Adhesion Characteristics and Dual Transcriptomic and Proteomic Analysis of Lactobacillus reuteri SH23 upon Gastrointestinal Fluid Stress

Interspecies interactions promote dual-species biofilm formation by Lactiplantibacillus plantarum and Limosilactobacillus fermentum: Phenotypic and metabolomic insights

Probiotics are live microorganisms offering various health benefits to hosts, but exposure to adverse conditions can compromise their viability during gastrointestinal transit. Probiotics in the biofilm state have been proven as an alternative way to the probiotic survival challenge; however, knowledge of mixed-species biofilms by probiotics is limited. This study aimed to examine the ecological interactions between Lactiplantibacillus plantarum LP-52 and Limosilactobacillus fermentum LF-56 from a phenotypic and metabolomics perspective during their mixed-species biofilm development. In specific, we investigated how their interaction changes bacterial growth, biofilm-forming capacity, biofilm structure, biofilm metabolic activity, EPS production, and biofilm tolerance under gastrointestinal conditions. Moreover, a comprehensive metabolomics analysis was conducted to identify different metabolic profiles and elucidate the underlying mechanisms during the development of mixed-species biofilm. Results showed that their cooperative interaction significantly promoted the planktonic cell growth of L. fermentum LF-56 and L. plantarum LP-52 during their co-cultivation. The synergistic effect also markedly improved the biofilm formation, with increased cell counts in biofilms and higher metabolic activity when compared to each single-species biofilm. Confocal laser scanning microscopy imaging showed denser and more diverse structures of mixed-species biofilm with higher coverage and thickness. In addition, dual-species biofilms were best tolerated under simulated gastric and intestinal conditions. Untargeted metabolomics assay identified 852 differential metabolites, primarily associated with seven pathways: two pathways of nucleotide metabolism (purine metabolism, pyrimidine metabolism), two pathways of carbohydrate metabolism (TCA cycle, glycolysis), alanine, aspartate, and glutamate metabolism, riboflavin metabolism, and ABC transporters, which an enhanced energy metabolism, stress adaptation, and potential biofunctional benefits. With this respect, this investigation underscores the benefits of mixed probiotics biofilms and contributes to further application of probiotics in the food and biotechnology industry.

Potential Probiotic Properties and Complete Genome Analysis of Limosilactobacillus reuteri LRA7 from Dogs

This study aimed to isolate and screen canine-derived probiotics with excellent probiotic properties. Strain characterization was conducted using a combination of in vitro and in vivo probiotic characterization and safety assessments, as well as complete genome analysis. The results showed that Limosilactobacillus reuteri LRA7 exhibited excellent bacteriostatic and antioxidant activities. The survival rate at pH 2.5 was 79.98%, and the viable counts after exposure to gastrointestinal fluid and 0.5% bile salts were 7.77 log CFU/mL and 5.29 log CFU/mL, respectively. The bacterium also exhibited high hydrophobicity, self-coagulation, and high temperature tolerance, was negative for hemolysis, and was sensitive to clindamycin. In vivo studies in mice showed that the serum superoxide dismutase activity level was 53.69 U/mL higher in the MR group of mice compared to that of the control group, the malondialdehyde content was 0.53 nmol/mL lower in the HR group, and the highest jejunal V/C value was 4.11 ± 1.05 in the HR group (p < 0.05). The L. reuteri LRA7 gene is 2.021 megabases in size, contains one chromosome and one plasmid, and is annotated with 1978 functional genes. In conclusion, L. reuteri LRA7 has good probiotic potential and is safe. It can be used as an ideal probiotic candidate strain of canine origin.

The ameliorative mechanism of Lactiplantibacillus plantarum NJAU-01 against D-galactose induced oxidative stress: a hepatic proteomics and gut microbiota analysis

