The Genus Lactobacillus: A Taxonomic Update

Lentilactobacillus farraginis FSI (3): a whole cell biocatalyst for the synthesis of kojic acid derivative under aquatic condition

Kojic acid derivatives are useful in the cosmetics and pharmaceutical industries. The current investigation focuses on the search for a safe and environmentally friendly newer whole-cell biocatalyst for the synthesis of kojic acid derivative especially 2-amino-6-(hydroxymethyl)-8-oxo-4-phenyl-4,8-dihydropyrano[3,2-b]pyran-3-carbonitrile (APhCN). In this context, a total of six cultures were isolated from fecal samples of infants and subjected to probiotic characterization followed by screening as whole cell biocatalyst (WCB). In this multicomponent reaction, benzaldehyde, malononitrile, and kojic acid were used to synthesize APhCN at room temperature under aqueous conditions. The screening of potent whole cell biocatalyst (WCB) from isolated cultures was done by comparing reaction time and percent yield. The potent WCB gave a good yield of 95% within 15 h of time and hence further characterized biochemically and identified as Lentilactobacillus farraginis by using 16S rRNA gene sequencing. Lactobacilli having GRAS (generally regarded as safe) status and being able to carry out this transformation under moderate reaction conditions with easy recovery of both product and biocatalyst, it has the potential to replace some of the chemical catalytic methods.

Biopurification using non-growing microorganisms to improve plant protein ingredients

Securing a sustainable global food supply for a growing population requires a shift toward a more plant-based diet. The application of plant-based proteins is therefore increasing, but unpleasant off-flavors complicate their use. Here, we screened 97 microorganisms for their potential to remove off-flavors in a process with limiting amounts of fermentable sugar. This allowed the production of a more neutral-tasting, purified food ingredient while limiting microbial growth and the production of typical fermentation end products. We demonstrate that various lactic acid bacteria (LAB) and yeasts remove "green" aldehydes and ketones. This conversion can be carried out in less than one hour in almond, pea, potato, and oat proteins. Heterofermentative LAB was best at aldehyde and ketone neutralization with minimum de novo formation of microbial volatiles such as ethylacetate (sweet, fruity) or alpha-diketones (butter- and cheese-like). While sensory properties were improved, changes in protein solubility, emulsification, foaming, and in vitro digestibility were limited.

Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants

Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.

Probiotics for Aquaculture: Hope, Truth, and Reality

The use of microorganisms as beneficial crops for human and animal health has been studied for decades, and these microorganisms have been in practical use for quite some time. Nowadays, in addition to well-known examples of beneficial properties of lactic acid bacteria, bifidobacteria, selected Bacillus spp., and yeasts, there are several other bacteria considered next-generation probiotics that have been proposed to improve host health. Aquaculture is a rapidly growing area that provides sustainable proteins for consumption by humans and other animals. Thus, there is a need to develop new technologies for the production practices associated with cleaner and environment-friendly approaches. It is a well-known fact that proper selection of the optimal probiotics for use in aquaculture is an essential step to ensure effectiveness and safety. In this critical review, we discuss the evaluation of host-specific probiotics in aquaculture, challenges in using probiotics in aquaculture, methods to improve the survival of probiotics under different environmental conditions, technological approach to improving storage, and delivery along with possible negative consequences of using probiotics in aquaculture. A critical analysis of the identified challenges for the use of beneficial microbes in aquaculture will help in sustainable aquafarming, leading to improved agricultural practices with a clear aim to increase protein production.

Probiotics: Shaping the gut immunological responses

Probiotics are live microorganisms exerting beneficial effects on the host's health when administered in adequate amounts. Among the most popular and adequately studied probiotics are bacteria from the families Lactobacillaceae, Bifidobacteriaceae and yeasts. Most of them have been shown, both in vitro and in vivo studies of intestinal inflammation models, to provide favorable results by means of improving the gut microbiota composition, promoting the wound healing process and shaping the immunological responses. Chronic intestinal conditions, such as inflammatory bowel diseases (IBD), are characterized by an imbalance in microbiota composition, with decreased diversity, and by relapsing and persisting inflammation, which may lead to mucosal damage. Although the results of the clinical studies investigating the effect of probiotics on patients with IBD are still controversial, it is without doubt that these microorganisms and their metabolites, now named postbiotics, have a positive influence on both the host's microbiota and the immune system, and ultimately alter the topical tissue microenvironment. This influence is achieved through three axes: (1) By displacement of potential pathogens via competitive exclusion; (2) by offering protection to the host through the secretion of various defensive mediators; and (3) by supplying the host with essential nutrients. We will analyze and discuss almost all the in vitro and in vivo studies of the past 2 years dealing with the possible favorable effects of certain probiotic genus on gut immunological responses, highlighting which species are the most beneficial against intestinal inflammation.

Initial culture media pH influences the antibacterial activity and metabolic footprint of Lactobacillus acidophilus BIOTECH 1900

This study investigated the impact of initial culture media pH on the antibacterial properties and metabolic profile of cell-free supernatants (CFSs) from Lactobacillus acidophilus BIOTECH 1900 (LAB1900). The CFSs harvested from LAB1900 grown in de Man, Rogosa, Sharpe broth with initial pH of 5.5 (CFS5.5) and 6.6 (CFS6.6) were tested. The two CFSs elicited varying degrees of activity against three gram-negative bacteria. In the agar-well diffusion against Pseudomonas aeruginosa, CFS5.5 and CFS6.6 recorded 14.36 ± 1.34 and 13.06 ± 1.29 mm inhibition, respectively. Interestingly, against Klebsiella pneumoniae, CFS5.5 showed 14.36 ± 1.56 mm inhibition which was significantly higher than the 12.22 ± 1.31 mm inhibition of CFS6.6 (p = 0.0464). While against Acinetobacter baumannii, significantly higher inhibition of 10.66 ± 0.51 mm was observed in CFS6.6 compared to the 7.58 ± 1.93 mm inhibition of CFS5.5 (p = 0.0087). Nonetheless, both CFSs were bactericidal, with a minimum inhibitory and bactericidal concentration range of 3.90625-7.8125 mg/mL. The varied antibacterial activities may be attributed to the metabolite compositions of CFSs. A total of 152 metabolites driving the separation between CFSs were noted, with the majority upregulated in CFS5.5. Furthermore, 15 were putatively identified belonging to acylcarnities, vitamins, gibberellins, glycerophospholipids, and peptides. In summary, initial culture media pH affects the production of microbial metabolites with antibacterial properties.

Detection of oxalyl-CoA decarboxylase (oxc) and formyl-CoA transferase (frc) genes in novel probiotic isolates capable of oxalate degradation in vitro

Oxalate degradation is one of lactic acid bacteria's desirable activities. It is achieved by two enzymes, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). The current study aimed to screen 15 locally isolated lactic acid bacteria to select those with the highest oxalate degradation ability. It also aimed to amplify the genes involved in degradation. MRS broth supplemented with 20 mM sodium oxalate was used to culture the tested isolates for 72 h. This was followed by an enzymatic assay to detect remaining oxalate. All isolates showed oxalate degradation activity to variable degrees. Five isolates demonstrated high oxalate degradation, 78 to 88%. To investigate the oxalate-degradation potential of the selected isolates, they have been further tested for the presence of genes that encode for enzymes involved in oxalate catabolism, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). Three strains showed bands with the specific OXC and FRC forward and reverse primers designated as (SA-5, 9 and 37). Species-level identification revealed Loigolactobacillus bifermentans, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum. Preliminary results revealed that the tested probiotic strains harbored both oxc and frc whose products are putatively involved in oxalate catabolism. The probiotic potential of the selected strains was evaluated, and they showed high survival rates to both simulated gastric and intestinal fluids and variable degrees of antagonism against the tested Gram-positive and negative pathogens and were sensitive to clarithromycin but resistant to both metronidazole and ceftazidime. Finally, these strains could be exploited as an innovative approach to establish oxalate homeostasis in humans and prevent kidney stone formation.

