Role of luxS in Stress Tolerance and Adhesion Ability in Lactobacillus plantarum KLDS1.0391

Engineered E. coli for Long-Term Oral Enzyme Delivery

Intestinal flora shows excellent affinity in the gut, and the adhesive property is borrowed for oral drug delivery. A facile strategy for bacteria engineering has been successfully developed by introducing metal-organic framework (MOF) mineralization. The MOF exoskeleton serves as an extendable platform for accommodating various cargoes with good Escherichia coli morphology maintained. The artificial exoskeleton surrounding E. coli is employed for encapsulating macromolecules as a therapeutic cargo, maintaining good bioactivity with high immobilization efficiency (60%) after systematic optimization of the MOF precursor. Leveraging the natural affinity of E. coli in the gut, the in-vivo tracking of MOF-engineered E. coli in the gastrointestinal tract confirmed excellent adhesion to the GI mucosa and a 17.9-fold increase in the gut retention half-time, demonstrating significant advantages in retention capability. In comparison, the control group without E. coli equipment resulted in quick gut passage. Furthermore, the artificially engineered E. coli serves as an effective carrier for macromolecules without notable oral toxicity, as evidenced by biocompatibility evaluations in cells and animals. Overall, the MOF-engineered E. coli provides an extendable platform for loading on-demand cargoes in versatile therapeutic functions with promising clinical transnationality for long-term applications.

Genome mining of Lactiplantibacillus plantarum PA21: insights into its antimicrobial potential

BACKGROUND

The dramatic increase of antimicrobial resistance in the healthcare realm has become inexorably linked to the abuse of antibiotics over the years. Therefore, this study seeks to identify potential postbiotic metabolites derived from lactic acid bacteria such as Lactiplantibacillus plantarum that could exhibit antimicrobial properties against multi-drug resistant pathogens.

RESULTS

In the present work, the genome sequence of Lactiplantibacillus plantarum PA21 consisting of three contigs was assembled to a size of 3,218,706 bp. Phylogenomic analysis and average nucleotide identity (ANI) revealed L. plantarum PA21 is closely related to genomes isolated from diverse niches such as dairy products, food, and animals. Genome mining through the BAGEL4 and antiSMASH database revealed four bacteriocins in a single cluster and four regions of biosynthetic gene clusters responsible for the production of bioactive compounds. The potential probiotic genes indirectly responsible for postbiotic metabolites production were also identified. Additionally, in vitro studies showed that the L. plantarum PA21 cell-free supernatant exhibited antimicrobial activity against all nine methicillin-resistant Staphylococcus aureus (MRSA) and three out of 13 Klebsiella pneumoniae clinical isolates tested.

CONCLUSION

Results in this study demonstrates that L. plantarum PA21 postbiotic metabolites is a prolific source of antimicrobials against multi-drug resistant pathogens with potential antimicrobial properties.

Lactiplantibacillus plantarum LOC1 Isolated from Fresh Tea Leaves Modulates Macrophage Response to TLR4 Activation

