Functional annotation of the genome unravels probiotic potential of Bacillus coagulans HS243

Exploring omics approaches in probiotics: Contemporary developments and prospective pathways

The application of omics technologies in combination with bench investigations has brought about a significant transformation in the field of probiotics, enabling a thorough investigation of the basic elements contributing to the probiotic activity. Genomics studies have decoded the complete set of genes of probiotic organisms, shedding light on beneficial traits and mechanisms of probiotic action. Transcriptomics analyses focus on gene expression patterns and investigate probiotic adaptation and functionality. Proteomic studies have revealed the intricate connections between proteins in probiotic cells and their relationship with the host environment. Metabolomic profiling has provided a comprehensive perspective on the metabolic pathways related to probiotic metabolism and the production of bioactive substances. The ongoing development of omics technology presents exciting opportunities for probiotic research, as it allows for a deeper exploration of probiotic-host interactions and the creation of advanced and tailored probiotics that offer specific health advantages. A comprehensive analysis of recent progress in genomics, transcriptomics, proteomics, and metabolomics related to probiotics is presented in this review.

Evaluation of the safety and probiotic properties of Limosilactobacillus fermentum BGI-AF16, a uric acid-lowering probiotic strain

Some beneficial microorganisms in the intestine have the potential to degrade uric acid, offering a novel strategy for the prevention of hyperuricemia. In this study, the safety and probiotic potentials of Limosilactobacillus fermentum BGI-AF16 were evaluated by whole genome sequence analysis and in vitro experiments. Based on the gene analysis of antibiotic resistance and virulence factors, L. fermentum BGI-AF16 has been shown to be safe. We identified probiotic-related genes by genome annotation tools and conducted in vitro experiments to evaluate the ability of L. fermentum BGI-AF16 to inhibit pathogenic bacteria, tolerate a simulated gastrointestinal environment, and degrade uric acid. The results from in vitro experiments showed that L. fermentum BGI-AF16 had inhibitory effects on four clinically relevant pathogens and was highly tolerant to the gastrointestinal environment. In addition, L. fermentum BGI-AF16 was able to rapidly degrade uric acid within the first hour, and the strain could degrade 56.36 ± 2.32 % of uric acid by the third hour. The genome of the strain contains genes encoding flavin adenine dinucleotide (FAD)-dependent urate hydroxylase (EC.1.14.13.113), an enzyme that directly metabolizes uric acid. And the strain has a complete uric acid metabolic pathway. These results suggest that L. fermentum BGI-AF16 is a probiotic candidate with significant potential for reducing uric acid level.

Whole Genome Analysis of Pediococcus acidilactici XJ-24 and Its Role in Preventing Listeria monocytogenes ATCC® 19115TM Infection in C57BL/6 Mice

Background/Objectives: As probiotics gain prominence in the prevention and treatment of intestinal diseases, their protective effects against pathogens and influence on host health have drawn significant attention. This study investigates the genomic characteristics and functional potential of Pediococcus acidilactici XJ-24 (XJ-24) in the prevention of Listeria monocytogenes (LM) infection in mice. Methods/Results: Whole-genome analysis confirmed the safety and probiotic properties of XJ-24, including acid and bile salt tolerance, antimicrobial activity, and safety. In vivo, C57BL/6 mice challenges indicated that XJ-24 significantly reduced LM colonization, suppressed pro-inflammatory cytokines (IL-1β, IL-6, TNF-α, IFN-γ), alleviated colon and spleen tissue damage, and maintained intestinal barrier integrity by upregulating tight junction proteins (Occludin, Claudin-1, ZO-1). Moreover, XJ-24 modulated gut microbiota composition by increasing beneficial taxa while reducing harmful bacteria. Correlation analysis highlighted a positive association between Lachnospiraceae and tight junction proteins. Conclusions: These findings demonstrate the potential of XJ-24 as a functional probiotic for preventing LM infection and provide a basis for further clinical exploration.

Pangenome analysis of Bacillus velezensis exploring the probiotic potential and plant growth promotion traits of strains isolated from fish intestines

New Bacillus velezensis strains with impressive antimicrobial activities are being continuously described. Here we performed genomic comparisons of five B. velezensis strains isolated from Amazonian fish intestines with other 266 genomes from the RefSeq database through a pangenome approach. We aimed to analyze the commonalities and specificities of each strain within this clade to explore their potential as probiotics and for promoting plant growth (PGP). High-quality draft genome sequences were obtained for strains P7 and P11, with genome metrics confirming their identification as B. velezensis. The evaluation of 271 B. velezensis genome sequences revealed an open pangenome composed of 14,918 homologs, while 16% of them represented the core genome. Therefore, the majority of genes belonged to the accessory variable genome, with many strains harboring numerous unique genes, including the Amazonian strain P45. This strain also stood out as carrying the potential to produce many hydrolytic enzymes and PGP traits. Genome mining of all five Amazonian strains annotated secondary metabolites with unknown identifications. The evaluated probiotic genes are mostly conserved in all B. velezensis strains. Moreover, the investigation of the mobilome, resistome, and virulence factors showed that these strains can be considered safe for probiotic and agricultural applications, corroborating our previous studies. This data will be useful to improve our understanding and biotechnological exploration of these strains and other B. velezensis as well.

Genome-Guided Identification and Characterisation of Broad-Spectrum Antimicrobial Compounds of Bacillus velezensis Strain PD9 Isolated from Stingless Bee Propolis

The emergence of multidrug-resistant pathogens presents a significant global health challenge, which is primarily fuelled by overuse and misuse of antibiotics. Bacteria-derived antimicrobial metabolites offer a promising alternative strategy for combating antimicrobial resistance issues. Bacillus velezensis PD9 (BvPD9), isolated from stingless bee propolis, has been reported to have antibacterial activities against methicillin-resistant Staphylococcus aureus (MRSA). This study aimed to characterise and identify the antimicrobial compounds (AMCs) synthesised by BvPD9 through integration of genome mining and liquid chromatography-mass spectrometry (LC-MS) analysis. The whole-genome sequence of BvPD9 contained 4,263,351 base pairs and 4101 protein-coding sequences, with 12 potential AMC biosynthetic gene clusters. Comparative genomic analysis highlighted the unique profile of BvPD9 that possesses the largest number of unknown proteins, indicating significant potential for further exploration. The combined genomics-metabolic profiling uncovered five AMCs in BvPD9 extract, including bacillibactin, bacilysin, surfactin A, fengycin A, and bacillomycin D. The extract exhibited a broad antibacterial spectrum against 25 pathogenic bacteria, including both Gram-positive and Gram-negative bacteria, with the lowest minimum inhibitory concentration (MIC, 0.032 mg/ml) against S. epidermidis ATCC 12228, and the lowest minimum bactericidal concentration (MBC; 0.128 mg/ml) against MRSA ATCC 700699 and Aeromonas hydrophilia. The robust stability of BvPD9 extract was demonstrated at high temperatures, over a wide range of pH conditions (6 to 12) and in the presence of various hydrolytic enzymes. Additionally, the extract showed 50% haemolytic and cytotoxicity activity at 0.158 and 0.250 mg/ml, respectively. These characteristics suggest potential applications of BvPD9 metabolites for tackling antimicrobial resistance and its applicability across diverse industries.