Lactiplantibacillus brownii sp. nov., a novel psychrotolerant species isolated from sauerkraut

A Gram-stain-positive, rod-shaped, facultatively anaerobic and homofermentative strain, named WILCCON 0030T, was isolated from sauerkraut (fermented cabbage) collected from a local market in the Moscow region of Russia. Comparative analyses based on 16S rRNA gene sequence similarity and whole genome relatedness indicated that strain WILCCON 0030T was most closely related to the type strains Lactiplantibacillus nangangensis NCIMB 15186T, Lactiplantibacillus daoliensis LMG 31171T and Lactiplantibacillus pingfangensis LMG 31176T. However, the average nucleotide identity and digital DNA-DNA hybridization prediction values with these closest relatives only ranged from 84.6 to 84.9 % and from 24.1 to 24.7 %, respectively, and were below the 95.0 and 70.0% thresholds for species delineation. Substantiated by further physiological and biochemical analyses, strain WILCCON 0030T represents a novel species within the genus Lactiplantibacillus for which we propose the name Lactiplantibacillus brownii sp. nov. (type strain WILCCON 0030T=DSM 116485T=LMG 33211T).

In silico prospection of Lactobacillus acidophilus strains with potential probiotic activity

Lactic acid bacteria (LAB) are fermentative microorganisms and perform different roles in biotechnological processes, mainly in the food and pharmaceutical industries. Among the LAB, Lactobacillus acidophilus is a species that deserves to be highlighted for being used both in prophylaxis and in the treatment of pathologies. Most of the metabolites produced by this species are linked to the inhibition of pathogens. In this study, we utilized a pangenomic and metabolic annotation analysis using Roary and BlastKOALA, ML-based probiotic activity prediction with iProbiotic and whole-genome similarity using ANI to identify strains of L. acidophilus with potential probiotic activity. According to the results in BlastKOALA and iProbiotics, L. acidophilus NCTC 13721 had the greatest potential among the 64 strains tested, both in terms of its ability to be a Lactobacillus spp. probiotic, when in the amount of genes involved in the metabolism of organic acids and quorum sensing. In addition, DSM 20079 proved to be promising for prospecting new probiotic Lactobacillus from BlastKOALA analyses, as they presented similar results in the number of genes involved in the production of lactic acid, acetic acid, hydrogen peroxide, except for quorum sensing where the NCTC 13721 strain had 14 more genes. L. acidophilus NCTC 13721 and L. acidophilus La-5 strains showed greater ability to be Lactobacillus spp. probiotic capacity, showing 84.8% and 51.9% capacity in the iProbiotics tool, respectively. When analyzed in ANI, none of the evaluated strains showed genomic similarity with NCTC 13721. In contrast, the DSM 20079 strain showed genomic similarity with all evaluated strains except NCTC 13721. Furthermore, eight strains with characteristics with approximately 100% genomic similarity to La-5 were listed: S20_1, LA-5, FSI4, APC2845, LA-G80-111, DS1_1A, LA1, and BCRC 14065. Therefore, according to the findings in iProbiotics and BlastKoala, among the 64 strains evaluated, NCTC 13721 is the most promising strain to be used for future in vitro studies.

Evaluation of Lentilactobacillus parafarraginis A6-2 strain for aluminum removal and anti-inflammatory effects: implications for alleviating Al toxicity

AIM

To assess the effectiveness of Lentilactobacillus parafarraginis A6-2 cell lysate for the removal of aluminum (Al), which induces neurotoxicity, and its protective effect at cellular level.

METHODS AND RESULTS

The cell lysate of the selected L. parafarraginis A6-2 strain demonstrated superior Al removal compared to live or dead cells. The Al removal efficiency of L. parafarraginis A6-2 cell lysate increased with decreasing pH and increasing temperature, primarily through adsorption onto peptidoglycan. Neurotoxicity mitigation potential of L. parafarraginis A6-2 was evaluated using C6 glioma cells. C6 cells exposed with increasing concentration of Al led to elevated toxicity and inflammation, which were gradually alleviated upon treatment with L. parafarraginis A6-2. Moreover, Al-induced oxidative stress in C6 cells showed a concentration-dependent reduction upon treatment with L. parafarraginis A6-2.

CONCLUSIONS

This study demonstrated that L. parafarraginis A6-2 strain, particularly in its lysate form, exhibited enhanced capability for Al removal. Furthermore, it effectively mitigated Al-induced toxicity, inflammation, and oxidative stress.

Shaping Future Foods through Fermentation of Side Streams: Microbial, Chemical, and Physical Characteristics of Fermented Blends from Sunflower Seed Press Cake and Cheese Whey

The current food system suffers from the inefficient use of resources, including the generation of side streams of low economic value that still contain nutritional components. One potential approach to reach a more sustainable food system is to reintroduce such side streams into a circular value chain and valorise them in novel food products, preferably in an unrefined or minimally refined manner. Blending side streams from different industries might be a suitable way to improve the nutritional value of the final matrix. In this study, sunflower seed press cake and cheese whey were combined to obtain matrices containing valuable proteins, structuring polysaccharides, as well as lactose and minerals facilitating fermentation with three different co-cultures of lactic acid bacteria and yeasts. Fermentation for 48 h at 26 °C decreased the pH from ~6.3 to ~4.7 and enhanced the storage stability of the blends with no effect on their rheological properties and microstructure. This research demonstrates the potential of fermentation as a mean to stabilise side stream blends while only minimally affecting their physical appearance.

Screening and Constructing a Library of Promoter-5'-UTR Complexes with Gradient Strength in Pediococcus acidilactici

The GRAS (generally recognized as safe) strain Pediococcus acidilactici is well known for its antibacterial and probiotic functions. Furthermore, as P. acidilactici has excellent high temperature and salt resistance, it is an ideal host for the production of food enzymes, food additives, and pharmaceuticals. In this regard, it is desirable and feasible to enhance the production of these products through the metabolic engineering of P. acidilactici. However, the rare gene expression elements greatly obstruct the development of engineering P. acidilactici. In this study, we screened and constructed a library of promoter-5'-UTR (PUTR) complexes in P. acidilactici DY15 for regulating gene expression at the transcription and translation levels. In the post-log phase, the mRNA and protein expression level ranges of the 90 screened native PUTRs were 0.059-2010% and 0.77-245%, respectively, of the P32 promoter. Besides, several PUTRs exhibited great expression stability under high temperature, salt, and ethanol stress. We analyzed the structure of PUTRs and obtained the conserved regions of the promoter and 5'-UTR. Based on the identified core regions of PUTRs, we constructed a panel of combinatorial PUTRs with higher and stable protein expression levels. The strongest combinatorial PUTR was 853% of the P32 promoter in the protein expression level. Finally, the obtained PUTRs were applied to optimize the expression level of aminotransferase and improve the phenyllactic acid (PLA) production in P. acidilactici DY15. The achieved yield was 950.6 mg/L, which was 79.2% higher than the wild-type strain. These results indicated that the obtained PUTRs with gradient strength had great potential for precisely regulating gene expression to achieve various goals in P. acidilactici.