Previously, we demonstrated that Lactiplantibacillus plantarum LOC1, originally isolated from fresh tea leaves, was able to improve epithelial barrier integrity in in vitro models, suggesting that this strain is an interesting probiotic candidate. In this work, we aimed to continue characterizing the potential probiotic properties of the LOC1 strain, focusing on its immunomodulatory properties in the context of innate immunity triggered by Toll-like receptor 4 (TLR4) activation. These studies were complemented by comparative and functional genomics analysis to characterize the bacterial genes involved in the immunomodulatory capacity. We carried out a transcriptomic study to evaluate the effect of L. plantarum LOC1 on the response of murine macrophages (RAW264.7 cells) to the activation of TLR4. We demonstrated that L. plantarum LOC1 exerts a modulatory effect on lipopolysaccharide (LPS)-induced inflammation, resulting in a differential regulation of immune factor expression in macrophages. The LOC1 strain markedly reduced the LPS-induced expression of some inflammatory cytokines (IL-1β, IL-12, and CSF2) and chemokines (CCL17, CCL28, CXCL3, CXCL13, CXCL1, and CX3CL1), while it significantly increased the expression of other cytokines (TNF-α, IL-6, IL-18, IFN-β, IFN-γ, and CSF3), chemokines (IL-15 and CXCL9), and activation markers (H2-k1, H2-M3, CD80, and CD86) in RAW macrophages. Our results show that L. plantarum LOC1 would enhance the intrinsic functions of macrophages, promoting their protective effects mediated by the stimulation of the Th1 response without affecting the regulatory mechanisms that help control inflammation. In addition, we sequenced the LOC1 genome and performed a genomic characterization. Genomic comparative analysis with the well-known immunomodulatory strains WCSF1 and CRL1506 demonstrated that L. plantarum LOC1 possess a set of adhesion factors and genes involved in the biosynthesis of teichoic acids and lipoproteins that could be involved in its immunomodulatory capacity. The results of this work can contribute to the development of immune-related functional foods containing L. plantarum LOC1.

Mechanism of gastrointestinal adaptability and antioxidant function of infant-derived Lactobacillus plantarum BF_15 through genomics

Lactobacillus plantarum is an essential probiotic in the human gastrointestinal tract. L. plantarum BF_15, a functional probiotic isolated from the feces of breast-fed infants, has been reported in many in vitro and in vivo studies with strong gastrointestinal adaptability and outstanding anti-oxidative activities. Therefore, the whole genome of L. plantarum BF_15 was sequenced. Several genes, encoding the gastrointestinal adaptability-related proteins, were identified, including genes related to gastrointestinal environment-induced stress resistance, adhesive performance, and ability to transport and metabolize resistant starch and oligosaccharides. Genes related to alleviating oxidative stress were also found. Further functional verification was carried out by RT-qPCR on the 10 and 12 key adhesion and antioxidant genes. Overall, this study might provide a critical basis for L. plantarum BF_15 as a potential candidate for probiotics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01132-w.

Arcobacter butzleri Biofilms: Insights into the Genes Beneath Their Formation

Arcobacter butzleri, the most prevalent species of the genus, has the demonstrated ability to adhere to various surfaces through biofilm production. The biofilm formation capability has been related to the expression of certain genes, which have not been characterized in A. butzleri. In order to increase the knowledge of this foodborne pathogen, the aim of this study was to assess the role of six biofilm-associated genes in campylobacteria (flaA, flaB, fliS, luxS, pta and spoT) in the biofilm formation ability of A. butzleri. Knockout mutants were constructed from different foodborne isolates, and static biofilm assays were conducted on polystyrene (PS), reinforced glass and stainless steel. Additionally, motility and Congo red binding assays were performed. In general, mutants in flaAB, fliS and luxS showed a decrease in the biofilm production irrespective of the surface; mutants in spoT showed an increase on stainless steel, and mutants in pta and spoT showed a decrease on reinforced glass but an increase on PS. Our work sheds light on the biofilm-related pathogenesis of A. butzleri, although future studies are necessary to achieve a satisfactory objective.

AI-2E Family Transporter Protein in Lactobacillus acidophilus Exhibits AI-2 Exporter Activity and Relate With Intestinal Juice Resistance of the Strain

The function of the autoinducer-2 exporters (AI-2E) family transporter protein of Lactobacillus acidophilus is still unclear. The phylogenetic analysis was used to analyze the relationship between the AI-2E protein of the L. acidophilus CICC 6074 strain and other AI-2E family members. Escherichia coli KNabc strain was used to verify whether the protein has Na⁺ (Li⁺)/H⁺ antiporter activity. The AI-2E protein overexpression strain was constructed by using the pMG36e expression vector, and the overexpression efficiency was determined by real-time quantitative PCR. The vitality and AI-2 activity of L. acidophilus CICC 6074 strains were determined. The results showed that the AI-2E protein of Lactobacillus formed a single branch on the phylogenetic tree and was closer to the AI-2E family members whose function was AI-2 exporter group I. The expression of AI-2E protein in the E. coli KNabc strain did not recover the resistance of the bacteria to the saline environment. Overexpression of AI-2E protein in L. acidophilus CICC 6074 could promote the AI-2 secretion of L. acidophilus CICC 6074 strain and enhance their survival ability in intestinal juice.

Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3

Spore-forming Bacillus species are gaining interest in human health recently, due to their ability to withstand the harsh environment of the gastrointestinal tract. The present study explores probiotic features of Bacillus paranthracis strain MHSD3 through genomic analysis and in vitro probiotic assays. The draft genome of strain MHSD3 contained genes associated with tolerance to gastrointestinal stress and adhesion. Cluster genes responsible for the synthesis of antimicrobial non-ribosomal peptide synthetases, bacteriocins, and linear azole-containing peptides were identified. Additionally, strain MHSD3 was able to survive in an acidic environment, had the tolerance to bile salt, and exhibited the capability to tolerate gastric juices. Moreover, the isolate was found to possess strong cell surface traits such as high auto-aggregation and hydrophobicity indices of 79 and 54%, respectively. Gas chromatography-mass spectrometry analysis showed that the strain produced secondary metabolites such as amino acids, phenolic compounds, and organic acid, known to exert health-promoting properties, including the improvement of gastrointestinal tract health.

Acetic acid acting as a signaling molecule in the quorum sensing system increases 2,3-butanediol production in Saccharomyces cerevisiae

2,3-Butanediol (2,3-BD) has been extensively used in chemical syntheses. This study aimed to explore acetic acid as a signaling molecule that activates a quorum sensing (QS) system to promote the production of 2,3-BD. The yield of 2,3-BD is proportional to the cell density. Saccharomyces cerevisiae W141 does not produce 2,3-BD when the cell density is lower than the threshold concentration (OD_600 nm = 10 or cell density 4.4 × 10⁸ CFU/mL). When 1.5 g/L acetic acid is added, the yield of 2,3-BD is 3.01 ± 0.04 g/L. Subsequently, S. cerevisiae W141 was cocultured with Acetobacter pasteurianus Huniang 1.01 under the optimal conditions, the acetic acid production was increased by 76.7% and 30.6% compared with the original strain and the strain cultivated with 1.5 g/L acetic acid, and the yield of 2,3-BD was increased by 81.9% and 3.3%, respectively. This difference is due to the activity of acetyl lactic acid synthase (ILV2) and 2,3-BD dehydrogenase (BDH1), as the relative expression of the ilv2 and bdh1 genes is increased. The results showed that the biosynthesis of 2,3-BD was regulated by acetic acid as a signaling molecule. S. cerevisiae is a promising host for producing 2,3-BD for industrial applications.

Comparative proteomic analysis of three Lactobacillus plantarum strains under salt stress by iTRAQ

BACKGROUND

Lactobacillus plantarum, a common species of lactic acid bacteria, is used to improve the flavor of traditional fermented food. Under salt stress, different strains of L. plantarum can respond differently. In this work, proteomics and bioinformatics analysis of L. plantarum strains (ATCC14917, FS5-5, and 208) grown under salt stress (240 g L^-1 sodium chloride (NaCl)) were investigated based on the isobaric tags for relative and absolute quantitation method.

RESULTS

Although 171 differentially expressed proteins (DEPs) were observed, only 44, 57, and 112 DEPs were identified in the strains ATCC14917, FS5-5, and 208 respectively. There were 33, 191, and 179 specific DEPs in ATCC14917 versus FS5-5, in 208 versus FS5-5, and in strain 208 versus ATCC14917 in 240 g L^-1 NaCl. These DEPs indicate that the three strains, from pickles, fermented soybean paste, and fermented milk, may have different salt stress responses. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis showed that most DEPs observed were involved in protein biosynthesis, nucleotide metabolism, and sugar metabolism. Twenty-six significantly different DEPs that were possibly associated with salt response were selected and further analyzed for gene expression level and pattern by quantitative reverse transcription polymerase chain reaction. Pyruvate kinase and cysteine desulfurase had similar expression patterns in all three strains; glutamate decarboxylase expression was upregulated in FS5-5 and significantly upregulated in strain 208; RNA polymerase subunit alpha was downregulated in FS5-5 but upregulated in strain 208.