Probiotic intervention is an effective strategy to alleviate oxidative stress-related diseases. Our previous studies found that Lactiplantibacillus plantarum NJAU-01 (NJAU-01) exhibited antioxidant effects in a D-galactose (D-gal)-induced aging mouse model. However, the underlying mechanism remains to be unveiled. This study was aimed to investigate the ameliorative effect and mechanism of NJAU-01 against oxidative stress induced by D-gal. The results showed that NJAU-01 could reverse the tendency of a slow body weight gain induced by D-gal. NJAU-01 relieved hepatic oxidative stress via increasing the hepatic total antioxidant capacity and antioxidant enzyme activities including superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT). Moreover, the malondialdehyde (MDA) level was reversed after NJAU-01 supplementation. The proteomic results showed that there were 201 differentially expressed proteins (DEPs) between NJAU-01 and D-gal groups. NJAU-01 regulated the expressions of glutathione S-transferase Mu 5 (Gstm5), glutathione S-transferase P2 (Gstp2) and NADH dehydrogenase 1α subcomplex subunit 7 (Ndufa7) related to oxidative stress, and autophagy protein 5 (Atg5) and plasma alpha-L-fucosidase (Fuca2) involved in autophagy, etc. 16S rDNA sequencing results showed that NJAU-01 supplementation could regulate the gut microbiota dysbiosis induced by D-gal via increasing the relative abundances of the phylum Firmicutes and the genus Lactobacillus and reducing the relative abundances of the phylum Bacteroidetes and the genera Lachnospiraceae_NK4A136_group as well as Prevotellaceae_UCG-001, etc.. Spearman correlation analysis results showed that the altered gut microbiota composition had a significant correlation with antioxidant enzyme activities and the DEPs related to oxidative stress. Overall, NJAU-01 alleviated hepatic oxidative stress induced by D-gal via manipulating the gut microbiota composition and hepatic protein expression profile.

Invited review: Current perspectives for analyzing the dairy biofilms by integrated multiomics

Biofilms formed by pathogenic or spoilage microorganisms have become serious issues in the dairy industry, as this mode of life renders such microorganisms highly resistant to cleaning-in-place (CIP) procedures, disinfectants, desiccation, and other control strategies. The advent of omics techniques, especially the integration of different omics tools, has greatly improved our understanding of the features of microbial biofilms, and provided in-depth knowledge on developing effective methods that are directly against deleterious biofilms. This review provides novel insights into the single use of each omics tool and the application of multiomics tools to unravel the mechanisms of biofilm formation, specific molecular phenotypes exhibited by biofilms, and biofilm control strategies. Challenges and future perspective on the integration of omics tools for biofilm studies are also addressed.

Multifunctional properties of the transmembrane LPxTG-motif protein derived from Limosilactobacillus reuteri SH-23

The LPxTG-motif protein is an important transmembrane protein with high hydrophilicity and stability, as evidenced by its stress tolerance and adhesion ability. In this study, a novel LPxTG-motif protein with esterase activity (LEP) was expressed, and the multifunctional properties such as adhesion properties and esterase activity were also investigated. When cocultured with Limosilactobacillus reuteri SH-23, the adhesion ability of L. reuteri SH-23 to HT-29 cells was improved, and this adhesion was further found relating to the potential target protein Pyruvate kinase M1/2 (PKM) of HT-29 cells. In addition, as a multifunctional protein, LEP can promote the hydrolysis of bovine milk lipids with its esterase activity, and the activity was enhanced in the presence of Zn2+ and Mn2+ at pH 7. Furthermore, the polyunsaturated fatty acids (PUFA) such as linoleic acid and eicosapentaenoic acid were found to increase during the hydrolyzing process. These unique properties of LEP provide a comprehensive understanding of the adhesion function and PUFA releasing properties of the multifunctional protein derived from L. reuteri SH-23 and shed light on the beneficial effect of this Lactobacillus strain on the colonization of the gastrointestinal tract.

The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare

The symbiosis of probiotic bacteria with humans has rendered various health benefits while providing nutrition and a suitable environment for their survival. However, the probiotics must survive unfavorable gut conditions to exert beneficial effects. The intrinsic resistance of probiotics to survive harsh conditions results from a myriad of proteins. Interaction of microbial proteins with the host is indispensable for modulating the gut microbiome, such as interaction with cell receptors and protective action against pathogens. The complex interplay of proteins should be unraveled by utilizing metaproteomic strategies. The contribution of probiotics to health is now widely accepted. However, due to the inconsistency of generalized probiotics, contemporary research toward precision probiotics has gained momentum for customized treatment. This review explores the application of metaproteomics and AI/ML algorithms in resolving multiomics data analysis and in silico prediction of microbial features for screening specific beneficial probiotic organisms. Implementing these integrative strategies could augment the potential of precision probiotics for personalized healthcare.