Tisochrysis lutea as a Substrate for Lactic Acid Fermentation: Biochemical Composition, Digestibility, and Functional Properties

Microalgae, because of their high nutritional value and bioactive molecule content, are interesting candidates for functional foods, including fermented foods, in which the beneficial effects of probiotic bacteria combine with those of biomolecules lying in microalgal biomass. The aim of this work was to evaluate the potential of Tisochrysis lutea F&M-M36 as a substrate for Lactiplantibacillus plantarum ATCC 8014 and to verify fermentation effects on functionality. Bacterium selection among three lactobacilli was based on growth and resistance to in vitro digestion. Microalgal raw biomass and its digested residue were fermented in two matrixes, water and diluted organic medium, and analysed for biochemical composition and antioxidant activity along with their unfermented counterparts. Bacterial survivability to digestion and raw biomass digestibility after fermentation were also evaluated. Fucoxanthin was strongly reduced (>90%) in post-digestion residue, suggesting high bioavailability. Raw biomass in diluted organic medium gave the highest bacterial growth (8.5 logCFU mL^-1) and organic acid production (5 mg L^-1), while bacterial survivability to digestion (<3%) did not improve. After fermentation, the antioxidant activity of lipophilic extracts increased (>90%). Fermentation appears an interesting process to obtain T. lutea-based functional foods, although further investigations are needed to optimize bacterial growth and fully evaluate its effects on functionality and organoleptic features.

Analysis of CRISPR-Cas Loci and their Targets in Levilactobacillus brevis

The CRISPR‒Cas system acts as a bacterial defense mechanism by conferring adaptive immunity and limiting genetic reshuffling. However, under adverse environmental hazards, bacteria can employ their CRISPR‒Cas system to exchange genes that are vital for adaptation and survival. Levilactobacillus brevis is a lactic acid bacterium with great potential for commercial purposes because it can be genetically manipulated to enhance its functionality and nutritional value. Nevertheless, the CRISPR‒Cas system might interfere with the genetic modification process. Additionally, little is known about the CRISPR‒Cas system in this industrially important microorganism. Here, we investigate the prevalence, diversity, and targets of CRISPR‒Cas systems in the genus Levilactobacillus, further focusing on complete genomes of L. brevis. Using the CRISPRCasFinder webserver, we identified 801 putative CRISPR-Cas systems in the genus Levilactobacillus. Further investigation focusing on the complete genomes of L. brevis revealed 54 putative CRISPR-Cas systems. Of these, 46 were orphan CRISPRs, and eight were CRISPR‒Cas systems. The type II-A CRISPR‒Cas system is the most common in Levilactobacillus and L. brevis complete genomes. Analysis of the spacer's target showed that the CRISPR‒Cas systems of L. brevis mainly target the enterococcal plasmids. Comparative analysis of putative CRISPR-Cas loci in Levilactobacillus brevis.

The Effects of Probiotics on Small Intestinal Microbiota Composition, Inflammatory Cytokines and Intestinal Permeability in Patients with Non-Alcoholic Fatty Liver Disease

The prevalence of non-alcoholic fatty liver disease (NAFLD) has soared globally. As our understanding of the disease grows, the role of the gut-liver axis (GLA) in NAFLD pathophysiology becomes more apparent. Hence, we focused mainly on the small intestinal area to explore the role of GLA. We looked at how multi-strain probiotics (MCP^® BCMC^® strains) containing six different Lactobacillus and Bifidobacterium species affected the small intestinal gut microbiota, inflammatory cytokines, and permeability in NAFLD patients. After six months of supplementation, biochemical blood analysis did not show any discernible alterations in either group. Five predominant phyla known as Actinobacteria, Proteobacteria, Firmicutes, Bacteroidota and Fusobacteria were found in NAFLD patients. The probiotics group demonstrated a significant cluster formation of microbiota composition through beta-diversity analysis (p < 0.05). This group significantly reduced three unclassifiable species: unclassified_Proteobacteria, unclassified_Streptococcus, and unclassified_Stenotrophomonas. In contrast, the placebo group showed a significant increase in Prevotella_melaninogenica and Rothia_mucilaginosa, which were classified as pathogens. Real-time quantitative PCR analysis of small intestinal mucosal inflammatory cytokines revealed a significant decrease in IFN-γ (-7.9 ± 0.44, p < 0.0001) and TNF-α (-0.96 ± 0.25, p < 0.0033) in the probiotics group but an increase in IL-6 (12.79 ± 2.24, p < 0.0001). In terms of small intestinal permeability analysis, the probiotics group, unfortunately, did not show any positive changes through ELISA analysis. Both probiotics and placebo groups exhibited a significant increase in the level of circulating zonulin (probiotics: 107.6 ng/mL ± 124.7, p = 0.005 vs. placebo: 106.9 ng/mL ± 101.3, p = 0.0002) and a significant decrease in circulating zonula occluden-1 (ZO-1) (probiotics: -34.51 ng/mL ± 18.38, p < 0.0001 vs. placebo: -33.34 ng/mL ± 16.62, p = 0.0001). The consumption of Lactobacillus and Bifidobacterium suggested the presence of a well-balanced gut microbiota composition. Probiotic supplementation improves dysbiosis in NAFLD patients. This eventually stabilised the expression of inflammatory cytokines and mucosal immune function. To summarise, more research on probiotic supplementation as a supplement to a healthy diet and lifestyle is required to address NAFLD and its underlying causes.

Cisplatin conjugation with an exopolysaccharide extracted from Lactobacillus gasseri potentiates its efficacy and attenuates its toxicity

The development of newer cisplatin analogs is constantly being investigated owing to its low solubility, poor pharmacokinetics, and dose-related toxicity. In order to address the limitations of current cisplatin therapy, the present study was undertaken. Cisplatin conjugation with an exopolysaccharide extracted from Lactobacillus gasseri (LG-EPS) showed remarkably enhanced and selective anticancer activity by targeting tumor cells overexpressing glucose transporter 1 (GLUT1). The EPS-cisplatin complex exhibited a 600-fold increase in aqueous solubility with a better pharmacokinetic profile (longer half-life) in comparison to cisplatin. Cell viability assay and western blotting demonstrated a strong correlation between the cytotoxicity profile and GLUT1 expressions in different cell lines. The concentration of DNA-bound platinum was also found to be significantly higher in EPS-cisplatin-treated cells. Quercetin, a competitive inhibitor of GLUTs, was shown to prevent this selective uptake of EPS-cisplatin complex. Surprisingly, EPS-cisplatin complex showed an exceptionally safer profile (4 times the maximum tolerated dose of cisplatin) in the acute toxicity study and was also more efficacious against the xenograft mice model. The study suggests that this green glycoconjugation can be an effective and safer strategy to broaden the therapeutic potential of anti-cancer drugs in general and cisplatin in particular.

Application of 16S rRNA virtual RFLP for the discrimination of some closely taxonomic-related lactobacilli species

BACKGROUND

Several species in Lactobacillaceae family were recognized as potential probiotic bacteria. In this group of lactic acid bacteria, species are taxonomically closed and usually share similar 16S rRNA gene, thus, instead of so their identification and discrimination are too difficult.