CONCLUSIONS

These results also showed that the salt stress response of strain 208 may involve higher numbers of genes than the other strains. This research provides a theoretical basis for improvement of salt tolerance of L. plantarum in industrial production. © 2020 Society of Chemical Industry.

Deciphering the Probiotic Potential of Bacillus amyloliquefaciens COFCAU_P1 Isolated from the Intestine of Labeo rohita Through In Vitro and Genetic Assessment

In this study, a bacterial strain COFCAU_P1, isolated from the digestive tract of a freshwater teleost rohu (Labeo rohita), was identified as Bacillus amyloliquefaciens using 16S rRNA gene sequence analysis combined with amplification of species-specific BamHI and barnase genes. The probiotic potential of the strain was evaluated using an array of in vitro tests along with safety and genetic analyses. The isolate showed potent antimicrobial response against several fish pathogenic bacteria, survived a wide pH range (2-9), and was resistant up to 10% bile salt concentration. With regard to the in vitro adhesion properties, the strain showed significantly high in vitro adhesion to mucus, auto and co-aggregation capacity, and cell surface hydrophobicity. The strain was non-haemolytic, able to produce extracellular enzymes, viz., proteinase, amylase, lipase, and cellulase, and showed significant free radical scavenging activity. A challenge study in rohu revealed the strain COFCAU_P1 as non-pathogenic. The presence of putative probiotic marker genes including 2, 3-bisphosphoglycerate-independent phosphoglycerate mutase, arginine/ornithine antiporter ArcD, choloylglycine hydrolase, LuxS, and E1 β-subunit of the pyruvate dehydrogenase complex was confirmed by PCR, suggesting the molecular basis of the probiotic-specific functional attributes of the isolate. In conclusion, the in vitro and genetic approaches enabled the identification of a potential probiotic from autochthonous source with a potential of its utilization in the aquaculture industry.

Pangenome analyses of LuxS-coding genes and enzymatic repertoires in cocoa-related lactic acid bacteria

Lactobacillaceae presents potential for interspecific Quorum Sensing (QS) in spontaneous cocoa fermentation, correlated with high abundance of luxS. Three Brazilian isolates from cocoa fermentation were characterized by Whole Genome Sequencing and luxS gene was surveyed in their genomes, in comparison with public databases. They were classified as Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Pediococcus acidilactici. LuxS genes were conserved in core genomes of the novel isolates, but in some non-cocoa related Lactic Acid Bacteria (LAB) it was accessory and plasmid-borne. The conservation and horizontal acquisition of luxS reinforces that QS is determinant for bacterial adaptation in several environments, especially taking into account the luxS has been correlated with modulation of bacteriocin production, stress tolerance and biofilm formation. Therefore, in this paper, new clade and species-specific primers were designed for future application for screening of luxS gene in LAB to evaluate the adaptive potential to diverse food fermentations.

Research on the role of LuxS/AI-2 quorum sensing in biofilm of Leuconostoc citreum 37 based on complete genome sequencing

