The dnaJ gene as a molecular discriminator to differentiate among species and strain within the Lactobacillus casei group

Enhanced preservation of viability and species stratification in Lacticaseibacillus group using levan-fortified skim milk as a cryoprotectant during freeze-drying

Ensuring the viability and accurate stratification of Lacticaseibacillus group (LCG) species after freeze-drying is essential for their effective use as probiotics. This study investigates the use of reconstituted skim milk (RSM) as a cryoprotectant base, supplemented with fructans such as inulin and diverse forms of levan from Halomonas smyrnensis, to maintain the viability of Lacticaseibacillus casei ATCC 334, Lacticaseibacillus paracasei ATCC 25302, and Lacticaseibacillus rhamnosus ATCC 53103. Cellular viability was enhanced with levan-based cryoprotectants, motivating the use of levan-based hydrogels (gHLs) for freeze-drying LCG species. Throughout freeze-drying, the species-specific molecular masses (m/z) were preserved irrespective of the cryoprotectant used, with markers 3445 and 6664 m/z identified as potential species-specific molecular mass indicators for Lc. paracasei and Lc. rhamnosus, respectively. This study is the first to utilize levan in various forms as a cryoprotective agent alongside RSM, highlighting its promise as an effective cryoprotectant for LCG and potentially other probiotics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01802-x.

In Vitro Characterization of Indigenous Probiotic Strains Isolated from Colombian Creole Pigs

Three lactic acid strains were isolated from feces of the native Zungo Pelado breed of pigs (n = 5) and presumably identified as belonging to the Lactobacillaceae family by morphological techniques showing that they were Gram-positive/rod-shaped and catalase- and oxidase-negative. They were then identified by biochemical tests using API 50CHL as Lactobacillus plantarum (CAM6), Lactobacillus brevis (CAM7), and Lactobacillus acidophilus (CL4). However, 16S rRNA identification showed that all three strains were Lactobacillus plantarum. Additionally, all three isolates were able to grow in pH 3 and 4. Interestingly, the growth of the CAM7 strain decreased at pH 5.6 compared to that of the CAM6 strain (p < 0.05), and the growth of the CL4 strain was reduced at pH 7(p < 0.05). All three candidates showed good growth on bile salts (≥0.15%), and CAM6 and CAM7 showed better tolerance at higher concentrations (0.30%). Similarly, all strains tolerated sodium chloride (NaCl) concentrations from 2 to 10%. These strains also grew well at all temperatures tested (30, 37, and 42 °C). The CAM6 strain showed in vitro antibacterial activity against selected enteropathogenic bacteria (Escherichia coli strain NBRC 102203 and Salmonella enterica serovar Typhimurium 4.5.12) and commensal bacteria (Klebsiella pneumoniae ATCC BAA-1705D-5 and Pseudomonas aeruginosa ATCC 15442) and resistance to all antibiotics except amoxicillin. Further studies to evaluate the effects of these probiotic candidate strains in commercial pigs are currently underway.

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

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

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Background

Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods.

Results

To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label.

Conclusions

The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus, and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have

Background

Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.

Results

When aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes.

Conclusions

The positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1365-8) contains supplementary material, which is available to authorized users.

The Lactobacillus casei Group: History and Health Related Applications

The Lactobacillus casei group (LCG), composed of the closely related Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are some of the most widely researched and applied probiotic species of lactobacilli. The three species have been extensively studied, classified and reclassified due to their health promoting properties. Differentiation is often difficult by conventional phenotypic and genotypic methods and therefore new methods are being continually developed to distinguish the three closely related species. The group remain of interest as probiotics, and their use is widespread in industry. Much research has focused in recent years on their application for health promotion in treatment or prevention of a number of diseases and disorders. The LCG have the potential to be used prophylactically or therapeutically in diseases associated with a disturbance to the gut microbiota. The group have been extensively researched with regard to stress responses, which are crucial for their survival and therefore application as probiotics.

A novel real-time PCR assay for highly specific detection and quantification of vaginal lactobacilli

PCR detection and quantification of vaginal lactobacilli remains problematic because of the high level of genetic heterogeneity and taxonomic complexity within the genus Lactobacillus. The aim of the present study was to identify conserved sequences among the genomes of major species of vaginal lactobacilli that could be used for the development of a PCR-based method for quantitative determination of vaginal microbiota-specific lactobacilli. Comparative analysis of the genomes of several species of vaginal lactobacilli allowed us to identify conserved regions in the rplK gene, which encodes ribosomal protein L11, and to design group-specific PCR primers and a probe for selected species from the L. acidophilus complex, including major vaginal lactobacilli Lactobacillus crispatus, L. gasseri, L. iners and L. jensenii as well as other species that are less common in vaginal microbiota. The applicability of the new assay in routine diagnostic testing was evaluated using a set of clinical samples. The assay was able to detect and quantify vagina-associated lactobacilli within a wide range of initial DNA template concentrations, indicating promising potential for clinical applications.