METHOD

In the present study, virtual restriction fragment length polymorphism (RFLP) is instead of was used as a tool to discriminate between the closely related species Lactiplantibacillus plantarum (L plantarum), Lactiplantibacillus paraplantarum (L paraplantarum), and Lactiplantibacillus pentosus (L pentosus); Latilactobacillus sakei (L sakei), Latilactobacillus curvatus(L curvatus), and Latilactobacillus graminis (L graminis); Lacticaseibacillus casei (L casei), Lacticaseibacillus paracasei (L paracasei), Lacticaseibacillus zeae, and Lacticaseibacillus rhamnosus; Lactobacillus gasseri (L gasseri) and Lactobacillus johnsonii (L johnsonii). In silico comparative analysis of 16S rRNA sequences digested by 280 restriction enzymes was performed in order to search the key enzymes which gives different profiles.

RESULTS

Results revealed that L casei, L paracasei, L zeae, and Lb rhamnosus could be separated from each other on the basis of AlwI, BpuEI, BsgI, BsrDI, BstYI, EarI, MluCI, and NsPI RFLP. Results showed also that different RFLP patterns were obtained from L sakei, L graminis and L curvatus by using both AflI and NspI endonucleases (in separated restriction) and L plantarum, L paraplantarum, and L pentosus were distinguished each one from the other by MucI, NspI, and TspDTI PCR-RFLP. Lb gasseri and L johnsonii were also separated on the basis of Mse I, Taq I, and Dra I RFLP.

CONCLUSION

In this study, we proved that too closely related species could be separated in virtual analysis on basis of their 16S rRNA RFLP patterns using key restriction enzymes method.

Novel Horizons in Postbiotics: Lactobacillaceae Extracellular Vesicles and Their Applications in Health and Disease

Lactobacillus probiotics contained in dietary supplements or functional foods are well-known for their beneficial properties exerted on host health and diverse pathological situations. Their capacity to improve inflammatory bowel disease (IBD) and regulate the immune system is especially remarkable. Although bacteria-host interactions have been thought to occur directly, the key role that extracellular vesicles (EVs) derived from probiotics play on this point is being unveiled. EVs are lipid bilayer-enclosed particles that carry a wide range of cargo compounds and act in different signalling pathways. Notably, these EVs have been recently proposed as a safe alternative to the utilisation of live bacteria since they can avoid the possible risks that probiotics may entail in vulnerable cases such as immunocompromised patients. Therefore, this review aims to give an updated overview of the existing knowledge about EVs from different Lactobacillus strains, their mechanisms and effects in host health and different pathological conditions. All of the information collected suggests that EVs could be considered as potential tools for the development of future novel therapeutic approaches.

Characterization and Identification of Probiotic Features in Lacticaseibacillus Paracasei Using a Comparative Genomic Analysis Approach

Lacticaseibacillus paracasei species are widely used for their health-promoting properties in food and agricultural applications. These bacteria have been isolated from various habitats such as the oral cavity, cereals, vegetables, meats, and dairy products conferring them the ability to consume different carbohydrates. Two subspecies are recognized, Lacticaseibacillus paracasei subsp. paracasei and Lacticaseibacillus paracasei subsp. tolerans according to their acid production from carbohydrates. Some strains are currently used as probiotics. In this study, we performed a comparative genomic analysis of 181 genomes of the Lacticaseibacillus paracasei species to reveal genomic differences at the subspecies level and to reveal adaptive and probiotic features, and special emphasis is given to inulin consumption. No clear distinction at the subspecies level for L. paracasei was shown using a phylogenetic tree with orthologous genes from the core-genome set. In general, a good correlation was observed between genomic distance and isolation origin, suggesting that L. paracasei strains are adapted to their natural habitat, giving rise to genetic differences at the genomic level. A low frequency of undesirable characteristics such as plasmids, prophages, antibiotic resistance genes, absence of virulence factors, and frequent bacteriocin production supports these species being good candidates for use as probiotics. Lastly, we found that the inulin gene cluster in L. paracasei strains seems to differ slightly in the presence or absence of some genes but maintains a core defined by at least three fructose-PTS proteins, one hypothetical protein, and extracellular β-fructosidase. Finally, we conclude that further work has to be done for L. paracasei subspecies classification. Improving outgroup selection criteria is a key factor for their correct subspecies assignation.

Selenium Nanoparticle-Enriched and Potential Probiotic, Lactiplantibacillus plantarum S14 Strain, a Diet Supplement Beneficial for Rainbow Trout

Simple Summary

Potential probiotic bacteria for aquacultured species should be naturally occurring and non-pathogenic in the native habitat of the host, easy to culture, and able to grow in the intestine of the host. Se nanoparticles (Se⁰Nps) can be effectively used as a growth promoter, antioxidant, and immunostimulant agent in aquacultured species. Dietary supplementation with probiotics and Se⁰Nps contributes to the balance of the intestinal microbiota and probiotics have been proposed as an alternative to chemotherapeutants and antibiotics to prevent disease outbreaks, to mitigate the negative effects of stress and to strengthen the antioxidant capacity and the immune system of fish. Our results reported the isolation of a probiotic strain obtained from healthy rainbow trout. The strain was identified as Lactiplantibacillus plantarum species. This strain showed characteristics typically present in probiotics and, concurrently, the capacity to biosynthesize Se⁰Nps. The supplementation of the rainbow trout fish diet with LABS14-Se⁰Nps showed a positive effect on innate immune response parameters, oxidative status, well-being, and a better growth performance than the supplementation of the diet with the bacterium LABS14 alone. Therefore, we propose LABS14-Se⁰Nps as a promising alternative for the nutritional supplementation for rainbow trout or even other salmonids.

Abstract

Lactic acid bacteria (LAB), obtained from rainbow trout (Oncorhynchus mykiss) intestine, were cultured in MRS medium and probiotic candidates. Concurrently, producers of elemental selenium nanoparticles (Se⁰Nps) were selected. Probiotic candidates were subjected to morphological characterization and the following tests: antibacterial activity, antibiotic susceptibility, hemolytic activity, catalase, hydrophobicity, viability at low pH, and tolerance to bile salts. Two LAB strains (S4 and S14) satisfied the characteristics of potential probiotics, but only strain S14 reduced selenite to biosynthesize Se⁰Nps. S14 strain was identified, by 16S rDNA analysis, as Lactiplantibacillus plantarum. Electron microscopy showed Se⁰Nps on the surface of S14 cells. Rainbow trout diet was supplemented (10⁸ CFU g⁻¹ feed) with Se⁰Nps-enriched L. plantarum S14 (LABS14-Se⁰Nps) or L. plantarum S14 alone (LABS14) for 30 days. At days 0, 15, and 30, samples (blood, liver, and dorsal muscle) were obtained from both groups, plus controls lacking diet supplementation. Fish receiving LABS14-Se⁰Nps for 30 days improved respiratory burst and plasmatic lysozyme, (innate immune response) and glutathione peroxidase (GPX) (oxidative status) activities and productive parameters when compared to controls. The same parameters also improved when compared to fish receiving LABS14, but significant only for plasmatic and muscle GPX. Therefore, Se⁰Nps-enriched L. plantarum S14 may be a promising alternative for rainbow trout nutritional supplementation.