Clinical and In Vitro Safety of Heyndrickxia coagulans AO 1167B: A Double-Blind, Placebo-Controlled Trial

(1) Background: Heyndrickxia coagulans, a lactic acid-producing bacterium, displays characteristics of both Lactobacillus and Bacillus genera. Clinical evidence suggests its potential health benefits. This study evaluated the safety of H. coagulans AO1167B as a candidate probiotic supplement. (2) Methods: Strain identification was confirmed through morphological, cultural, and genomic analyses, including 16S RNA and whole genome sequencing to assess antimicrobial resistance and virulence factors. Phenotypic tests, such as disk diffusion for antimicrobial resistance, and safety assays for cytotoxicity and hemolytic activity, were conducted. In a phase I, double-blind, placebo-controlled clinical trial, healthy adults were randomized into H. coagulans AO1167B and placebo groups for 60 days. Daily capsule consumption was monitored through clinical and hematological evaluations, adverse event tracking, and health surveys. (3) Results: The genome of H. coagulans AO1167B revealed no concerning features. Disk diffusion tests showed no antimicrobial resistance. The strain exhibited no cytotoxic or hemolytic activity, indicating in vitro safety. No significant differences in clinical or hematological parameters were observed between groups. The most common adverse event, gas, diminished over time. (4) Conclusions: H. coagulans AO1167B demonstrates a suitable safety profile, genetic stability, and probiotic potential for gastrointestinal health, justifying further clinical research.

A review on the diversity of antimicrobial peptides and genome mining strategies for their prediction

Antibiotic resistance has become one of the most serious threats to human health in recent years. In response to the increasing microbial resistance to the antibiotics currently available, it is imperative to develop new antibiotics or explore new approaches to combat antibiotic resistance. Antimicrobial peptides (AMPs) have shown considerable promise in this regard, as the microbes develop low or no resistance against them. The discovery and development of AMPs still confront numerous obstacles such as finding a target, developing assays, and identifying hits and leads, which are time-consuming processes, making it difficult to reach the market. However, with the advent of genome mining, new antibiotics could be discovered efficiently using tools such as BAGEL, antiSMASH, RODEO, etc., providing hope for better treatment of diseases in the future. Computational methods used in genome mining automatically detect and annotate biosynthetic gene clusters in genomic data, making it a useful tool in natural product discovery. This review aims to shed light on the history, diversity, and mechanisms of action of AMPs and the data on new AMPs identified by traditional as well as genome mining strategies. It further substantiates the various phases of clinical trials for some AMPs, as well as an overview of genome mining databases and tools built expressly for AMP discovery. In light of the recent advancements, it is evident that targeted genome mining stands as a beacon of hope, offering immense potential to expedite the discovery of novel antimicrobials.

Advances in characterization of probiotics and challenges in industrial application

An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.

Genome Analysis of Potential Probiotic Levilactobacillus brevis AcCh91 Isolated from Indian Home-Made Fermented Milk Product (Chhurpi)

Consumption of naturally fermented milk (NFM) products is the dietary culture in India. The mountainous people of Arunachal Pradesh in India prepare the assorted artisanal home-made NFM products from cow and yak milk. Previously, we isolated and identified 76 strains of lactic acid bacteria (LAB) from NFM products of Arunachal Pradesh, viz. mar, chhurpi and churkam. We hypothesized that some of these LAB strains may possess probiotic potentials; hence, we investigated the probiotic potentials of these strains. On the basis of in vitro and genetic screening for probiotic attributes including haemolytic ability, 20 LAB strains were selected out of 76 strains, for further analysis. Using in silico analysis, viz. multivariate heatmap and PCA (principal component analysis) biplot, Levilactobacillus brevis AcCh91 was selected as the most promising probiotic strain, which was further characterized by the whole-genome analysis. Lev. brevis AcCh91 showed the highest survival rate of 93.38% in low pH and 86.68 ± 2.69% in low bile and the highest hydrophobicity average of 86.34 ± 5.53%. This strain also showed auto-aggregation and co-aggregation with antimicrobial properties against the pathogens, showed ability to produce beta-galactosidase and cholesterol reduction property and, most importantly, produced GABA, an important psychobiotic element. Genomic analysis of Lev. brevis AcCh91 showed the presence of genes corresponding to GABA, vitamins, amino acids, cholesterol reduction, immunomodulation, bioactive peptides and antioxidant activity. The absence of antimicrobial-resistant genes and virulence factors was observed. Hence, genome analysis supports the probiotic potentials of Lev. brevis AcCh91, which may be further investigated to understand its health-promoting properties.

Pig-Derived Probiotic Bacillus tequilensis YB-2 Alleviates Intestinal Inflammation and Intestinal Barrier Damage in Colitis Mice by Suppressing the TLR4/NF-κB Signaling Pathway

The search for new probiotics has been regarded as an important approach to improving intestinal health in animals. Bacillus has many advantages, such as strong resistance to harmful external factors, wide distribution, and easy colonization of the intestine. Hence, this study aims to screen for a probiotic Bacillus strain that improves animal intestinal health and to elucidate its probiotic mechanism so as to provide probiotic resources for the development of feed-using probiotic formulations. In this research, a strain of Bacillus was isolated from adult pig feces and named B. tequilensis YB-2. In vitro probiotic experiments showed that B. tequilensis YB-2 had strong acid and bile salt resistance, indicating that this strain can customize in the intestine. To further explore the effect of B. tequilensis YB-2 upon animal intestinal health, DSS-induced murine colitis models were established, and the body weight, colonic morphology, inflammatory cytokines level, and intestinal-barrier- and TLR4/NF-κB-pathway-related protein were determined. The results showed that mice receiving drinking water with 3% DSS were found to develop colitis symptoms, including body weight loss and increased disease activity index (DAI); colon length and microvilli shedding were shortened; tight junctions were disrupted; goblet cells decreased; anti-inflammatory cytokines were inhibited; and pro-inflammatory cytokines and the TLR4/NF-κB signaling pathway were activated. Notably, orally received B. tequilensis YB-2 alleviated symptoms of DSS-induced colitis in mice. The above results indicated that B. tequilensis YB-2 was capable of improving colitis in mice by weakening inflammation and intestinal barrier damage, and its mechanism may involve the TLR4/NF-κB pathway. Overall, this research suggests that B. tequilensis YB-2 has the potential to serve as an animal feed additive to prevent intestinal inflammation.

Genomic and Phenotypic Safety Assessment of Probiotic Bacillus coagulans Strain JBI-YZ6.3

Spore-forming Bacillus coagulans has been widely recognized as an important probiotic, which is commonly used in products for human consumption and animal feeds. B. coagulans exhibits beneficial traits from both Bacillus and lactic acid-producing Lactobacillus. The present study evaluated the safety of the newly isolated B. coagulans strain JBI-YZ6.3, using combined genomic and phenotypic analysis approaches. The taxonomic classification based on genome sequence and biochemical tests identified strain JBI-YZ6.3 as B. coagulans. Comprehensive genome-based analyses established JBI-YZ6.3 as a novel strain of B. coagulans. Antibiotic susceptibility testing showed that the strain JBI-YZ6.3 was sensitive to a panel of fourteen antibiotics, and no genes related to antibiotic resistance were found in its genome. The spores of strain JBI-YZ6.3 exhibited tolerance to acid and bile salts, as well as stability at ambient and elevated conditions of temperature and relative humidity. There were no homologs of Bacillus toxin genes identified in the genome of JBI-YZ6.3, and the strain exhibited no cytotoxicity towards Vero cells and human peripheral blood mononuclear cells. In conclusion, findings from this study support the safety of B. coagulans strain JBI-YZ6.3, which can be developed into new probiotic products for preventive and therapeutic benefits in human and animal hosts.