Leuconostoc citreum, a type of food-grade probiotic bacteria, plays an important role in food fermentation and intestinal probiotics. Biofilms help bacteria survive under adverse conditions, and LuxS/AI-2-dependent quorum sensing (QS) plays an important role in the regulation of their biofilm-forming activities. L. citreum 37 was a biofilm-forming strain isolated from dairy products. The aim of this study was to analyze genes involved in the LuxS/AI-2 system based on genome sequencing and biofilm formation of L. citreum 37. Genome assembly yielded two contigs (one chromosome and one plasmid), and the complete genome contained 1,946,279 base pairs (bps) with a G + C content of 38.91%. The genome sequence analysis showed that there were several pathways such as the two-component system, QS, and seven other signal pathways, and 26 genes (including luxS, pfs, and 24 other genes) may participate in QS related to biofilm formation. All these results showed that the LuxS/AI-2 system is complete in the genome of L. citreum 37. The quantitative polymerase chain reaction (qPCR) of pfs, luxS genes, and AI-2 production of L. citreum 37 in planktonic state and biofilm state showed that the expression of pfs and luxS genes was consistent with the production of AI-2 and was positively correlated with biofilm formation. After luxS of L. citreum 37 expressed in Escherichia coli BL21, AI-2 production was detected, suggesting that the luxS gene played an important role in AI-2 synthesis, Therefore, luxS may regulate the biofilm formation of L. citreum 37 by participating in AI-2 synthesis. It is projected that results of this study could help facilitate further understanding and application of L. citreum 37.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02747-2.

Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced by Lactobacillus acidophilus PNW3

The genome of Lactobacillus acidophilus PNW3 was assessed for probiotic and safety potentials. The genome was completely sequenced, assembled using SPAdes, and thereafter annotated with NCBI prokaryotic genome annotation pipeline (PGAP) and rapid annotation using subsystem technology (RAST). Further downstream assessment was determined using appropriate bioinformatics tools. The production of biogenic amines was confirmed through HPLC analysis and the evolutionary trend of the strain was determined through the Codon Tree pipeline. The strain was predicted as a non-human pathogen. A plethora of encoding genes for lactic acids and bioactive peptides production, adhesion molecules, resistance to the harsh gut environmental conditions, and improvement of the host metabolism, which are putative for important probiotic functionalities, were located at different loci within the genome. A bacteriocin predicted to be helveticin J was identified as one of the secondary metabolites. The maximum zone of inhibition exhibited by the crude bacteriocin against STEC E. coli O177 was 21.7 ± 0.58 mm and 24.3 ± 1.15 mm after partial purification (250 µg/mL). Three coding sequences were identified for insertion sequences and one for the CRISPR-Cas fragment. The protein-encoding sequence for Ornithine decarboxylase was found within the genome. L. acidophilus PNW3 presents important features categorizing it as a viable and safe probiotic candidate, though further safety investigations are necessary. The application of probiotics in livestock-keeping would ensure improved public health and food security.

Plasmids encode niche-specific traits in Lactobacillaceae

Species belonging to the family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbour plasmids that encode important genes. In this study, we performed comparative genomic analysis of publicly available data for 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-thirds of the species had at least one plasmid-harbouring strain. Plasmid abundance and GC content were significantly lower in vertebrate-adapted species as compared to nomadic and free-living species. Hierarchical clustering highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-adapted species. EggNOG-assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin–antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters and the major facilitator superfamily were overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures correlate with the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to their respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.

Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis

Purpose

The aim of this study was to identify salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains, isolated from Chinese traditional fermented food, by genomic analysis.

Methods

Tolerance of L. plantarum D31 and T9 strains was evaluated at different stress conditions (temperatures, acid, osmolality, and artificial gastrointestinal fluids). Draft genomes of the two strains were determined using the Illumina sequencing technique. Comparative genomic analysis and gene transcriptional analysis were performed to identify and validate the salt tolerance-related genes.

Results

Both L. plantarum D31 and T9 strains were able to withstand high osmotic pressure caused by 5.0% NaCl, and L. plantarum D31 even to tolerate 8.0% NaCl. L. plantarum D31 genome contained 3,315,786 bp (44.5% GC content) with 3106 predicted protein-encoding genes, while L. plantarum T9 contained 3,388,070 bp (44.1% GC content) with 3223 genes. Comparative genomic analysis revealed a number of genes involved in the maintenance of intracellular ion balance, absorption or synthesis of compatible solutes, stress response, and modulation of membrane composition in L. plantarum D31 and or T9 genomes. Gene transcriptional analysis validated that most of these genes were coupled with the stress-resistance phenotypes of the two strains.