Phenotype-genotype analysis of Latilactobacills curvatus from different niches: Carbohydrate metabolism, antibiotic resistance, bacteriocin, phage fragments and linkages with CRISPR-Cas systems

The potential probiotic function of Latilactobacills curvatus has attracted the attention of researchers. To explore the differences in the genomes of L. curvatus, nine strains were isolated from various sources, including feces and fermented vegetables and compared with 25 strains from the NCBI database. The findings indicated that the average genome size, GC content, and CDS of L. curvatus were 1.94 MB, 41.9%, and 1825, respectively. Its core genome is associated with transcription, translation, carbohydrate transport and metabolism, and defense functions. The pan-genome of L. curvatus was in a closed state. The genetic diversity of L. curatus is mainly manifested in its ability to use carbohydrates, antibiotic resistance, bacteriocin operon, and polymeric regularly interspaced short palindromic repeats (CRISPR)-Cas for bacterial immunity. The CRISPR system of 34 strains of L. curvatus was predominantly found to be of the IIA type with a few IIC and IE types. These findings will contribute to a better understanding of this species.

Characterization of microbial communities in anaerobic acidification reactors fed with casein and/or lactose

Abstract

Protein-rich agro-industrial waste streams are high in organic load and represent a major environmental problem. Anaerobic digestion is an established technology to treat these streams; however, retardation of protein degradation is frequently observed when carbohydrates are present. This study investigated the mechanism of the retardation by manipulating the carbon source fed to a complex anaerobic microbiota and linking the reactor performance to the variation of the microbial community. Two anaerobic acidification reactors were first acclimated either to casein (CAS reactor) or lactose (LAC reactor), and then fed with mixtures of casein and lactose. Results showed that when lactose was present, the microbial community acclimated to casein shifted from mainly Chloroflexi to Proteobacteria and Firmicutes, the degree of deamination in the CAS reactor decreased from 77 to 15%, and the VFA production decreased from 75 to 34% of the effluent COD. A decrease of 75% in protease activity and 90% in deamination activity of the microbiota was also observed. The microorganisms that can ferment both proteins and carbohydrates were predominant in the microbial community, and from a thermodynamical point of view, they consumed carbohydrates prior to proteins. The frequently observed negative effect of carbohydrates on protein degradation can be mainly attributed to the substrate preference of these populations.

Keypoints

• The presence of lactose shifted the microbial community and retarded anaerobic protein degradation.

• Facultative genera were dominant in the presence and absence of lactose.

• Substrate-preference caused retardation of anaerobic protein degradation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12132-5.

The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People

Obesity is a problem of modern health care that causes the occurrence of many concomitant diseases: arterial hypertension, diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. New strategies for the treatment and prevention of obesity are being developed that are based on using probiotics for modulation of the gut microbiota. Our study aimed to evaluate the bacterial composition of the gut of obese patients before and after two weeks of lactic acid bacteria (Lactobacillus acidophilus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and Lactobacillus delbrueckii) intake. The results obtained showed an increase in the number of members of the phylum Actinobacteriota in the group taking nutritional supplements, while the number of phylum Bacteroidota decreased in comparison with the control group. There has also been an increase in potentially beneficial groups: Bifidobacterium, Blautia, Eubacterium, Anaerostipes, Lactococcus, Lachnospiraceae ND3007, Streptococcus, Escherichia-Shigella, and Lachnoclostridium. Along with this, a decrease in the genera was demonstrated: Faecalibacterium, Pseudobutyrivibrio, Subdoligranulum, Faecalibacterium, Clostridium sensu stricto 1 and 2, Catenibacterium, Megasphaera, Phascolarctobacterium, and the Oscillospiraceae NK4A214 group, which contribute to the development of various metabolic disorders. Modulation of the gut microbiota by lactic acid bacteria may be one of the ways to treat obesity.

Lactic Acid Bacteria in Raw-Milk Cheeses: From Starter Cultures to Probiotic Functions

Traditional cheeses produced from raw milk exhibit a complex microbiota, characterized by a sequence of different microorganisms from milk coagulation and throughout maturation. Lactic acid bacteria (LAB) play an essential role in traditional cheese making, either as starter cultures that cause the rapid acidification of milk or as secondary microbiota that play an important role during cheese ripening. The enzymes produced by such dynamic LAB communities in raw milk are crucial, since they support proteolysis and lipolysis as chief drivers of flavor and texture of cheese. Recently, several LAB species have been characterized and used as probiotics that successfully promote human health. This review highlights the latest trends encompassing LAB acting in traditional raw milk cheeses (from cow, sheep, and goat milk), and their potential as probiotics and producers of bioactive compounds with health-promoting effects.

Genomic Characterization of Lactobacillus delbrueckii Strains with Probiotics Properties

Probiotics are health-beneficial microorganisms with mainly immunomodulatory and anti-inflammatory properties. Lactobacillus delbrueckii species is a common bacteria used in the dairy industry, and their benefits to hosting health have been reported. This study analyzed the core genome of nine strains of L. delbrueckii species with documented probiotic properties, focusing on genes related to their host health benefits. For this, a combined methodology including several software and databases (BPGA, SPAAN, BAGEL4, BioCyc, KEEG, and InterSPPI) was used to predict the most important characteristics related to L. delbrueckii strains probiose. Comparative genomics analyses revealed that L. delbrueckii probiotic strains shared essential genes related to acid and bile stress response and antimicrobial activity. Other standard features shared by these strains are surface layer proteins and extracellular proteins-encoding genes, with high adhesion profiles that interacted with human proteins of the inflammatory signaling pathways (TLR2/4-MAPK, TLR2/4-NF-κB, and NOD-like receptors). Among these, the PrtB serine protease appears to be a strong candidate responsible for the anti-inflammatory properties reported for these strains. Furthermore, genes with high proteolytic and metabolic activity able to produce beneficial metabolites, such as acetate, bioactive peptides, and B-complex vitamins were also identified. These findings suggest that these proteins can be essential in biological mechanisms related to probiotics’ beneficial effects of these strains in the host.

Acids produced by lactobacilli inhibit the growth of commensal Lachnospiraceae and S24-7 bacteria

The Lactobacillaceae are an intensively studied family of bacteria widely used in fermented food and probiotics, and many are native to the gut and vaginal microbiota of humans and other animals. Various studies have shown that specific Lactobacillaceae species produce metabolites that can inhibit the colonization of fungal and bacterial pathogens, but less is known about how Lactobacillaceae affect individual bacterial species in the endogenous animal microbiota. Here, we show that numerous Lactobacillaceae species inhibit the growth of the Lachnospiraceae family and the S24-7 group, two dominant clades of bacteria within the gut. We demonstrate that inhibitory activity is a property common to homofermentative Lactobacillaceae species, but not to species that use heterofermentative metabolism. We observe that homofermentative Lactobacillaceae species robustly acidify their environment, and that acidification alone is sufficient to inhibit growth of Lachnospiraceae and S24-7 growth, but not related species from the Clostridiales or Bacteroidales orders. This study represents one of the first in-depth explorations of the dynamic between Lactobacillaceae species and commensal intestinal bacteria, and contributes valuable insight toward deconvoluting their interactions within the gut microbial ecosystem.