Whole genome sequencing analysis of Limosilactobacillus reuteri from the intestinal tract of mice recovering from ulcerative colitis and preliminary study on anti-inflammatory effects of its derived peptides

Limosilactobacillus reuteri is an indigenous inhabitant of the animal gut known for its probiotic effects on the host. In our previous study, a large number of L. reuteri strains were isolated from the gastrointestinal tract of mice recovering from ulcerative colitis, from which we randomly selected L. reuteri RE225 for whole genome sequencing to explore its probiotic properties. The results of next-generation sequencing and third-generation single molecule sequencing showed that L. reuteri RE225 contained many genes encoding functional proteins associated with adhesion, anti-inflammatory and pathogen inhibition. And compared to other L. reuteri strains in NCBI, L. reuteri RE225 has unique gene families with probiotic functions. In order to further explore the probiotic effect of the L. reuteri RE225, the derived peptides were identified by LC-MS/MS, and the peptides with tumor necrosis factor-α binding ability were screened by reverse molecular docking and microscale thermophoresis. Finally, cell experiments demonstrated the anti-inflammatory ability of the peptides. Western blotting and qPCR analyses confirmed that the selected peptides might alleviate LPS-induced inflammation in NCM460 cells by inhibiting JAK2/STAT3 pathway activation.

Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice

Introduction

In recent years, a large number of studies have shown that Bacillus velezensis has the potential as an animal feed additive, and its potential probiotic properties have been gradually explored.

Methods

In this study, Illumina NovaSeq PE150 and Oxford Nanopore ONT sequencing platforms were used to sequence the genome of Bacillus velezensis TS5, a fiber-degrading strain isolated from Tibetan sheep. To further investigate the potential of B. velezensis TS5 as a probiotic strain, in vivo experiments were conducted using 40 five-week-old male specific pathogen-free C57BL/6J mice. The mice were randomly divided into four groups: high fiber diet control group (H group), high fiber diet probiotics group (HT group), low fiber diet control group (L group), and low fiber diet probiotics group (LT group). The H and HT groups were fed high-fiber diet (30%), while the L and LT groups were fed low-fiber diet (5%). The total bacteria amount in the vegetative forms of B. velezensis TS5 per mouse in the HT and LT groups was 1 × 109 CFU per day, mice in the H and L groups were given the same volume of sterile physiological saline daily by gavage, and the experiment period lasted for 8 weeks.

Results

The complete genome sequencing results of B. velezensis TS5 showed that it contained 3,929,788 nucleotides with a GC content of 46.50%. The strain encoded 3,873 genes that partially related to stress resistance, adhesion, and antioxidants, as well as the production of secondary metabolites, digestive enzymes, and other beneficial nutrients. The genes of this bacterium were mainly involved in carbohydrate metabolism, amino acid metabolism, vitamin and cofactor metabolism, biological process, and molecular function, as revealed by KEGG and GO databases. The results of mouse tests showed that B. velezensis TS5 could improve intestinal digestive enzyme activity, liver antioxidant capacity, small intestine morphology, and cecum microbiota structure in mice.

Conclusion

These findings confirmed the probiotic effects of B. velezensis TS5 isolated from Tibetan sheep feces and provided the theoretical basis for the clinical application and development of new feed additives.

Unveiling the Probiotic Potential of the Anaerobic Bacterium Cetobacterium sp. nov. C33 for Enhancing Nile Tilapia (Oreochromis niloticus) Cultures

The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent techniques, the adaptability of the C33 strain to the host gastrointestinal conditions, its antibacterial activity against aquaculture bacterial and its antibiotic susceptibility were assessed. The genome of C33 was sequenced, assembled, annotated, and subjected to functional inference, particularly regarding pinpointed probiotic activities. Furthermore, phylogenomic comparative analyses were performed including closely reported strains/species relatives. Comparative genomics with closely related species disclosed that the isolate is not phylogenetically identical to other Cetobacterium species, displaying an approximately 5% sequence divergence from C. somerae and a 13% sequence divergence from Cetobacterium ceti. It can be distinguished from other species through physiological and biochemical criteria. Whole-genome annotation highlighted that Cetobacterium sp. nov. C33 possesses a set of genes that may contribute to antagonism against competing bacteria and has specific symbiotic adaptations in fish. Additional in vivo experiments should be carried out to verify favorable features, reinforcing its potential as a probiotic bacterium.

Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products

The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations, Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei, and Bifidobacterium animalis exhibited two to three genomic alterations, while Streptococcus equinus was found in one. TYGS and GDTB discovered E. faecium and L. paracasei in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for Bifidobacterium strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of L. reuteri (NPLps01.et_L.r and NPLps02.uf_L.r), Lactobacillus delbrueckii (NPLps01.et_L.d), Streptococcus thermophilus (NPLps06.ab_S.t), and E. faecium (NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.

Effects of Dietary Bacillus coagulans and Tributyrin on Growth Performance, Serum Antioxidants, Intestinal Morphology, and Cecal Microbiota of Growing Yellow-Feathered Broilers

This study investigated the impact of Bacillus coagulans (BC) and tributyrin (TB) supplementation on the growth performance, serum antioxidant capacity, intestinal morphology, and cecal microbiota of yellow-feathered broilers. Using a 2 × 2 factorial design, 480 broilers were randomly assigned to four experimental diets, comprising two levels of BC (0 and 1 g/kg) and two levels of TB (0 and 1 g/kg), over a 36-day period. A significant interaction was observed between BC and TB, impacting the average daily feed intake (ADFI) of broilers aged between 26 and 40 days (p < 0.01). BC and TB also displayed a significant interaction in relation to serum malondialdehyde levels and total antioxidant capacity (p < 0.05). Additionally, there was a significant interaction between BC and TB concerning the duodenal villus-to-crypt ratio, crypt depth, and jejunal villus-to-crypt ratio (p < 0.05). The addition of BC and TB significantly enhanced the richness and diversity of cecal microbiota, with a notable interactive effect observed for the abundance of Faecalibacterium, Ruminococcus_torques_group, and Phascolarctobacterium. In conclusion, supplementation with BC and TB can effectively improve the growth performance, serum antioxidant capacity, intestinal morphology, and cecal microbiota composition of yellow-feathered broilers, indicating the presence of an interactive effect.

Maternal and infant microbiome: next-generation indicators and targets for intergenerational health and nutrition care

Microbes are commonly sensitive to shifts in the physiological and pathological state of their hosts, including mothers and babies. From this perspective, the microbiome may be a good indicator for diseases during pregnancy and has the potential to be used for perinatal health monitoring. This is embodied in the application of microbiome from multi body sites for auxiliary diagnosis, early prediction, prolonged monitoring, and retrospective diagnosis of pregnancy and infant complications, as well as nutrition management and health products developments of mothers and babies. Here we summarized the progress in these areas and explained that the microbiome of different body sites is sensitive to different diseases and their microbial biomarkers may overlap between each other, thus we need to make a diagnosis prudently for those diseases. Based on the microbiome variances and additional anthropometric and physical data, individualized responses of mothers and neonates to meals and probiotics/prebiotics were predictable, which is of importance for precise nutrition and probiotics/prebiotics managements and developments. Although a great deal of encouraging performance was manifested in previous studies, the efficacy could be further improved by combining multi-aspect data such as multi-omics and time series analysis in the future. This review reconceptualizes maternal and infant health from a microbiome perspective, and the knowledge in it may inspire the development of new options for the prevention and treatment of adverse pregnancy outcomes and bring a leap forward in perinatal health care.

Bioprocess development for endospore production by Bacillus coagulans using an optimized chemically defined medium

Bacillus coagulans is a promising probiotic, because it combines probiotic properties of Lactobacillus and the ability of Bacillus to form endospores. Due to this hybrid relationship, cultivation of this organism is challenging. As the probiotics market continues to grow, there is a new focus on the production of these microorganisms. In this work, a strain-specific bioprocess for B. coagulans was developed to support growth on one hand and ensure sporulation on the other hand. This circumstance is not trivial, since these two metabolic states are contrary. The developed bioprocess uses a modified chemically defined medium which was further investigated in a one-factor-at-a-time assay after adaptation. A transfer from the shake flask to the bioreactor was successfully demonstrated in the scope of this work. The investigated process parameters included temperature, agitation and pH-control. Especially the pH-control improved the sporulation in the bioreactor when compared to shake flasks. The bioprocess resulted in a sporulation efficiency of 80%-90%. This corresponds to a sevenfold increase in sporulation efficiency due to a transfer to the bioreactor with pH-control. Additionally, a design of experiment (DoE) was conducted to test the robustness of the bioprocess. This experiment validated the beforementioned sporulation efficiency for the developed bioprocess. Afterwards the bioprocess was then scaled up from a 1 L scale to a 10 L bioreactor scale. A comparable sporulation efficiency of 80% as in the small scale was achieved. The developed bioprocess facilitates the upscaling and application to an industrial scale, and can thus help meet the increasing market for probiotics.

