Whole-genome sequence and comparative genome analysis of Lactobacillus paracasei DTA93, a promising probiotic lactic acid bacterium

Probiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap

This study focused on L. paracasei strains isolated from fermented palm sap in southern Thailand that exhibit potential probiotic characteristics, including antibiotic susceptibility, resistance to gastrointestinal stresses, and antimicrobial activity against various pathogens. However, a thorough investigation of the whole genome sequences of L. paracasei isolates is required to ensure their safety and probiotic properties for human applications. This study aimed to sequence the genome of L. paracasei isolated from fermented palm sap, to assess its safety profile, and to conduct a comprehensive comparative genomic analysis with other Lacticaseibacillus species. The genome sizes of the seven L. paracasei strains ranged from 3,070,747 bp to 3,131,129 bp, with a GC content between 46.11% and 46.17% supporting their classification as nomadic lactobacilli. In addition, the minimal presence of cloud genes and a significant number of core genes suggest a high degree of relatedness among the strains. Meanwhile, phylogenetic analysis of core genes revealed that the strains possessed distinct genes and were grouped into two distinct clades. Genomic analysis revealed key genes associated with probiotic functions, such as those involved in gastrointestinal, oxidative stress resistance, vitamin synthesis, and biofilm disruption. This study is consistent with previous studies that used whole-genome sequencing and bioinformatics to assess the safety and potential benefits of probiotics in various food fermentation processes. Our findings provide valuable insights into the potential use of seven L. paracasei strains isolated from fermented palm sap as probiotic and postbiotic candidates in functional foods and pharmaceuticals.

Lacticaseibacillus paracasei AD22 Stress Response in Brined White Cheese Matrix: In Vitro Probiotic Profiles and Molecular Characterization

Functionalizing foods involve discovering and integrating new candidate health-promoting bacteria into the food matrix. This study aimed (i) to reveal the probiotic potential of autochthonous Lacticaseibacillus paracasei AD22 by a series of in vitro tests and molecular characterization and (ii) to evaluate its application to the matrix of brined white cheese, which is the most common cheese in Türkiye, in terms of survival and stress response. To evaluate in vitro probiotic characteristics, L. paracasei AD22 was exposed to functional, technological, and safety tests. Pilot scale production was conducted to integrate L. paracasei AD22 into the brined white cheese matrix. The expression levels of stress-related genes (dnaK, groES, ftsH, argH, and hsp20) were detected by reverse-transcriptase polymerase chain reaction to determine the transcriptional stress response during ripening. The presence of genes encoding stress-related proteins was determined by whole-genome sequence analysis using a subsystem approach; the presence of antibiotic resistance and virulence genes was determined by ResFinder4.1 and VirulenceFinder 2.0 databases. The BAGEL4 database determined the presence of bacteriocin clusters. L. paracasei AD22 was found to survive in pH 2 and medium with 12% NaCl and did not cause hemolysis. Adhesion of the strain to Caco2 cells was 76.26 ± 4.81% and it had coaggregation/autoaggregation properties. It was determined that L. paracasei AD22 exceeded 7 log cfu/g in the cheese matrix at the end of the ripening period. Total mesophilic aerobes decreased in the cheese inoculated with L. paracasei AD22 after the 45th day of ripening. While hsp20 and groES genes were downregulated during ripening, argH was upregulated. Both downregulation and upregulation were observed in dnaK and ftsH. Fold changes indicating the expression levels of dnaK, groES, ftsH, argH, and hsp20 genes were not statistically significant during ripening (p > 0.05). Whole-genome sequence profiles revealed that the strain did not contain antibiotic and virulence genes but bacteriocin clusters encoding Enterolysin A (Class III bacteriocin), Carnosine CP52 (class II bacteriocin), Enterocin X beta chain (Class IIc bacteriocin), and the LanT region. Subsystems approach manifested that the most functional part of the genomic distribution belonged to metabolism, protein processing, and stress response functions. The study findings highlight that L. paracasei AD22 will provide biotechnological innovation as a probiotic adjunct because it contains tolerance factors and probiotic characteristics to produce new functional foods.