Developing the Limosilactobacillus reuteri Chassis through an Endogenous Programmable Endonuclease-Based Genome Editing Tool

Using genetically tractable probiotics to engineer live biotherapeutic products (LBPs) for disease treatment is urgently needed. Limosilactobacillus reuteri is an important vertebrate gut symbiont, which has great potential for developing LBPs. However, in L. reuteri, synthetic biology work is largely limited by the long editing cycle. In this study, we identified a subtype II-A CRISPR-Cas9 system in L. reuteri 03 and found the endogenous Cas9 (LrCas9) recognizing a broad protospacer-adjacent motif (PAM) sequence (3'-NDR; N = A, G, T, C; D = A, G, T; R = A, G). We reprogrammed the LrCas9 for efficient gene deletion (95.46%), point mutation (86.36%), large fragment deletion (40 kb), and gene integration (1743 bp, 73.9%), which uncovered the function of the repeated conserved domains in mucus-binding protein. Moreover, we analyzed the distribution of endogenous endonucleases in 304 strains of L. reuteri and found the existence of programmable endonucleases in 98.36% of L. reuteri strains suggesting the potential to reprogram endogenous endonucleases for genetic manipulation in the majority of L. reuteri strains. In conclusion, this study highlights the development of a new probiotic chassis based on endogenous endonucleases in L. reuteri 03, which paves the way for the development of genome editing tools for functional genetic studies in other L. reuteri. We believe that the development of an endogenous endonuclease-based genetic tool will greatly facilitate the construction of LBPs.

Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15

Bifidobacterium is a predominant and important genus in the bacterial population of the human gut microbiota. Despite the increasing number of studies on the beneficial functionality of bifidobacteria for human health, knowledge about their antioxidant potential is still insufficient. Several in vivo and in vitro studies of Bifidobacterium strains and their cellular components have shown good antioxidant capacity that provided a certain protection of their own and the host's cells. Our work presents the data of transcriptomic, proteomic, and metabolomic analyses of the growing and stationary culture of the probiotic strain B. longum subsp. longum GT15 after exposure to hydrogen peroxide for 2 h and oxygen for 2 and 4 h. The results of the analysis of the sequenced genome of B. longum GT15 showed the presence of 16 gene-encoding proteins with known antioxidant functions. The results of the full transcriptomic analysis demonstrated a more than two-fold increase of levels of transcripts for eleven genes, encoding proteins with antioxidant functions. Proteomic data analysis showed an increased level of more than two times for glutaredoxin and thioredoxin after the exposure to oxygen, which indicates that the thioredoxin-dependent antioxidant system may be the major redox homeostasis system in B. longum bacteria. We also found that the levels of proteins presumably involved in global stress, amino acid metabolism, nucleotide and carbohydrate metabolism, and transport had significantly increased in response to oxidative stress. The metabolic fingerprint analysis also showed good discrimination between cells responding to oxidative stress and the untreated controls. Our results provide a greater understanding of the mechanism of oxidative stress response in B. longum and the factors that contribute to its survival in functional food products.

The regulation of simulated artificial oro-gastrointestinal transit stress on the adhesion of Lactobacillus plantarum S7

BACKGROUND

Oro-gastrointestinal stress in the digestive tract is the main stress to which orally administered probiotics are exposed. The regulation of oro-gastrointestinal transit (OGT) stress on the adhesion and survival of probiotics under continuous exposure to simulated salivary-gastric juice-intestinal juice was researched in this study.

RESULTS

Lactobacillus plantarum S7 had a higher survival rate after exposure to simulated OGT1 (containing 0.15% bile salt) stress and OGT2 (containing 0.30% bile salt) stress. The adhesion ability of L. plantarum S7 was significantly increased by OGT1 stress (P < 0.05) but was not changed significantly by OGT2 stress (P > 0.05), and this trend was also observed in terms of the thickness of the surface material of L. plantarum S7 cells. The expression of surface proteins of L. plantarum S7, such as the 30 S ribosomal proteins, mucus-binding protein and S-layer protein, was significantly downregulated by OGT stress (P < 0.05); meanwhile, the expression of moonlight proteins, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycorate kinase (PGK), beta-phosphoglucomutase (PGM1), GroEL and glucose-6-phosphate isomerase (PGI), was significantly upregulated (P < 0.05). However, the upregulation of GAPDH, PGK, PGM1 and PGI mediated by OGT1 stress was greater than those mediated by OGT2 stress. The quorum sensing pathway of L. plantarum S7 was changed significantly by OGT stress compared with no OGT stress cells (P < 0.05), and the expression of Luxs in the pathway was significantly upregulated by OGT1 stress (P < 0.05). The ABC transportation pathway was significantly altered by OGT1 stress (P < 0.05), of which the expression of the peptide ABC transporter substrate-binding protein and energy-coupling factor transporter ATP-binding protein EcfA was significantly upregulated by OGT stress (P < 0.05). The glycolide metabolism pathway was significantly altered by OGT1 stress compared with that in response to OGT2 stress (P < 0.05).

CONCLUSION

L. plantarum S7 had a strong ability to resist OGT stress, which was regulated by the proteins and pathways related to OGT stress. The adhesion ability of L. plantarum S7 was enhanced after continuous exposure to OGT1 stress, making it a potential probiotic with a promising future for application.