Genome-Assisted Probiotic Characterization and Application of Lactiplantibacillus plantarum 18 as a Candidate Probiotic for Laying Hen Production

Probiotics gained significant attention for their potential to improve gut health and enhance productivity in animals, including poultry. This comprehensive study focused on the genetic analysis of Lactiplantibacillus plantarum 18 (LP18) to understand its survival and colonization characteristics in the gastrointestinal tract. LP18 was supplemented in the late-stage diet of laying hens to investigate its impact on growth performance, egg quality, and lipid metabolism. The complete genome sequence of LP18 was determined, consisting of 3,275,044 base pairs with a GC content of 44.42% and two circular plasmids. Genomic analysis revealed genes associated with adaptability, adhesion, and gastrointestinal safety. LP18 supplementation significantly improved the daily laying rate (p < 0.05) during the late-production phase and showed noteworthy advancements in egg quality, including egg shape index (p < 0.05), egg albumen height (p < 0.01), Haugh unit (p < 0.01), and eggshell strength (p < 0.05), with notable improvements in eggshell ultrastructure. Additionally, LP18 supplementation resulted in a significant reduction in serum lipid content, including LDL (p < 0.01), FFA (p < 0.05), and Gly (p < 0.05). These findings provide valuable insights into the genomic characteristics of LP18 and the genes that support its survival and colonization in the gastrointestinal tract. Importantly, this study highlights the potential of LP18 as a probiotic candidate to enhance productivity, optimize egg quality, and modulate lipid metabolism in poultry production.

Whole genome sequence analysis enabled affirmation of the probiotic potential of marine sporulater Bacillus amyloliquefaciens BTSS3 isolated from Centroscyllium fabricii

Probiotics are microorganisms when administered in adequate amounts, confer health benefits on the host. Many probiotics find application in various industries however, probiotic bacteria linked to marine environments are less explored.Although Bifidobacteria, Lactobacilli, and Streptococcus thermophilus are the most frequently used probiotics, Bacillus spp. have acquired much acceptance in human functional foods due to their increased tolerance and enduring competence in harsh environments like the gastrointestinal (GI) tract. In this study, the 4 Mbp genome sequence of Bacillus amyloliquefaciens strain BTSS3, a marine spore former isolated from deep-sea shark Centroscyllium fabricii, with antimicrobial and probiotic properties was sequenced, assembled, and annotated. Analysis revealed the presence of numerous genes presenting probiotic traits like production of vitamins, secondary metabolites, amino acids, secretory proteins, enzymes and other proteins that allow survival in GI tract as well as adhesion to intestinal mucosa. Adhesion by colonization in the gut was studied in vivo in zebrafish (Danio rerio) using FITC labelled B.amyloliquefaciens BTSS3. Preliminary study revealed the ability of the marine Bacillus to attach to the intestinal mucosa of the fish gut. The genomic data and the in vivo experiment affirms that this marine spore former is a promising probiotic candidate with potential biotechnological applications.

Whole-genome sequence analysis and probiotic characteristics of Lactococcus lactis Subsp. lactis strain Lac3 isolated from traditional fermented buffalo milk (Dadih)

BACKGROUND

Probiotics are live microorganisms that provide beneficial effects on the host's health when exploited in adequate amounts. This study aimed at carrying out whole-genome sequence analysis and in vitro potential probiotic characteristics of Lactococcus lactis subsp. lactis strain Lac3 isolated from the spontaneously fermented buffalo milk named Dadih.

RESULTS

The results from de novo assembly indicated that the assembled genome consisted of 55 contigs with a genome size of 2,441,808 bp ~ (2.44 Mb), and GC % content of 34.85%. The evolution history result showed that the strain Lac3 was closely related to Lactococcus lactis species deposited in NCBI with a sequence similarity ≥ 99.93%. L. lactis subsp. lactis Lac3 was non-pathogenic with a probability of 0.21 out of 1 and had a pathogenicity score of zero (0), and neither harbored virulence factors nor acquired antibiotic resistance phenotypes. L. lactis subsp. lactis Lac3 exhibited the potential probiotic characteristics to tolerate acid at pH (2.0 and 5.0), salinity (1-5% NaCl), bile salt of (0.3-1.0%) and had auto-aggregation capacity increased from 6.0 to 13.1%.

CONCLUSION

This study described a novel strain of Lactococcus lactis subsp. lactis called Lac3, which exhibits probiotic properties that could be beneficial in the development of probiotics.

Probiotics: insights and new opportunities for Clostridioides difficile intervention

Clostridioides difficile infection (CDI) is a life-threatening disease caused by the Gram-positive, opportunistic intestinal pathogen C. difficile. Despite the availability of antimicrobial drugs to treat CDI, such as vancomycin, metronidazole, and fidaxomicin, recurrence of infection remains a significant clinical challenge. The use of live commensal microorganisms, or probiotics, is one of the most investigated non-antibiotic therapeutic options to balance gastrointestinal (GI) microbiota and subsequently tackle dysbiosis. In this review, we will discuss major commensal probiotic strains that have the potential to prevent and/or treat CDI and its recurrence, reassess the efficacy of probiotics supplementation as a CDI intervention, delve into lessons learned from probiotic modulation of the immune system, explore avenues like genome-scale metabolic network reconstructions, genome sequencing, and multi-omics to identify novel strains and understand their functionality, and discuss the current regulatory framework, challenges, and future directions.

In vitro characterization of lactic acid bacterial strains isolated from fermented foods with anti-inflammatory and dipeptidyl peptidase-IV inhibition potential

Probiotics are known to stimulate, modulate, and regulate host immune response by regulating specific sets of genes and improve glucose homeostasis through regulating dipeptidyl peptidase (DPP-IV) activity, but the mechanism behind their protective role is not clearly understood. Therefore, the present study was designed to isolate indigenous lactic acid bacterial (LAB) strains from different fermented food samples, vegetables, and human infant feces exhibiting anti-inflammatory, antioxidant, and DPP-IV inhibitory activity. A total of thirty-six Gram-positive, catalase-negative, and rod-shaped bacteria were isolated and screened for their anti-inflammatory activity using lipopolysaccharide (LPS)-induced inflammation on the murine (RAW264.7) macrophages. Among all, sixteen strains exhibited more than 90% reduction in nitric oxide (NO) production by the LPS-treated RAW264.7 cells. Prioritized strains were characterized for their probiotic attributes as per the DBT-ICMR guidelines and showed desirable probiotic attributes in a species and strain-dependent manner. Accordingly, Lacticaseibacillus rhamnosus LAB3, Levilactobacillus brevis LAB20, Lactiplantibacillus plantarum LAB31, Pediococcus acidilactici LAB8, and Lactiplantibacillus plantarum LAB39 were prioritized. Furthermore, these strains when co-supplemented with LPS and treated on RAW264.7 cells inhibited the mitogen-activated protein kinases (MAPKs), i.e., p38 MAPK, ERK1/2, and SAPK/JNK, cyclooxygenase-2 (COX-2), relative to the LPS-alone-treated macrophages. LAB31 and LAB39 also showed 64 and 95% of DPP-IV inhibitory activity relative to the Lacticaseibacillus rhamnosus GG ATCC 53103, which was used as a reference strain in all the studies. Five prioritized strains ameliorated the LPS-induced inflammation by downregulating the JNK/MAPK pathway and could be employed as an alternative bio-therapeutic strategy in mitigating gut-associated inflammatory conditions. The potential mechanism of action of prioritized LAB strains in preventing the LPS-induced inflammation in RAW 264.7 macrophage cells.