Conclusions

L. plantarum D31 and T9 strains tolerated 5.0% NaCl, and D31 even tolerated 8.0% NaCl. The draft genomes of these two strains were determined, and comparative genomic analysis revealed multiple molecular coping strategies for the salt stress tolerance in L. plantarum D31 and T9 strains.

Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone

The bacterial quorum sensing phenomenon has been well studied since its discovery and has traditionally been considered to include signaling pathways recognized exclusively within either Gram-positive or Gram-negative bacteria. These groups of bacteria synthesize structurally distinct signaling molecules to mediate quorum sensing, where Gram-positive bacteria traditionally utilize small autoinducing peptides (AIPs) and Gram-negatives use small molecules such as acyl-homoserine lactones (AHLs). The structural differences between the types of signaling molecules have historically implied a lack of cross-talk among Gram-positive and Gram-negative quorum sensing systems. Recent investigations, however, have demonstrated the ability for AIPs and AHLs to be produced by non-canonical organisms, implying quorum sensing systems may be more universally recognized than previously hypothesized. With that in mind, our interests were piqued by the organisms Lactobacillus plantarum, a Gram-positive commensal probiotic known to participate in AIP-mediated quorum sensing, and Pseudomonas aeruginosa, a characterized Gram-negative pathogen whose virulence is in part controlled by AHL-mediated quorum sensing. Both health-related organisms are known to inhabit the human gut in various instances, both are characterized to elicit distinct effects on host immunity, and some studies hint at the putative ability of L. plantarum to degrade AHLs produced by P. aeruginosa. We therefore wanted to determine if L. plantarum cultures would respond to the addition of N-(3-oxododecanoyl)-L-homoserine lactone (3OC12) from P. aeruginosa by analyzing changes on both the transcriptome and proteome over time. Based on the observed upregulation of various two-component systems, response regulators, and native quorum sensing related genes, the resulting data provide evidence of an AHL recognition and response by L. plantarum.

Overexpression of luxS Promotes Stress Resistance and Biofilm Formation of Lactobacillus paraplantarum L-ZS9 by Regulating the Expression of Multiple Genes

Probiotics have evoked great interest in the past years for their beneficial effects. The aim of this study was to investigate whether luxS overexpression promotes the stress resistance of Lactobacillus paraplantarum L-ZS9. Here we show that overexpression of luxS gene increased the production of autoinducer-2 (AI-2, quorum sensing signal molecule) by L. paraplantarum L-ZS9. At the same time, overexpression of luxS promoted heat-, bile salt-resistance and biofilm formation of the strain. RNAseq results indicated that multiple genes encoding transporters, membrane proteins, and transcriptional regulator were regulated by luxS. These results reveal a new role for LuxS in promoting stress resistance and biofilm formation of probiotic starter.

The LuxS/AI-2 system of Streptococcus suis

Quorum sensing (QS) is an important protective mechanism that allows bacteria to adapt to its environment. A limited number of signal molecules play the key role of transmitting information in this mechanism. Signals are transmitted between individual bacterium through QS systems, resulting in the expression of specific genes. QS plays an important role in a variety of bacterial processes, including drug resistance, biofilm formation, motility, adherence, and virulence. Most Gram-positive and Gram-negative bacteria possess QS systems, mainly the LuxS/AI-2-mediated QS system. Evidence has been brought that LuxS/AI-2 system controls major virulence determinants in Streptococcus suis and, as such, the ability of this bacterial species to cause infections in humans and pigs. Understanding the S. suis LuxS/AI-2 system may open up novel avenues for decreasing the drug resistance and infectivity of S. suis. This article focuses on the progress made to date on the S. suis LuxS/AI-2-mediated QS system.