The role of potential probiotic strains Lactobacillus reuteri in various intestinal diseases: New roles for an old player

Lactobacillus reuteri (L. reuteri), a type of Lactobacillus spp., is a gut symbiont that can colonize many mammals. Since it was first isolated in 1962, a multitude of research has been conducted to investigate its function and unique role in different diseases as an essential probiotic. Among these, the basic functions, beneficial effects, and underlying mechanisms of L. reuteri have been noticed and understood profoundly in intestinal diseases. The origins of L. reuteri strains are diverse, with humans, rats, and piglets being the most common. With numerous L. reuteri strains playing significant roles in different intestinal diseases, DSM 17938 is the most widely used in humans, especially in children. The mechanisms by which L. reuteri improves intestinal disorders include protecting the gut barrier, suppressing inflammation and the immune response, regulating the gut microbiota and its metabolism, and inhibiting oxidative stress. While a growing body of studies focused on L. reuteri, there are still many unknowns concerning its curative effects, clinical safety, and precise mechanisms. In this review, we initially interpreted the basic functions of L. reuteri and its related metabolites. Then, we comprehensively summarized its functions in different intestinal diseases, including inflammatory bowel disease, colorectal cancer, infection-associated bowel diseases, and pediatric intestinal disorders. We also highlighted some important molecules in relation to the underlying mechanisms. In conclusion, L. reuteri has the potential to exert a beneficial impact on intestinal diseases, which should be further explored to obtain better clinical application and therapeutic effects.

The Bioavailability of Glycyrrhizinic Acid Was Enhanced by Probiotic Lactobacillus rhamnosus R0011 Supplementation in Liver Fibrosis Rats

Glycyrrhizinic acid (GL) is clinically applied to treat liver injury, and the bioavailability of orally administered GL is closely related to the gut microbiota. Therefore, the dysbiosis of gut flora in liver injury could significantly influence GL bioavailability. Still, less is known about the impact of probiotic supplementation on the bio-absorption process of oral medication, especially under a pathological state. Herein, probiotic L. rhamnosus R0011 (R0011) with a high viability in the harsh gastrointestinal environment was selected, and the effect of R0011 on the GL bioavailability in rats was investigated. Four groups of rats (n = 6 per group) were included: the normal group (N group), the normal group supplemented with R0011 (NLGG group), CCl4-induced chronic liver injury model (M group), and the model group supplemented with R0011 (MLGG group). Our results showed that liver injury was successfully induced in the M and MLGG groups via an intraperitoneal injection of 50% (v/v) CCl4 solution. Healthy rats supplemented with R0011 could increase the bioavailability of GL by 1.4-fold compared with the normal group by plasma pharmacokinetic analysis. Moreover, the GL bioavailability of MLGG group was significantly increased by 4.5-fold compared with the model group. R0011 directly improved gut microbial glucuronidase and downregulated the host intestinal drug transporter gene expression of multidrug resistance protein 2 (MRP2). More critically, R0011 restored the gut microbiota composition and regulated the metabolic function, significantly enhancing the microbial tryptophan metabolic pathway compared with the pathological state, which may indirectly promote the bioavailability of GL. Overall, these data may provide possible strategies by which to address the low bioavailability of traditional medicine through probiotic intervention.

Antioxidant peptides derived from hydrolyzed milk proteins by Lactobacillus strains: A BIOPEP-UWM database-based analysis

Milk-derived peptides have been identified as the essential ingredients in the food industry for the health-promoting properties. Some bioactive peptides in the milk product can be released by the specific protease system of lactic acid bacteria (LAB) during the fermentation processing. In this research, the bioactive peptides released from the casein and whey protein are investigated by the hydrolyzing ability of the Lactobacillus brevis CGMCC15954, Lactobacillus reuteri WQ-Y1 and Lactobacillus plantarum A3. Results found that the hydrolysates of casein/whey protein generated by L. reuteri WQ-Y1 have the potential antioxidant activity. Furthermore, milk-derived peptides identified by the liquid chromatography-mass spectrometry (LC-MS/MS) with the BIOPEP-UWM database showed the YLGYLEQLLR (α_S1-casein), VKEAMAPK (β-casein), YIPIQYVLSR (κ-casein) fragment had the promising antioxidant activity, especially VKEAMAPK, which exhibited IC₅₀ of 0.63 and 0.86 mg/mL in DPPH and ABTS free radical scavenging activity. The finding of this study sheds some light of obtaining milk-derived peptides by using the Lactobacillus strains and proves the potential bioactive function of the LAB fermented milk products.