Complete Genomic Sequence of Bacillus coagulans Strain JBI-YZ6.3: a Natural Spore-Forming Isolate from Food-Grade Tapioca Starch

Bacillus coagulans strain JBI-YZ6.3 is a safe probiotic bacterium isolated from food-grade tapioca starch. The complete genome of B. coagulans JBI-YZ6.3 comprises one circular chromosome of 3.5 Mb and contains no toxigenic and antibiotic resistance genes, providing molecular information to support the strain's safety and usage as a probiotic.

In vitro and in silico assessment of probiotic and functional properties of Bacillus subtilis DE111®

Bacillus subtilis DE111® is a safe, well-tolerated commercially available spore-forming probiotic that has been clinically shown to support a healthy gut microbiome, and to promote digestive and immune health in both adults and children. Recently it was shown that this spore-forming probiotic was capable of germinating in the gastrointestinal tract as early as 3 h after ingestion. However, a better understanding of the mechanisms involved in the efficacy of DE111® is required. Therefore, the present investigation was undertaken to elucidate the functional properties of DE111® through employing a combination of in vitro functional assays and genome analysis. DE111® genome mining revealed the presence of several genes encoding acid and stress tolerance mechanisms in addition to adhesion proteins required to survive and colonize harsh gastrointestinal environment including multi subunit ATPases, arginine deiminase (ADI) pathway genes (argBDR), stress (GroES/GroEL and DnaK/DnaJ) and extracellular polymeric substances (EPS) biosynthesis genes (pgsBCA). DE111® harbors several genes encoding enzymes involved in the metabolism of dietary molecules (protease, lipases, and carbohyrolases), antioxidant activity and genes associated with the synthesis of several B-vitamins (thiamine, riboflavin, pyridoxin, biotin, and folate), vitamin K2 (menaquinone) and seven amino acids including five essential amino acids (threonine, tryptophan, methionine, leucine, and lysine). Furthermore, a combined in silico analysis of bacteriocin producing genes with in vitro analysis highlighted a broad antagonistic activity of DE111® toward numerous urinary tract, intestinal, and skin pathogens. Enzymatic activities included proteases, peptidases, esterase's, and carbohydrate metabolism coupled with metabolomic analysis of DE111® fermented ultra-high temperature milk, revealed a high release of amino acids and beneficial short chain fatty acids (SCFAs). Together, this study demonstrates the genetic and phenotypic ability of DE111® for surviving harsh gastric transit and conferring health benefits to the host, in particular its efficacy in the metabolism of dietary molecules, and its potential to generate beneficial SCFAs, casein-derived bioactive peptides, as well as its high antioxidant and antimicrobial potential. Thus, supporting the use of DE111® as a nutrient supplement and its pottential use in the preparation of functional foods.

Complete Genome Sequencing Revealed the Potential Application of a Novel Weizmannia coagulans PL-W Production with Promising Bacteriocins in Food Preservative

Weizmannia coagulans is an important potential probiotic with dual characteristics of Bacillus and Lactobacillus. This study describes a novel Weizmannia coagulans PL-W with excellent antibacterial activity isolated from Mongolian traditional cheese, in which safety and probiotic potential were evaluated by complete genome sequencing. The crude bacteriocins of W. coagulans PL-W showed antibacterial activity against various foodborne pathogens, including Listeria monocytogenes CMCC 54,004, Bacillus cereus ATCC 14,579, and Staphylococcus aureus ATCC 25,923. Moreover, the crude bacteriocins have outstanding stability against pH, temperature, surfactants, and are sensitive to protease. The complete genome sequencing revealed W. coagulans PL-W consists of 3,666,052-base pair (bp) circular chromosomes with a GC content of 46.24% and 3485 protein-coding genes. It contains 84 tRNA, 10 23S rRNA, 10 16S rRNA, and 10 5S rRNA. In addition, no risk-related genes such as acquired antibiotic resistance genes, virulence, and pathogenic factors were identified, demonstrating that W. coagulans PL-W is safe to use. Furthermore, the presence of gene clusters involved in bacteriocin synthesis, adhesion-related genes, and genes contributing to acid and bile tolerance indicate that W. coagulans PL-W is a potential candidate probiotic. Thus, antimicrobial activity and genome characterization of W. coagulans PL-W demonstrate that it has extensive potential applications as a food protective culture.

In vitro assessment of probiotic attributes for strains contained in commercial formulations

Although probiotics are often indiscriminately prescribed, they are not equal and their effects on the host may profoundly differ. In vitro determination of the attributes of probiotics should be a primary concern and be performed even before clinical studies are designed. In fact, knowledge on the biological properties a microbe possesses is crucial for selecting the most suitable bacteriotherapy for each individual. Herein, nine strains (Bacillus clausii NR, OC, SIN, T, Bacillus coagulans ATCC 7050, Bifidobacterium breve DSM 16604, Limosilactobacillus reuteri DSM 17938, Lacticaseibacillus rhamnosus ATCC 53103, and Saccharomyces boulardii CNCM I-745) declared to be contained in six commercial formulations were tested for their ability to tolerate simulated intestinal conditions, adhere to mucins, and produce β-galactosidase, antioxidant enzymes, riboflavin, and D-lactate. With the exception of B. breve, all microbes survived in simulated intestinal fluid. L. rhamnosus was unable to adhere to mucins and differences in mucin adhesion were evidenced for L. reuteri and S. boulardii depending on oxygen levels. All microorganisms produced antioxidant enzymes, but only B. clausii, B. coagulans, B. breve, and L. reuteri synthesize β-galactosidase. Riboflavin secretion was observed for Bacillus species and L. rhamnosus, while D-lactate production was restricted to L. reuteri and L. rhamnosus. Our findings indicate that the analyzed strains possess different in vitro biological properties, thus highlighting the usefulness of in vitro tests as prelude for clinical research.

Application of Weizmannia coagulans in the medical and livestock industry

Purpose

Products enriched with probiotics have always been fashionable. Weizmannia coagulans has become a hot research topic in the academic community due to their multiple functional properties and high resistance to stress, which can retain their activity in a variety of harsh environments. This review aims to evaluate the probiotic effects of different strains of Weizmannia coagulans in animals and humans and to inspire better exploitation of the value of this strain.

Methods

This review summarizes the latest research progress of Weizmannia coagulans from two major applications in animal breeding and human health.

Results

The functional properties of Weizmannia coagulans are extensively recognized. In animals, the strain can promote nutrient absorption, reduce mortality, and enhance the slaughter rate in livestock and poultry. In humans, the strain can be used to treat gastrointestinal disorders, immunomodulation, depressive symptoms, and non-alcoholic fatty liver. Weizmannia coagulans is projected as an ideal substitute for antibiotics and other chemical drugs.

Conclusion

Despite the outstanding functional properties of Weizmannia coagulans, there are numerous strains of Weizmannia coagulans and significant differences between strains in functional and physiological properties. Currently, there are few literature reports on the probiotic mechanism and functional gene identification of Weizmannia coagulans, which is crucial for the commercialization of Weizmannia coagulans and the benefit of human society.