Draft Genome Sequence and Comparative Genome Analysis Reveal Potential Functional Properties in Lacticaseibacillus paracasei ItalPN16

Nowadays, there is a great interest on rapid and effective methods for initial identification of probiotic bacteria. In this work, potential probiotic features of the lactic acid bacteria strain ItalPN16 isolated from a traditional Brazilian cheese were studied using bioinformatic tools. The complete genome sequence was obtained, and in silico analyses were carried out to identify the strain and its potential probiotic properties. The sequenced genome (3.02 Mb) presented 3126 protein-coding sequences distributed on 244 SEED subsystems, classifying the strain as nomadic lactobacilli. Phylogenetic and ANI analyses allowed to locate the ItalPN16 strain as a member of the Lacticaseibacillus paracasei group, due to the highest number of orthologous genes in common with reference L. paracasei strains (>98%). In silico analyses revealed the presence of CDSs related to microbe-host interactions, such as adhesion proteins and exopolysaccharide biosynthesis genes. The comparative analysis reveals the presence of a strain-specific glycosyl transferases, compared with other three L. paracasei strains and a high level of protein expression (92%) with the probiotic L. paracasei BL29. The results obtained here indicated interesting probiotic features of the strain L. paracasei ItalPN16 that could favor a future application in the food industry.

Bioinformatics and its role in the study of the evolution and probiotic potential of lactic acid bacteria

Due to their numerous well-established applications in the food industry, there have been many studies regarding the adaptation and evolution of lactic acid bacteria (LAB) in a wide variety of hosts and environments. Progress in sequencing technology and continual decreases in its costs have led to the availability of LAB genome sequence data. Bioinformatics has been central to the extraction of valuable information from these raw genome sequence data. This paper presents the roles of bioinformatics tools and databases in understanding the adaptation and evolution of LAB, as well as the bioinformatics methods used in the initial screening of LAB for probiotic potential. Moreover, the advantages, challenges, and limitations of employing bioinformatics for these purposes are discussed.

Genomic and Phenotypic Evaluation of Potential Probiotic Pediococcus Strains with Hypocholesterolemic Effect Isolated from Traditional Fermented Food

The use of probiotic microorganisms in food with the aim to confer health benefits to the host is one of the most critical roles of functional foods. Many pediococci bacteria frequently related to the meat environment, have technological properties, and are therefore commercially used as starter in the production of fermented meat products, such as different types of sausages. In this study, different lactic acid bacteria were isolated, identified to the species level, and then evaluated for their safety and functionality as possible probiotics. Different properties, such as resistance to simulated human gastrointestinal conditions, antimicrobial activity, and cholesterol-lowering effects, have been studied. Finally, the complete genome of one strain, namely P. acidilactici IRZ12B, which showed interesting features as a promising probiotic candidate, was sequenced and further studied. The results revealed that IRZ12B possesses interesting probiotic properties, particularly cholesterol-lowering capability and antimicrobial activity. In silico analysis evidenced the absence of plasmids, transmissible antibiotic resistance genes, and virulence factors. We also detected a bacteriocin encoding gene and a cholesterol assimilation-related protein. The phenotypical and genomic outcomes described in this study make P. acidilactici IRZ12B a very interesting cholesterol-lowering potential probiotic strain to be considered for the development of novel non-dairy-based functional foods.

Potential of New Bacterial Strains for a Multiproduct Bioprocess Application: A Case Study Using Isolates of Lactic Acid Bacteria from Pineapple Silage of Costa Rican Agro-Industrial Residues