Comprehensive characterization of the bacterial community structure and metabolite composition of food waste fermentation products via microbiome and metabolome analyses

Few studies have characterized the microbial community and metabolite profile of solid food waste fermented products from centralized treatment facilities, which could potentially be processed into safe animal feeds. In this study, 16S rRNA gene sequencing and liquid/gas chromatography-mass spectrometry were conducted to investigate the bacterial community structure and metabolite profile of food waste samples inoculated with or without 0.18% of a commercial bacterial agent consisting of multiple unknown strains and 2% of a laboratory-made bacterial agent consisting of Enterococcus faecalis, Bacillus subtilis and Candida utilis. Our findings indicated that microbial inoculation increased the crude protein content of food waste while reducing the pH value, increasing lactic acid production, and enhancing aerobic stability. Microbial inoculation affected the community richness, community diversity, and the microbiota structure (the genera with abundances above 1.5% in the fermentation products included Lactobacillus (82.28%) and Leuconostoc (1.88%) in the uninoculated group, Lactobacillus (91.85%) and Acetobacter (2.01%) in the group inoculated with commercial bacterial agents, and Lactobacillus (37.11%) and Enterococcus (53.81%) in the group inoculated with homemade laboratory agents). Microbial inoculation reduced the abundance of potentially pathogenic bacteria. In the metabolome, a total of 929 substances were detected, 853 by LC-MS and 76 by GC-MS. Our results indicated that inoculation increased the abundance of many beneficial metabolites and aroma-conferring substances but also increased the abundance of undesirable odors and some harmful compounds such as phenol. Correlation analyses suggested that Leuconostoc, Lactococcus, and Weissella would be promising candidates to improve the quality of fermentation products. Taken together, these results indicated that inoculation could improve food waste quality to some extent; however, additional studies are required to optimize the selection of inoculation agents.

Extracellular Vesicles from Gram-positive and Gram-negative Probiotics Remediate Stress-Induced Depressive Behavior in Mice

Chronic stress causes maladaptive changes in the brain that lead to depressive behavior. In the present study, we investigate whether chronic stress alters gut microbiota compositions that are related to stress-induced maladaptive changes in the brain. Mice treated with daily 2-h restraint for 14 days (CRST) exhibit depressive-like behavior. Sequence readings of 16S rRNA genes prepared from fecal samples taken from CRST-treated mice suggest that chronic stress induces gut microbiota changes that are pronounced in the post-stress period, relative to those that occur in the 14-day stress phase. The genus Lactobacillus is one such microbiota substantially changed following chronic stress. In contrast, intraperitoneal injection of extracellular vesicles (EVs) isolated from culture media of the Gram-positive probiotic Lactobacillus plantarum is sufficient to ameliorate stress-induced depressive-like behavior. Interestingly, EVs from the Gram-positive probiotic Bacillus subtilis and EVs from the Gram-negative probiotic Akkermansia muciniphila also produce anti-depressive-like effects. While chronic stress decreases the expression of MeCP2, Sirt1, and/or neurotrophic factors in the hippocampus, EVs from the three selected probiotics differentially restore stress-induced changes of these factors. These results suggest that chronic stress produces persistent changes in gut microbiota composition, whereas purified EVs of certain probiotics can be used for treatment of stress-induced depressive-like behavior.

Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest

Winemaking is a complex process involving two successive fermentations: alcoholic fermentation, by yeasts, and malolactic fermentation (MLF), by lactic acid bacteria (LAB). During MLF, LAB can contribute positively to wine flavor through decarboxylation of malic acid with acidity reduction and other numerous enzymatic reactions. However, some microorganisms can have a negative impact on the quality of the wine through processes such as biogenic amine production. For these reasons, monitoring the bacterial community profiles during MLF can predict and control the quality of the final product. In addition, the selection of LAB from a wine-producing area is necessary for the formulation of native malolactic starter cultures well adapted to local winemaking practices and able to enhance the regional wine typicality. In this sense, molecular biology techniques are fundamental tools to decipher the native microbiome involved in MLF and to select bacterial strains with potential to function as starter cultures, given their enological and technological characteristics. In this context, this work reviews the different molecular tools (both culture-dependent and -independent) that can be applied to the study of MLF, either in bacterial isolates or in the microbial community of wine, and of its dynamics during the process.

Characterization and Evaluation of the Probiotic Potential In Vitro and In Situ of Lacticaseibacillus paracasei Isolated from Tenate Cheese

ABSTRACT

The objectives of this investigation were (i) to isolate bacteria from various foods (dairy products, fruits, and vegetables) and evaluate their probiotic potential and (ii) to select, identify, and characterize the bacterial strain(s) with the highest probiotic potential. From 14 food samples, 117 bacterial strains were isolated; however, only 42 (T1 to T42) had the correct characteristics (gram positive, coccoid, and bacilliform) and were catalase and oxidase negative to be considered presumptive lactic acid bacteria (LAB). The antagonistic activity of the 42 strains was evaluated against Escherichia coli (O157:H7E09), Listeria monocytogenes (ATCC 19115), Staphylococcus aureus (ATCC 25923), and Salmonella enterica serotype Typhimurium (ATCC 14028). The nine strains with the highest antagonistic activity were recovered from the following foods: pulque (T1), sprouted beans (T26), Ranchero cheese (T30, T31, T32, T33, T35, and T36), and Tenate cheese (T40). The inhibition zones on culture and sensitivity plates were 17.0 ± 1.2 to 19.3 ± 2.8 mm in diameter. Based on the antagonistic activity against pathogenic bacteria and resistance to low pH and bile salts, strain T40 had the highest probiotic potential. A 16S rRNA technique was used to identify strain T40 as Lacticaseibacillus paracasei (renamed from Lactobacillus paracasei in April 2020). This strain had no resistance to ampicillin, gentamicin, erythromycin, and tetracycline. The antagonistic activity was evaluated in situ (fresh cheese) against pathogenic bacteria, supporting the probiotic potential of L. paracasei. Isolates of this LAB recovered from Tenate cheese had characteristics of a probiotic microorganism with high potential for use in food technology.

HIGHLIGHTS

Nutritional and Health Potential of Probiotics: A Review

Several products consist of probiotics that are available in markets, and their potential uses are growing day by day, mainly because some strains of probiotics promote the health of gut microbiota, especially Furmicutes and Bacteroidetes, and may prevent certain gastrointestinal tract (GIT) problems. Some common diseases are inversely linked with the consumption of probiotics, i.e., obesity, type 2 diabetes, autism, osteoporosis, and some immunological disorders, for which the disease progression gets delayed. In addition to disease mitigating properties, these microbes also improve oral, nutritional, and intestinal health, followed by a robust defensive mechanism against particular gut pathogens, specifically by antimicrobial substances and peptides producing probiotics (AMPs). All these positive attributes of probiotics depend upon the type of microbial strains dispensed. Lactic acid bacteria (LAB) and Bifidobacteria are the most common microbes used, but many other microbes are available, and their use depends upon origin and health-promoting properties. This review article focuses on the most common probiotics, their health benefits, and the alleviating mechanisms against chronic kidney diseases (CKD), type 1 diabetes (T1D), type 2 diabetes (T2D), gestational diabetes mellitus (GDM), and obesity.

Dietary supplementation of red-osier dogwood polyphenol extract changes the ileal microbiota structure and increases Lactobacillus in a pig model

Red-osier dogwood (ROD) extract contains a lot of polyphenols that have the potential for modulation of gut microbiota. However, little information is available about its prebiotic properties. This study investigated the impact of ROD polyphenol extract on the ileal microbiota with dietary supplementation of ROD polyphenol extract in a pig model. The data indicated that supplementation of ROD polyphenol extract significantly increased class Bacilli, order Lactobacillales and family lactobacillaceae. Within family lactobacillaceae, Lactobacillus was the main responder by increasing from 5.92% to 35.09%. Further analysis showed that ROD polyphenol extract improved two species Lactobacillus delbrueckii and Lactobacillus mucus. The results of this study suggested that ROD polyphenol extract has the potential to play prebiotic role and confer health benefit through modifying gut microbiota.