Bacillus coagulans BACO-17 Alone or in Combination with Galacto-Oligosaccharide Ameliorates Salmonella-Induced Diarrhea and Intestinal Inflammation

In this study, a diarrhea model was established by exposing rats to appropriate antibiotics and Salmonella. After an in vitro screening of prebiotics, fructo-oligosaccharide and galacto-oligosaccharide (GOS) were selected; their synbiotic potential and ability to ameliorate diarrhea symptoms and intestinal inflammation with Bacillus coagulans BACO-17 were evaluated in vivo. After a 27-day feeding experiment including antibiotic intervention and Salmonella infection, it was found that using B. coagulans BACO-17 alone and in combination with GOS as a synbiotic could render a better recovery by lowering diarrhea indexes by 26.9% and 18.7%, respectively. Compared with the negative control, the administration of this synbiotic mixture resulted in the most significant increase in fecal concentrations of total short-chain fatty acids (about 2-fold higher), with a promising improvement in disrupted gut microbial balance. It was worth noting that the administration of B. coagulans BACO-17 alone or in combination with GOS effectively reduced intestinal inflammation (27–31%) and mucosal necrosis (82%) over the negative control. These results suggested that B. coagulans BACO-17 and GOS could be exploited as a promising synbiotic mixture to relieve intestinal inflammatory diseases and improve gut health.

Integrated genome-based assessment of safety and probiotic characteristics of Lactiplantibacillus plantarum PMO 08 isolated from kimchi

Lactiplantibacillus plantarum PMO 08 has been used as a probiotic starter culture for plant-based fermented beverages, with various health-promoting effects such as cholesterol-lowering and anti-inflammatory activities. This study aimed to analyze the genome sequence of Lp. plantarum PMO 08 and identify its safety and probiotic characteristics at the genomic level. For this, complete genome sequencing was conducted to investigate the genes associated with risk and probiotic characteristics by using Pacbio combined with Illumina HiSeq. This bacterial strain has one circular chromosome of 3,247,789 bp with 44.5% G + C content and two plasmids of 50,296 bp with 39.0% G + C content and 19,592 bp with 40.5% G + C content. Orthologous average nucleotide identity analysis showed that PMO 08 belongs to the Lp. plantarum group with 99.14% similarity to Lp. plantarum WCFS1. No deleterious genes were determined in the virulence factor analysis, and no hemolysin activity or secondary bile salt synthesis were detected in vitro test. In the case of antibiotic resistance analysis, PMO 08 was resistant to ampicillin in vitro test, but these genes were not transferable. In addition, the strain showed same carbohydrate utilization with Lp. plantarum WCFS1, except for mannopyranoside, which only our strain can metabolize. The strain also harbors a gene for inositol monophosphatase family protein related with phytate hydrolysis and have several genes for metabolizing various carbohydrate which were rich in plant environment. Furthermore, in probiotic characteristics several genes involved in phenotypes such as acid/bile tolerance, adhesion ability, and oxidative stress response were detected in genome analysis. This study demonstrates that Lp. plantarum PMO 08 harbors several probiotic-related genes (with no deleterious genes) and is a suitable probiotic starter for plant-based fermentation.

Analysis and Characterization of Lactobacillus paragasseri and Lacticaseibacillus paracasei: Two Probiotic Bacteria that Can Degrade Intestinal Oxalate in Hyperoxaluric Rats

In the present study, we characterized the probiotic properties of two commercially available bacterial strains, Lactobacillus paragasseri UBLG-36 and Lacticaseibacillus paracasei UBLPC-87, and evaluated their ability to degrade oxalate in vitro and in a hyperoxaluria-induced nephrolithiasis rat model. UBLG-36 harboring two oxalate catabolizing genes, oxalyl coenzyme A decarboxylase (oxc) and formyl coenzyme A transferase (frc), was previously shown to degrade oxalate in vitro effectively. Here, we show that UBLPC-87, lacking both oxc and frc, could still degrade oxalate in vitro. Both these strains harbored several potential putative probiotic genes that may have conferred them the ability to survive in low pH and 0.3% bile, resist antibiotic stress, show antagonistic activity against pathogenic bacteria, and adhere to epithelial cell surfaces. We further evaluated if UBLG-36 and UBLPC-87 could degrade oxalate in vivo and prevent hyperoxaluria-induced nephrolithiasis in rats. We observed that rats treated with 4.5% sodium oxalate (NaOx) developed hyperoxaluria and renal stones. However, when pre-treated with UBLG-36 or UBLPC-87 before administering 4.5% NaOx, the rats were protected against several pathophysiological manifestations of hyperoxaluria. Compared to the hyperoxaluric rats, the probiotic pre-treated rats showed reduced urinary excretion of oxalate and urea (p < 0.05), decreased serum blood urea nitrogen and creatinine (p < 0.05), alleviated stone formation and renal histological damage, and an overall decrease in renal tissue oxalate and calcium content (p < 0.05). Taken together, both UBLG-36 and UBLPC-87 are effective oxalate catabolizing probiotics capable of preventing hyperoxaluria and alleviating renal damage associated with nephrolithiasis.

Bacillus licheniformis MCC 2514 genome sequencing and functional annotation for providing genetic evidence for probiotic gut adhesion properties and its applicability as a bio-preservative agent

Bacillus licheniformis is a well-known probiotic that can be found in a variety of foods. The strain Bacillus licheniformis MCC 2514 was previously characterized by our group for its bio-physiological capabilities establishing it as a promising probiotic, but information on the genetic evidence for its attributes was lacking. In the current study, whole genome analysis identified the underlying molecular determinants responsible for its probiotic potential. The circular genome of MCC 2514 was 4,230,480 bp with 46.2% GC content, 24 rRNA, and 83 tRNA genes. The pangenome analysis between B. licheniformis MCC 2514 and 12 other B. licheniformis strains revealed a pangenome of 6008 genes and core genome of 3775 genes. Genome mining revealed NRPS and bacteriocins producing gene clusters indicating its biocontrol properties. Several genes encoding carbohydrate degrading enzymes, which aid in proper food degradation in the intestine, were also observed. Stress tolerance, vitamin, and essential amino acids biosynthesis related genes were found, which are important characteristics of a probiotic strain. Additionally, vital genes responsible for gut adhesion and biofilm formation were observed in its genome. The bacterium has been shown to improve the shelf life of idli batter by preventing whey separation, CO_2, and odour production while maintaining the pH of 3.96-4.29, especially at cold temperatures. It has significantly reduced coliform contamination at both room and low temperatures, demonstrating its bio-preservative ability, which is also corroborated by the presence of the NRPS and bacteriocin gene clusters in its genome. The present study helped to understand both, the ability of B. licheniformis MCC 2514 to adapt the intestinal gut environment and its probiotic functionality for food preservation.

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.

Discovery and delivery strategies for engineered live biotherapeutic products

Genetically engineered microbes that secrete therapeutics, sense and respond to external environments, and/or target specific sites in the gut fall under an emergent class of therapeutics, called live biotherapeutic products (LBPs). As live organisms that require symbiotic host interactions, LBPs offer unique therapeutic opportunities, but also face distinct challenges in the gut microenvironment. In this review, we describe recent approaches (often demonstrated using traditional probiotic microorganisms) to discover LBP chassis and genetic parts utilizing omics-based methods and highlight LBP delivery strategies, with a focus on addressing physiological challenges that LBPs encounter after oral administration. Finally, we share our perspective on the opportunity to apply an integrated approach, wherein discovery and delivery strategies are utilized synergistically, towards tailoring and optimizing LBP efficacy.