Lactic acid bacteria (LAB) with potential for the development of multi-product processes are necessary for the valorization of side streams obtained during the biotechnological production of lactic acid (LA). In this study, 14 LAB strains isolated from pineapple agro-industrial residues in Costa Rica were cultivated in microplates, and the six strains with the highest growth were selected for fermentation in microbioreactors to evaluate the production of LA and acetic acid, and the consumption of glucose. Lacticaseibacillus paracasei 6710 and L. paracasei 6714 presented the highest OD600 values (1.600 and 1.602, respectively); however, the highest LA (in g/L) production was observed in L. paracasei 6714 (14.50 ± 0.20) and 6712 (14.67 ± 0.42). L. paracasei 6714 was selected for bioreactor fermentation and reached a maximum OD600 of 6.3062 ± 0.141, with a LA yield of 84.9% and a productivity of 1.06 g L−1 h−1 after 21 h of fermentation. Finally, lipoteichoic acid (LTA) detection from biomass was performed and the antimicrobial activity of the compounds present in the supernatant was studied. LTA was detected from L. paracasei 6714 biomass, and its supernatant caused significant inhibition of foodborne surrogate microorganisms. LAB isolated from pineapple silage have biotechnological potential for multiproduct processes.

Safety evaluation and anti-inflammatory activity of Lactobacillus johnsonii IDCC 9203 isolated from feces of breast-fed infants

This study evaluated the safety of Lactobacillus johnsonii IDCC 9203 and investigated its anti-inflammatory activity in lipopolysaccharide (LPS)-induced RAW 264.7 macrophages. Genomic analysis revealed that this strain has no virulence and antibiotic resistance gene except tetW, which is a tetracycline resistance gene. Minimum inhibitory concentration data showed that the strain is resistant to tetracycline and aminoglycosides. Further analysis indicated that the transferability of the tetW gene is extremely low, and resistance to aminoglycosides is due to the intrinsic resistance of L. johnsonii IDCC 9203. Phenotypic safety assessment showed that the strain has neither β-hemolytic nor β-glucuronidase activity, and no biogenic amine production. When LPS-induced RAW 264.7 cells were treated with L. johnsonii IDCC 9203, the level of nitric oxide and expression of pro-inflammatory cytokines significantly decreased (p < 0.05). Therefore, L. johnsonii IDCC 9203 strain is considered as safe and beneficial probiotic for human consumption.

Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud

AIMS

Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates.

METHODS AND RESULTS

Using high-throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche-specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci.

CONCLUSIONS

Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.

Limosilactobacillus fermentum ING8, a Potential Multifunctional Non-Starter Strain with Relevant Technological Properties and Antimicrobial Activity

Lactic acid bacteria (LAB) have gained particular attention among different exopolysaccharide-producing microorganisms due to their safety status and effects on human health and food production. Exopolysaccharide-producing LAB play a crucial role in different ways, such as improving texture, mouthfeel, controlling viscosity, and for low-calorie food production. In this study, we isolated a multifunctional strain with good exopolysaccharide production properties. Limosilactobacillus fermentum ING8 was isolated from an Indian traditional fermented milk (Dahi) and evaluated for its safety, enzymatic activity, NaCl resistance and temperature tolerance, milk coagulation, and storage stability. Finally, the complete genome of this strain was sequenced and subjected to safety in silico evaluation and genomic analysis. The results revealed that L. fermentum ING8 possesses relevant technological properties, such as exopolysaccharide production, antimicrobial activity, and galactose utilization. Besides, this strain showed very high stability to storage conditions at refrigeration temperature. In addition, the genomic analysis did not evidence any possible deleterious elements, such as acquired antibiotic resistance genes, virulence genes, or hemolysis-related genes. However, all structural genes related to the galactose operon and EPS production were detected. Therefore, L. fermentum ING8 can be considered a promising multifunctional bacterium to be proposed as non-starter in different types of dairy productions.