A Method of Direct Quantitation of Lactobacillus spp. in Intestinal Contents Based on Real-Time PCR

The method of direct quantitation of Lactobacillus spp. and L. acidophilus in intestinal contents based on real-time PCR was developed. It does not require culturing and allows estimating the number of living lactobacilli cells (measured in lg CFU) in absolute quantitative PCR format.

Identification of Type II Toxin-Antitoxin Loci in Levilactobacillus brevis

Levilactobacillus brevis are present in various environments, such as beer, fermented foods, silage, and animal host. Like other lactic acid bacteria, L. brevis might adopt the viable but nonculturable (VBNC) state under unfavorable conditions. The toxin-antitoxin (TA) system, known to regulate cell growth in response to environmental stresses, is found to control the dynamic of the VBNC state. Here, we investigate the type II TA locus prevalence and compare the TA diversity in L. brevis genomes. Using the TAfinder software, we identified a total of 273 putative type II TA loci in 110 replicons of 21 completely sequenced genomes. Genome size does not appear to correlate with the amount of putative type II TA in L. brevis. Besides, type II TA loci are distributed differently among the chromosomes and plasmids. The most prevalent toxin domain is MazF-like in the chromosomes, and RelE/RelE-like in the plasmids; while for antitoxin, Xre-like and Phd-like domains are the most common in the chromosomes and plasmids, respectively. We also observed a unique GNAT-like/ArsR-like TA pair that presents only in the L. brevis chromosome. Detection of 273 putative type II TA loci in 21 complete genomes of Levilactobacillus brevis.

Genomic analysis revealed conserved acid tolerance mechanisms from native micro-organisms in fermented feed

AIMS

Fermented feed is an agricultural practice used in many regions of the world to improve the growth performance of farm animals. This study aimed to identify and evaluate the lactic acid bacteria and yeast involved in the production of fermented feed.

METHODS AND RESULTS

We isolated and described two micro-organisms from autochthonous microbiota origin present in a regional feed product, Lactobacillus paracasei IBR07 (Lacticaseibacillus paracasei) and Kazachstania unispora IBR014 (Saccharomyces unisporum). Genome sequence analyses were performed to characterize both micro-organisms. Potential pathways involved in the acid response, tolerance and persistence were predicted in both genomes. Although L. paracasei and K. unispora are considered safe for animal feed, we analysed the presence of virulence factors, antibiotic resistance and pathogenicity islands. Furthermore, the Galleria mellonella model was used to support the safety of both isolates.

CONCLUSIONS

We conclude that IBR07 and IBR014 strains are good candidates to be used as starter cultures for feed fermentation.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data presented here will be helpful to explore other biotechnological aspects and constitute a starting point for further studies to establish the consumption benefit of fermented feed in farm animal production.

LrpCBA pilus proteins of gut-dwelling Ligilactobacillus ruminis: crystallization and X-ray diffraction analysis

Adhesion to host surfaces for bacterial survival and colonization involves a variety of molecular mechanisms. Ligilactobacillus ruminis, a strict anaerobe and gut autochthonous (indigenous) commensal, relies on sortase-dependent pili (LrpCBA) for adherence to the intestinal inner walls, thereby withstanding luminal content flow. Here, the LrpCBA pilus is a promiscuous binder to gut collagen, fibronectin and epithelial cells. Structurally, the LrpCBA pilus displays a representative hetero-oligomeric arrangement and consists of three types of pilin subunit, each with its own location and function, i.e. tip LrpC for adhesion, basal LrpB for anchoring and backbone LrpA for length. To provide further structural insights into the assembly, anchoring and functional mechanisms of sortase-dependent pili, each of the L. ruminis pilus proteins was produced recombinantly for crystallization and X-ray diffraction analysis. Crystals of LrpC, LrpB, LrpA and truncated LrpA generated by limited proteolysis were obtained and diffracted to resolutions of 3.0, 1.5, 2.2 and 1.4 Å, respectively. Anomalous data were also collected from crystals of selenomethionine-substituted LrpC and an iodide derivative of truncated LrpA. Successful strategies for protein production, crystallization and derivatization are reported.

D- and l-amino acid concentrations in culture broth of Lactobacillus are highly dependent on the phylogenetic group of Lactobacillus

d-amino acids produced by Lactobacillus are thought to contribute to the taste quality and health functions; however, no studies have comprehensively evaluated the concentrations of the D- and L-forms of amino acids separately in individual Lactobacillus strains. To gain insight into amino acid concentrations in Lactobacillus, we evaluated amino acid concentrations in culture broth of Lactobacillus separately for the D- and L-forms. Lactobacillus strains were cultured in culture broth, and the amino acid concentrations in supernatant were assessed. The amino acid concentrations obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were subjected to cluster analysis based on Bray-Curtis distance with Ward's minimum variance method. In the analysis of amino acid concentrations under culture with different monosaccharides, the distances among strains cultured with the same monosaccharide were significantly greater than those among cultures of the same strain under different monosaccharides (p < 0.01). The cluster analysis of amino acid concentrations under culture with the same monosaccharide suggested that strains belonging to the same phylogenetic group of Lactobacillus exhibited similar concentrations of amino acids. Data analyses of 70 strains belonging to 17 Lactobacillus taxa indicated that the concentrations of amino acids were highly dependent on the phylogenetic group of Lactobacillus and that the group differences in amino acid concentration were strongly driven by differences in l-serine and d-alanine concentrations. Our results indicate that it is important to evaluate D- and l-amino acids separately when evaluating variations in amino acid concentrations. Because d-alanine has the potential to affect taste quality, the results of this study may provide insight into the taste quality of fermented food produced by Lactobacillus.

Genomic and proteomic comparisons of bacteriocins in probiotic species Lactobacillus and Bifidobacterium and inhibitory ability of Escherichia coli MG 1655

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The genomes and proteomes of 12 Bifidobacterium and 46 Lactobacillus were reviewed and then compared for bacteriocin identification.

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NCBI-Genome, UniProt-Proteome, Bactibase, and BAGL4 databases, as well as BLASTP, and Clustal Omega can be used for bacteriocin mining.

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Lactobacillus species have more diversity and abundance of bacteriocin compared to Bifidobacterium species.

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Notably, L. sakei, L. plamtarum, L. reuteri, L. fermentum, and L. casei had the highest pathogen inhibition (E. coli MG 1655); respectively.

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A set of Lactobacillus bacteria including L. sakei, L. reuteri, L. fermentum, and L. casei can be proposed as a biosecure and safe solution to control gastrointestinal pathogens.

Bacteriocins are a large family of bacterial peptides or proteins, ribosomally synthesized with antimicrobial activity against other bacteria. We investigated and compared the genomes and proteomes of 12 Bifidobacterium and 46 Lactobacillus species for bacteriocins using NCBI-Genome, UniProt-Proteome, Bactibase, and BAGL4 databases. Selected Lactobacillus species were examined for bile salt resistance, acid and pH resistance, pepsin and trypsin enzyme resistance, and antibiotic resistance. Also, the antimicrobial activity of selected Lactobacillus species was evaluated against E. coli MG 1655. Results showed that Lactobacillus species have more diversity and abundance of bacteriocin compared to Bifidobacterium species. Notably, L. sakei, L. plamtarum, L. reuteri, L. fermentum, and L. casei had the highest pathogen inhibition; respectively. Therefore, a combination of these Lactobacillus species can be suggested as a biochemical and safe solution to control gastrointestinal pathogens and suitable alternatives to antibiotics and chemicals in food technology.