Draft Genome Sequence of Lactococcus lactis Subsp. cremoris WA2-67: A Promising Nisin-Producing Probiotic Strain Isolated from the Rearing Environment of a Spanish Rainbow Trout (Oncorhynchus mykiss, Walbaum) Farm

Probiotics are a viable alternative to traditional chemotherapy agents to control infectious diseases in aquaculture. In this regard, Lactococcus lactis subsp. cremoris WA2-67 has previously demonstrated several probiotic features, such as a strong antimicrobial activity against ichthyopathogens, survival in freshwater, resistance to fish bile and low pH, and hydrophobicity. The aim of this manuscript is an in silico analysis of the whole-genome sequence (WGS) of this strain to gain deeper insights into its probiotic properties and their genetic basis. Genomic DNA was purified, and libraries prepared for Illumina sequencing. After trimming and assembly, resulting contigs were subjected to bioinformatic analyses. The draft genome of L. cremoris WA2-67 consists of 30 contigs (2,573,139 bp), and a total number of 2493 coding DNA sequences (CDSs). Via in silico analysis, the bacteriocinogenic genetic clusters encoding the lantibiotic nisin Z (NisZ) and two new bacteriocins were identified, in addition to several probiotic traits, such as the production of vitamins, amino acids, adhesion/aggregation, and stress resistance factors, as well as the absence of transferable antibiotic resistance determinants and genes encoding detrimental enzymatic activities and virulence factors. These results unveil diverse beneficial properties that support the use of L. cremoris WA2-67 as a probiotic for aquaculture.

Bacillus coagulans TL3 Inhibits LPS-Induced Caecum Damage in Rat by Regulating the TLR4/MyD88/NF-κB and Nrf2 Signal Pathways and Modulating Intestinal Microflora

Background

Bacillus coagulans has been widely used in food and feed additives, which can effectively inhibit the growth of harmful bacteria, improve intestinal microecological environment, promote intestinal development, and enhance intestinal function, but its probiotic mechanism is not completely clear.

Aim

The aim of this study is to discuss the effect and mechanism of Bacillus coagulans TL3 on oxidative stress and inflammatory injury of cecum induced by LPS.

Method

The Wistar rats were randomly divided into four groups, each containing 7 animals. Two groups were fed with basic diet (the LPS and control, or CON, groups). The remaining groups were fed with basic diet and either a intragastric administration high or low dose of B. coagulans, forming the HBC and LBC groups, respectively. The rats were fed normally for two weeks. On the 15th day, those in the LPS, HBC, and LBC groups were injected intraperitoneally with LPS—the rats in the CON group were injected intraperitoneally with physiological saline. After 4 hours, all the rats were anesthetized and sacrificed by cervical dislocation, allowing samples to be collected and labeled. The inflammatory and antioxidant cytokine changes of the cecum were measured, and the pathological changes of the cecum were observed, determining the cecal antioxidant, inflammation, and changes in tight junction proteins and analysis of intestinal flora.

Result

The results show that LPS induces oxidative damage in the cecal tissues of rats and the occurrence of inflammation could also be detected in the serum. The Western blot results detected changes in the NF-κB- and Nrf2-related signaling pathways and TJ-related protein levels. Compared with the LPS group, the HBC group showed significantly downregulated levels of expression of Nrf2, NQO1, HO-1, GPX, and GCLC. The expression of TLR4, MYD88, NF-κB, IL-6, TNFα, and IL-1β was also significantly downregulated, while the expression of other proteins (ZO-1, occludin, and claudin-1) increased significantly. Bacillus coagulans TL3 was also found to increase the relative abundance of the beneficial bacterium Akkermansia muciniphila in the intestines. There is also a significant reduction in the number of harmful bacteria Escherichia coli and Shigella (Enterobacteriaceae).

Conclusion

Bacillus coagulans TL3 regulates the TLR4/MyD88/NF-κB and Nrf2 signaling pathways in the cecal tissue of rats, protects the intestine from inflammation and oxidative damage caused by LPS, and inhibits the reproduction of harmful bacteria and promotes beneficial effects by regulating the intestinal flora bacteria grow, thereby enhancing intestinal immunity.

Genome Characterization and Probiotic Potential of Corynebacterium amycolatum Human Vaginal Isolates

The vaginal microbiome of healthy women contains nondiphtheria corynebacteria. The role and functions of nondiphtheria corynebacteria in the vaginal biotope are still under study. We sequenced and analysed the genomes of three vaginal C. amycolatum strains isolated from healthy women. Previous studies have shown that these strains produced metabolites that significantly increased the antagonistic activity of peroxide-producing lactic acid bacteria against pathogenic and opportunistic microorganisms and had strong antimicrobial activity against opportunistic pathogens. Analysis of the C. amycolatum genomes revealed the genes responsible for adaptation and survival in the vaginal environment, including acid and oxidative stress resistance genes. The genes responsible for the production of H₂O₂ and the synthesis of secondary metabolites, essential amino acids and vitamins were identified. A cluster of genes encoding the synthesis of bacteriocin was revealed in one of the annotated genomes. The obtained results allow us to consider the studied strains as potential probiotics that are capable of preventing the growth of pathogenic microorganisms and supporting colonisation resistance in the vaginal biotope.

Indian oil sardine (Sardinella longiceps) gut derived Bacillus safensis SDG14 with enhanced probiotic competence for food and feed applications

Probiotics are considered as functional food as they provide health benefits along with traditional nutrition. Spore forming probiotic Bacillus are of commercial interest than Lactic Acid Bacillus due to their relatively lower cost of production and higher survivability. In the present study we identified the bacterial strain SDG14 isolated from Indian oil Sardine by Average Nucleotide Identity of whole genome sequence. The whole genome of SDG14 was also explored for pathogenicity, the presence of genes responsible for probiotic traits such as spore formation, resistance to host gastrointestinal tract conditions, adhesion to intestinal mucosa, interference in pathogen survival, expression of bacteriocins, oxidative and other stress responses, absorption of nutrition, production of essential amino acids and vitamins. Wet lab experiments for probiotic characterization were also conducted. The organism was confirmed to be Bacillus safensis SDG14. The possible pathogenicity of the organism was also ruled out by in silico analysis. Bacillus safensis SDG14 was able to survive at pH 3 and bile salt concentration of 0.5% (w/v). The adhesion index of Bacillus safensis SDG14 on HEp-2 was 36.82 ± 5.93 and 45.54 ± 9.55 respectively after 60 and 90 min of incubation and self aggregation percentage was 18.4 ± 0.48% after 3 h. Bacillus safensis SDG14 produced bacteriocin and co-aggregated with E. coli, Salmonella Typhimurium and Pseudomonas aeruginosa. The genomic data supported the findings of wet lab study and vice versa. Bacillus safensis SDG14 was proved to be a non-pathogenic, spore forming, pH and bile salt resistant, bacteriocin, amino acid and vitamin producing probiotic with proposed food and feed applications.

Genome assisted probiotic characterization and application of Bacillus velezensis ZBG17 as an alternative to antibiotic growth promoters in broiler chickens

The present study describes genome annotation and phenotypic characterization of Bacillus velezensis ZBG17 and evaluation of its performance as antibiotic growth promoter substitute in broiler chickens. ZBG17 comprises 3.89 Mbp genome with GC content of 46.5%. ZBG17 could tolerate simulated gastrointestinal juices prevalent in the animal gut. Some adhesion-associated genomic features of ZBG17 supported the experimentally determined cell surface hydrophobicity and cell aggregation results. ZBG17 encoded multiple secondary metabolite gene clusters correlating with its broad-spectrum antibacterial activity. Interestingly, ZBG17 completely inhibited Salmonella enterica and Escherichia coli within 6 h and 8 h in liquid co-culture assay, respectively. ZBG17 genome analysis did not reveal any genetic determinant associated with reported safety hazards for use as a poultry direct-fed microbial. Dietary supplementation of ZBG17 significantly improved feed utilization efficiency and humoral immune response in broiler chickens, suggesting its prospective application as a direct-fed microbial in broiler chickens.

Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius

Lactobacillus salivarius has drawn attention because of its promising probiotic functions. Tolerance to the gastrointestinal tract condition is crucial for orally administrated probiotics to exert their functions. However, previous studies of L. salivarius have only focused on the bile salt resistance of particular strains, without uncovering the common molecular mechanisms of this species. Therefore, in this study, we expanded our research to 90 L. salivarius strains to explore their common functional genes for bile salt resistance. First, the survival rates of the 90 L. salivarius strains in 0.3% bile salt solutions were determined. Comparative genomics analysis was then performed to screen for the potential functional genes related to bile salt tolerance. Next, real-time polymerase chain reaction and gene knockout experiments were conducted to further verify the tolerance-related functional genes. The results indicated that the strain-dependent bile salt tolerance of L. salivarius was mainly associated with four peptidoglycan synthesis-related genes, seven phosphotransferase system-related genes, and one chaperone-encoding gene involved in the stress response. Among them, the GATase1-encoding gene showed the most significant association with bile salt tolerance. In addition, four genes related to DNA damage repair and substance transport were redundant in the strains with high bile salt tolerance. Besides, cluster analysis showed that bile salt hydrolases did not contribute to the bile salt tolerance of L. salivarius. In this study, we determined the global regulatory genes, including LSL_1568, LSL_1716 and LSL_1709, for bile salt tolerance in L. salivarius and provided a potential method for the rapid screening of bile salt-tolerant L. salivarius strains, based on PCR amplification of functional genes.

Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity

Limosilactobacillus fermentum (ATCC 23271) was originally isolated from the human intestine and has displayed antimicrobial activity, primarily against Candida species. Complete genome sequencing and comparative analyses were performed to elucidate the genetic basis underlying its probiotic potential. The ATCC 23271 genome was found to contain 2,193,335 bp, with 2123 protein-coding sequences. Phylogenetic analysis revealed that the ATCC 23271 strain shares 941 gene clusters with six other probiotic strains of L. fermentum. Putative genes known to confer probiotic properties have been identified in the genome, including genes related to adhesion, tolerance to acidic pH and bile salts, tolerance to oxidative stress, and metabolism and transport of sugars and other compounds. A search for bacteriocin genes revealed a sequence 48% similar to that of enterolysin A, a protein from Enterococcus faecalis. However, in vitro assays confirmed that the strain has inhibitory activity on the growth of Candida species and also interferes with their adhesion to HeLa cells. In silico analyses demonstrated a high probability of the protein with antimicrobial activity. Our data reveal the genome features of L. fermentum ATCC 23271, which may provide insight into its future use given the functional benefits, especially against Candida infections.

Probiotic Properties of Bacillus proteolyticus Isolated From Tibetan Yaks, China

Yaks (Bos grunniens) live primarily in high-altitude hypoxic conditions and have a unique intestinal micro-ecosystem, remarkable adaptability, and strong climatic resistance. Accumulating evidence revealed the importance of probiotics in host metabolism, gut microbiota, growth performance, and health. The goal of this study was to screen out probiotics with excellent probiotic potential for clinical application. In this study, four strains of Bacillus, i.e., Bacillus proteolyticus (named Z1 and Z2), Bacillus amyloliquefaciens (named J), and Bacillus subtilis (named K), were isolated and identified. Afterward, their probiotic potential was evaluated. Antioxidant activity tests revealed that Z1 had the highest DPPH and hydroxyl radical scavenging activity, whereas Z2 had higher reducing power and inhibited lipid peroxidation. Additionally, the antibacterial testing revealed that all strains were antagonistic to three indicator pathogens, Escherichia coli C83902, Staphylococcus aureus BNCC186335, and Salmonella enteritidis NTNC13349. These isolates also had a higher hydrophobicity, autoaggregation, and acid and bile tolerance, all of which helped to survive and keep dangerous bacteria out of the host intestine. Importantly, all strains could be considered safe in terms of antibiotic susceptibility and lack of hemolysis. In conclusion, this is the first study to show that B. proteolyticus and B. amyloliquefaciens isolated from yaks have probiotic potential, providing a better foundation for future clinical use.

Use of probiotics for formation of microflora of gastrointestinal tract of calves

The results of the use of probiotic strains of microorganisms of the Bacillus family for the correction and formation of the microflora of the gastrointestinal tract and the impact on metabolism in calves are presented. The aim of the study. To analyze the effect of probiotics on the microflora of the gastrointestinal tract in calves and biochemical parameters of blood in calves up to one month. Materials and methods. The research was conducted during 2020 in the conditions of Ukrainian farms for cattle breeding. Five experimental groups of five one-week-old calves were formed in each and one control group. Calves were kept separately in the same conditions on the same diet, but with feeding together with colostrum substitute probiotics of five grams per animal: Bacillus amyloliquefaciense, Bacillus mucilaginosus, Bacillus coagulans, Bacillus megaterium, Bacillus pumilus. The strains are deposited and produced by “Kronos Agro” Ukraine. Results. It was found that as a result of studies when feeding calves B. coagulans, B. pumilus and B. mucilaginosus the number of Lactobacillus sp. was 80 % higher than in the control group. The level of opportunistic pathogens in the experimental group with B. coagulans had minimal values. Animals in the group where B. mucilaginosus was given had a higher amount of Candida - up to 300 CFU/g and Enterobacteriaceae – 200 CFU/g; which is 50 % less compared to control groups, but more than in the experiment with B. coagulans. According to the results of biochemical examination of blood serum in calves, the absence of toxic effects of probiotic strains: Bacillus amyloliquefaciense, Bacillus mucilaginosus, Bacillus coagulans, Bacillus megaterium, Bacillus pumilus on the internal organs of animals was established. Conclusions. It was found that the maximum positive effect on the microflora of the gastrointestinal tract of calves up to 30 days of age had B. coagulans (1×109) when fed at a dose of 5 g per animal. The amount of Lactobacillus sp. was the maximum and reached 800 CFU/g, which is 80 % more than in the control group. At the same time, the level of opportunistic pathogens in the experimental group with B. coagulans had minimal indicators and was: Clostridium by 20 %, Escherichia coli – by 70 %, Enterobacteriaceae, Staphylococcus and Candida – 100 % less than the control. In the study of biochemical parameters, it was found that the activity of enzymes, protein and glucose levels in the serum of experimental animals fed with B. coagulans were within the physiological norm, indicating a normal metabolic process and no toxic effects.

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

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

Bacillus coagulans R11 consumption influenced the abundances of cecum antibiotic resistance genes in lead-exposed laying hens

Bacillus coagulans is regarded as a clean, safe and helpful probiotic additive in the production of livestock and poultry breeds. Some studies have also shown that Bacillus coagulans can adsorb heavy metals in water, even in the gut of animals. However, whether Bacillus coagulans feeding influences antibiotic resistance gene (ARG) abundance in the gut of lead-exposed laying hens is unknown. To better apply such probiotics in the breeding industry, the present study employed Bacillus coagulans R11 and laying hens in model experiments to test ARG changes in the cecum of laying hens under lead exposure and B. coagulans R11 feeding. The results showed that there was the trend for ARG abundance decreasing in feeding B. coagulans R11 without lead exposure to laying hens in the cecum; however, feeding B. coagulans R11 to laying hens exposed to lead obviously increased the abundances of aminoglycoside and chloramphenicol ARGs. Further experiment found that hydroquinone, dodecanedioic acid, gibberellin A14, alpha-solanine, jasmonic acid and chitin were involved in the abundances of ARGs in the cecum, in addition the abundances of these compounds were also significantly enhanced by lead exposure or combination effects of lead and B. coagulans R11. As a result, the ARG hazards increased with feeding B. coagulans R11 to laying hens exposed to lead, and the key compounds which influenced by the combination effects of lead and B. coagulans R11 might influence the ARGs abundance.