Identification and Transferability of Tetracycline Resistance in Streptococcus thermophilus during Milk Fermentation, Storage, and Gastrointestinal Transit

The existence of antibiotic-resistant bacteria in food products, particularly those carrying acquired resistance genes, has increased concerns about the transmission of these genes from beneficial microbes to human pathogens. In this study, we evaluated the antibiotic resistance-susceptibility patterns of 16 antibiotics in eight S. thermophilus strains, whose genome sequence is available, using phenotypic and genomic approaches. The minimal inhibitory concentration values collected revealed intermediate resistance to aminoglycosides, whereas susceptibility was detected for different classes of β-lactams, quinolones, glycopeptide, macrolides, and sulfonamides in all strains. A high tetracycline resistance level has been detected in strain M17PTZA496, whose genome analysis indicated the presence of the tet(S) gene and the multidrug and toxic compound extrusion (MATE) family efflux pump. Moreover, an in-depth genomic analysis revealed genomic islands and an integrative and mobilizable element (IME) in the proximity of the gene tet(S). However, despite the presence of a prophage, genomic islands, and IME, no horizontal gene transfer was detected to Lactobacillus delbrueckii subsp. lactis DSM 20355 and Lactobacillusrhamnosus GG during 24 h of skim milk fermentation, 2 weeks of refrigerated storage, and 4 h of simulated gastrointestinal transit.

Whole genome and acid stress comparative transcriptome analysis of Lactiplantibacillus plantarum ZDY2013

Previous study has reported that Lactiplantibacillus plantarum ZDY2013 which was screened from traditional Chinese fermented soybeans has a strong acid resistance. The purpose of this study was to uncover the genes potentially related to its genetic adaptation and probiotic profiles, based on comparative genomic and comparative transcriptome analysis. We got the basic information about L. plantarum ZDY2013 and identified genes which are related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative transcriptome showed CK group (normal MRS culture L. plantarum ZDY2013) and SCL group (pH 3.0 MRS culture L. plantarum ZDY2013) had 652 significant differentially expressed genes including 310 up-regulated genes and 342 down-regulated genes. Besides that, these genes had been classified through KEGG and GO functional annotation. In addition, we also found top 20 KEGG pathways adjusted to acid stress. Then, some genes were selected to verify the transcriptome analysis and explore the mechanism of how L. plantarum ZDY2013 tolerate acid stress. We found that some genes of ABC transporter, phosphotransferase system, oxidation reduction process, membrane transporter and phosphorylation metabolism process had a significant change. These results suggested that comparative characterization of the L. plantarum ZDY2013 genome and transcriptome provided the genetic basis for further elucidating the functional mechanisms of it.

Lactobacillus paracasei DTA81, a cholesterol-lowering strain having immunomodulatory activity, reveals gut microbiota regulation capability in BALB/c mice receiving high-fat diet

Aims

In‐vitro/In‐vivo evaluation of cholesterol‐lowering probiotic strain Lactobacillus paracasei DTA81 and the possible connection with the gut microbiota modulation.

Methods and Results

In the present study, strain DTA81 has been evaluated for the possible influence on blood lipid and glucose concentrations, modulation of the immune system, gastrointestinal survivability and modulation of gut microbiota in BALB/c mice receiving a high‐fat diet. After 6 weeks of treatment, a significant reduction of total cholesterol and fasting blood sugar (FBS) among animals treated with L. paracasei DTA81 has been recorded. Comparison of colon tissue levels of different cytokines revealed a significant reduction of the inflammatory cytokine interleukin‐6. The comparison of gut microbiota using the 16S rRNA approach indicated that the treatment with L. paracasei DTA81 significantly increased the taxa Bacteroidetes and Coprococcus. Moreover, the genome of DTA81 was sequenced for the in‐silico assessment, and the analysis indicated the presence of cholesterol assimilation‐related genes as well as the absence of negative traits such as transmissible antibiotic resistance genes, plasmids and prophage regions.

Conclusion

The outcome of this study revealed the in‐vitro and in‐vivo properties of L. paracasei DTA81 and the possible mechanism between consumption of this strain, the abundance of Bacteriodetes/Coprococcus taxa, immunomodulatory activity and the subsequent reduction of cholesterol/FBS in BALB/c mice.

Significance and Impact of the Study

Lactobacillus paracasei DTA81 as a non‐pharmacological potential probiotic supplement can influence metabolic homeostasis in individuals, particularly those adopting high‐fat diets, and it can contribute to reduce coronary heart disease.