Health-Promoting Properties of Lactobacilli in Fermented Dairy Products

Bacteria of the genus Lactobacillus have been employed in food fermentation for decades. Fermented dairy products, such as cheese and yogurt, are products of high value known as functional food and widely consumed due to their positive health impact. Fermentation was originally based on conversion of carbohydrate into organic acids, mostly lactic acid, intended to preserve nutrient in milk, but then it develops in other disclosure of capabilities associates with health benefit. It is expected that during the manufacture of fermented dairy products, some bioactive peptides from milk protein are released through proteolysis. Lactobacilli have been recognized and received increasing attention as probiotics by balancing gut microbial population. Information of molecular mechanisms of genome sequence focusing on the microbial that normally inhabit gut may explain as to how these bacteria positively give impact on improving host health. Recent post-biotics concept revealed that health benefit can also be associated after bacterial lysis. This mini review focuses on the contribution of lactobacilli in dairy fermentation with health-promoting properties on human health.

Biogeochemical Alteration of an Aquifer Soil during In Situ Chemical Oxidation by Hydrogen Peroxide and Peroxymonosulfate

In this study, the effects of in situ chemical oxidation (ISCO) on the biogeochemical properties of an aquifer soil were evaluated. Microcosms packed with an aquifer soil were investigated for 4 months in two phases including oxidant exposure (phase I) and biostimulation involving acetate addition (phase II). The geochemical and microbial alterations from different concentrations (0.2 and 50 mM) of hydrogen peroxide (HP) and peroxymonosulfate (PMS) were assessed. The 50 mM PMS-treated sample exhibited the most significant geochemical changes, characterized by the decrease in pH and the presence of more crystalline phases. Microbial activity decreased for all ISCO-treated microcosms compared to the controls; particularly, the activity was severely inhibited at high PMS concentration exposure. The soil microbial community structures were shifted after the ISCO treatment, with the high PMS causing the most distinct changes. Microbes such as the Azotobacter chroococcum and Gerobacter spp. increased during phase II of the ISCO treatment, indicating these bacterial communities can promote organic degradation despite the oxidants exposure. The HP (low and high concentrations) and low concentration PMS exposure temporarily impacted the microbial activity, with recovery after some duration, whereas the microbial activity was less recovered after the high concentration PMS exposure. These results suggest that the use of HP and low concentration PMS are suitable ISCO strategies for aquifer soil bioattenuation.

Probiogenomics of Lactobacillus delbrueckii subsp. lactis CIDCA 133: In Silico, In Vitro, and In Vivo Approaches

Lactobacillus delbrueckii subsp. lactis CIDCA 133 (CIDCA 133) has been reported as a potential probiotic strain, presenting immunomodulatory properties. This study investigated the possible genes and molecular mechanism involved with a probiotic profile of CIDCA 133 through a genomic approach associated with in vitro and in vivo analysis. Genomic analysis corroborates the species identification carried out by the classical microbiological method. Phenotypic assays demonstrated that the CIDCA 133 strain could survive acidic, osmotic, and thermic stresses. In addition, this strain shows antibacterial activity against Salmonella Typhimurium and presents immunostimulatory properties capable of upregulating anti-inflammatory cytokines Il10 and Tgfb1 gene expression through inhibition of Nfkb1 gene expression. These reported effects can be associated with secreted, membrane/exposed to the surface and cytoplasmic proteins, and bacteriocins-encoding genes predicted in silico. Furthermore, our results showed the genes and the possible mechanisms used by CIDCA 133 to produce their beneficial host effects and highlight its use as a probiotic microorganism.

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.

Limosilactobacillus fermentum CECT5716: Mechanisms and Therapeutic Insights

Probiotics microorganisms exert their health-associated activities through some of the following general actions: competitive exclusion, enhancement of intestinal barrier function, production of bacteriocins, improvement of altered microbiota, and modulation of the immune response. Among them, Limosilactobacillus fermentum CECT5716 has become one of the most promising probiotics and it has been described to possess potential beneficial effects on inflammatory processes and immunological alterations. Different studies, preclinical and clinical trials, have evidenced its anti-inflammatory and immunomodulatory properties and elucidated the precise mechanisms of action involved in its beneficial effects. Therefore, the aim of this review is to provide an updated overview of the effect on host health, mechanisms, and future therapeutic approaches.

Biodiversity of Lactobacillus helveticus isolates from dairy and cereal fermentations reveals habitat-adapted biotypes

For the present study, we collected 22 Lactobacillus helveticus strains from different dairy (n = 10) and cereal (n  = 12) fermentations to investigate their biodiversity and to uncover habitat-specific traits. Biodiversity was assessed by comparison of genetic fingerprints, low-molecular-weight subproteomes, metabolic and enzymatic activities, growth characteristics and acidification kinetics in food matrices. A clear distinction between the dairy and cereal strains was observed in almost all examined features suggesting that the different habitats are domiciled by different L. helveticus biotypes that are adapted to the specific environmental conditions. Analysis of the low-molecular-weight subproteome divided the cereal isolates into two clusters, while the dairy isolates formed a separate homogeneous cluster. Differences regarding carbohydrate utilization were observed for lactose, galactose, sucrose and cellobiose as well as for plant-derived glucosides. Enzymatic differences were observed mainly for ß-galactosidase and ß-glucosidase activities. Further, growth temperature was optimal in the range from 33 to 37°C for the cereal strains, whereas the dairy strains showed optimal growth at 40°C. Taken together, adaptation of the various biotypes results in a growth benefit in the particular environment. Acidification and growth tests using either sterile skim milk or a wheat flour extract confirmed these results. Differentiation of these biotypes and their physiological characteristics enables knowledge-based starter culture development for cereal versus dairy products within one species.

Effects of fermented ginseng on the gut microbiota and immunity of rats with antibiotic-associated diarrhea

ETHNOPHARMACOLOGICAL RELEVANCE

Ginseng (Panax ginseng Meyer) is a well-known herb in traditional Chinese medicine and has been used to treat many diseases for thousands of years. Recent studies have shown that ginseng is a promising agent for improving the gut microbiota and treating ulcerative colitis. Fermentation is a common process in traditional Chinese medicine making that can be used to enhance efficacy and reduce toxicity.

AIM OF THE STUDY

The purpose of the present study was to research the efficacy of ginseng fermented with probiotics (Lactobacillus fermentum) on the gut microbiota and immunity of rats with antibiotic-associated diarrhea (AAD).

MATERIALS AND METHODS

SPF Sprague-Dawley rats were randomly divided into eight groups: control group, antibiotic group, natural recovery group, and five groups treated with different doses of fermented ginseng (FG1 to FG5). A model of AAD was established by treating the rats with triple antibiotics, and obvious symptoms of AAD were observed. A histopathological analysis of the colon was performed. The total bacteria in the intestinal microbiota and five types of gut microbes in the feces were detected by quantitative PCR. The expression levels of related immune factors TLR4 and NF-κB in the colon were assayed.

RESULTS

An appropriate dose of fermented ginseng (0.5 g/kg/d) relieved some of the symptoms of AAD and colon inflammation and reduced the expression of the immune factors TLR4 and NF-κB in the colon. The alteration of the gut microbiota observed in the rats treated with antibiotics also returned to normal after treatment with fermented ginseng. Moreover, different doses of fermented ginseng exerted different influences on the gut microbiota, and excessively high or low doses of fermented ginseng were disadvantageous for resolving the symptoms of AAD and promoting recovery.

CONCLUSIONS

These results demonstrate that fermented ginseng can treat AAD symptoms and colon inflammation and restore the gut microbiota to its original state.