable of replacing the conventional methods used for S. gallolyticus subspecies identification. The results of this study suggest that the biology and virulence of two pathogenic S. gallolyticus subspecies (i.e. S. gallolyticus subsp. gallolyticus and S. gallolyticus subsp. pasteurianus) are very different. The MLST scheme offers researchers a valuable typing tool that will promote further investigation of the epidemiology of S. gallolyticus.

Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso

Lactobacillus delbrueckii is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9T, was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA–DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species L. delbrueckii . The genome sequence of isolate ZN7a-9T was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9T together with 41 additional L. delbrueckii strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of L. delbrueckii represented by strain ZN7a-9T as it clustered with L. delbrueckii strains unassigned to any of the recognized subspecies of L. delbrueckii . Strain ZN7a-9T additionally differed from the recognized type strains of the subspecies of L. delbrueckii with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9T represents a novel subspecies of L. delbrueckii closely related to Lactobacillus delbrueckii subsp. lactis and Lactobacillus delbrueckii subsp. delbrueckii for which the name Lactobacillus delbrueckii subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9T = DSM 26046T = LMG 27067T.

Timely approaches to identify probiotic species of the genus Lactobacillus

Over the past decades the use of probiotics in food has increased largely due to the manufacturer’s interest in placing “healthy” food on the market based on the consumer’s ambitions to live healthy. Due to this trend, health benefits of products containing probiotic strains such as lactobacilli are promoted and probiotic strains have been established in many different products with their numbers increasing steadily. Probiotics are used as starter cultures in dairy products such as cheese or yoghurts and in addition they are also utilized in non-dairy products such as fermented vegetables, fermented meat and pharmaceuticals, thereby, covering a large variety of products.

To assure quality management, several pheno-, physico- and genotyping methods have been established to unambiguously identify probiotic lactobacilli. These methods are often specific enough to identify the probiotic strains at genus and species levels. However, the probiotic ability is often strain dependent and it is impossible to distinguish strains by basic microbiological methods.

Therefore, this review aims to critically summarize and evaluate conventional identification methods for the genus Lactobacillus, complemented by techniques that are currently being developed.

Population genetics of Lactobacillus sakei reveals three lineages with distinct evolutionary histories

Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products.

Development of a tiered multilocus sequence typing scheme for members of the Lactobacillus acidophilus complex

Members of the Lactobacillus acidophilus complex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of the L. acidophilus complex (L. acidophilus, L. amylovorus, L. crispatus, L. gallinarum, L. gasseri, and L. johnsonii) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of the hsp60 gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genes fusA, gpmA, gyrA, gyrB, lepA, pyrG, and recA, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of the L. acidophilus complex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection of Lactobacillus species.

Genetic diversity of dairy Geotrichum candidum strains revealed by multilocus sequence typing

The introduction of multilocus sequence typing (MLST) for strain characterization provided the first sequence-based approach for genotyping many fungi, leading to reproducible, reliable, and exchangeable data. A MLST scheme based on the analysis of six housekeeping genes was developed for genotyping Geotrichum candidum. The scheme was first developed using 18 isolates for which the complete sequences of the alanyl-tRNA synthetase (ALA1), pyruvate kinase (CDC19), acetyl-coA acetyltransferase (ERG10), glutaminyl-tRNA synthase (GLN4), phosphoglucoisomerase (PGI1), and phosphoglucomutase (PGM2) housekeeping genes were determined. Multiple sequence alignments of these genes were used to define a set of loci showing, as closely as possible, the same phylogenetic resolution level as complete gene sequences. This scheme was subsequently validated with 22 additional isolates from dairy and non-dairy sources. Overall, 58 polymorphic sites were indexed among 3,009 nucleotides analyzed. Depending on the loci, four to eight alleles were detected, generating 17 different sequence types, of which ten were represented by a single strain. MLST analysis suggested a predominantly clonal population for the 40 G. candidum isolates. Phylogenetic analysis of the concatenated sequences revealed a distantly related group of four isolates. Interestingly, this group diverged with respect to internal transcribed spacers 1 (ITS1), 5.8S, and ITS2 analysis. The reproducibility of the MLST approach was compared to random amplification of microsatellites by PCR (RAM-PCR), a gel profiling method previously proposed for G. candidum strain typing. Our results found MLST differentiation to be more efficient than RAM-PCR, and MLST also offered a non-ambiguous, unique language, permitting data exchange and evolutionary inference.

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology

Multi-locus sequence typing (MLST) is a high-resolution genetic typing approach to identify species and strains of pathogens impacting human health, agriculture (animals and plants), and biosafety. In this review, we outline the general concepts behind MLST, molecular approaches for obtaining MLST data, analytical approaches for MLST data, and the contributions MLST studies have made in a wide variety of areas. We then look at the future of MLST and their relative strengths and weaknesses with respect to whole genome sequence typing approaches that are moving into the research arena at an ever-increasing pace. Throughout the paper, we provide exemplar references of these various aspects of MLST. The literature is simply too vast to make this review comprehensive, nevertheless, we have attempted to include enough references in a variety of key areas to introduce the reader to the broad applications and complications of MLST data.

Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii , the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii . Together, the results of phenotypic characterization, DNA–DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7 %) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221T ( = JCM 17838T  = DSM 24966T).

Identification and classification of the genus Bacteroides by multilocus sequence analysis

Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.