Assessing the safety and probiotic characteristics of Bacillus coagulans 13002 based on complete genome and phenotype analysis

Dilute acid-assisted microbubbles-mediated ozonolysis of Eucheuma denticulatum phycocolloid for biobased L-lactic acid production

Biobased L-lactic acid (L-LA) appeals to industries; however, existing technologies are plagued by limited productivity and high energy consumption. This study established an integrated process for producing macroalgae-based L-LA from Eucheuma denticulatum phycocolloid (EDP). Dilute acid-assisted microbubbles-mediated ozonolysis (DAMMO) was selected for the ozonolysis of EDP to optimize D-galactose recovery. Through single-factor optimization of DAMMO treatment, a maximum D-galactose recovery efficiency (59.10 %) was achieved using 0.15 M H2SO4 at 80 °C for 75 min. Fermentation with 3 % (w/v) mixed microbial cells (Bacillus coagulans ATCC 7050 and Lactobacillus acidophilus-14) and fermented residues achieved a 97.67 % L-LA yield. Additionally, this culture approach was further evaluated in repeated-batch fermentation and showed an average L-LA yield of 93.30 %, providing a feasible concept for macroalgae-based L-LA production.

Safety Evaluation of Bifidobacterium animalis subsp. lactis BLa80 under In Vitro, and In Vivo Conditions

Bifidobacterium animalis subsp. lactis BLa80 is a new probiotic strain with extensive applications in food products both domestically and internationally. Given the rising consumption of this probiotic, its safety assessment is increasingly crucial in the food industry. This study evaluates the safety of strain BLa80 using a combination of in vitro and in vivo assays along with genomic analysis. Methods included exposing the strain to artificial gastric and intestinal fluids, as well as a medium containing bile salts, to stimulate human digestive conditions. The strain showed high tolerance to gastric fluid at pH of 2.5 and to 0.3% bile salts. It maintained a 99.92% survival rate in intestinal fluid. Additional tests assessed hemolytic activity, antibiotic susceptibility (revealing sensitivity to 7 antibiotics), and biogenic amine production using HPLC-ELSD, confirming the absence of histamine, and other harmful amines. Bile salt hydrolase activity was demonstrated qualitatively, and metabolic byproducts were quantitatively analyzed using a D-/L-lactic acid assay kit, showing that BLa80 produces 1.48 mg/mL of L-lactic acid and no harmful D-lactic acid. Genomic analysis confirmed the absence of virulence or pathogenicity genes, and a 90-day oral toxicity study in rats confirmed no toxic effects at various doses. Overall, these findings support the safety classification of the strain BLa80.

Probiotic functional gene explorations in the genome of Limosilactobacillus fermentum GD5MG

Limosilactobacillus fermentum is an isolate obtained from oral gingival samples of healthy human individuals. The whole genome of Lb. fermentum GD5MG is composed of a circular DNA molecule containing 1,834,134 bp and exhibits a GC content of 52.80 %. The sequencing effort produced 38.6 million reads, each 150 bp in length, resulting in a sequencing depth of 2912.48x. Our examination unveiled a total of 1961 protein-coding genes, 27 rRNA genes, 24 tRNA genes, 3 non-coding RNA genes, and 63 pseudogenes with the use of gene annotations in NCBI Prokaryotic Genome Annotation tool. RAST revealed 1863 coding genes distributed across 209 subsystems, with a predominant involvement in amino acid, carbohydrate, and protein metabolism. Phylogenetic analysis infers that the Lb. fermentum GD5MG shares 281 gene clusters. Furthermore, the genome features showed a single CRISPR locus of 45 bp in length. Three genes associated with adhesion ability (strA, dltD, and dltA) and 26 genes related to acid tolerance, digestive enzyme secretion, and bile salt resistance were identified. Numerous genes associated with oral probiotic properties, comprising adhesion, acid and bile salt tolerance, oxidative stress tolerance, and sugar metabolism, were identified in the genome. Our findings shed light on the genomic characteristics of Lb. fermentum GD5MG, which are probable probiotics with functional benefits in humans.

Whole-genome sequencing of Pseudoalteromonas piscicida 2515 revealed its antibacterial potency against Vibrio anguillarum: a preliminary invitro study

Pseudoalteromonas piscicida 2515, isolated from Litopenaeus vannamei culture water, is a potential marine probiotic with broad anti-Vibrio properties. However, genomic information on P. piscicida 2515 is scarce. In this study, the general genomic characteristics and probiotic properties of the P. piscicida 2515 strain were analysed. In addition, we determined the antibacterial mechanism of this bacterial strain by scanning electron microscopy (SEM). The results indicated that the whole-genome sequence of P. piscicida 2515 contained one chromosome and one plasmid, including a total length of 5,541,406 bp with a G + C content of 43.24%, and 4679 protein-coding genes were predicted. Various adhesion-related genes, amino acid and vitamin metabolism and biosynthesis genes, and stress-responsive genes were found with genome mining tools. The presence of genes encoding chitin, bromocyclic peptides, lantibiotics, and sactipeptides showed the strong antibacterial activity of the P. piscicida 2515 strain. Moreover, in coculture with Vibrio anguillarum, P. piscicida 2515 displayed vesicle/pilus-like structures located on its surface that possibly participated in its bactericidal activity, representing an antibacterial mechanism. Additionally, 16 haemolytic genes and 3 antibiotic resistance genes, including tetracycline, fluoroquinolone, and carbapenem were annotated, but virulence genes encoding enterotoxin FM (entFM), cereulide (ces), and cytotoxin K were not detected. Further tests should be conducted to confirm the safety characteristics of P. piscicida 2515, including long-term toxicology tests, ecotoxicological assessment, and antibiotic resistance transfer risk assessment. Our results here revealed a new understanding of the probiotic properties and antibacterial mechanism of P. piscicida 2515, in addition to theoretical information for its application in aquaculture.

Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs

This study aims to screen for potential probiotic lactic acid bacteria from the intestines of meat-type pigeon squabs. Ligilactobacillus salivarius YZU37 was identified as the best comprehensive performed strain. Being acid- and bile salt-tolerant, it displayed growth-inhibition activities against Staphylococcus aureus ATCC25923, Escherichia coli ATCC25922, and Salmonella typhimurium SL1344, exhibited sensitivity to 6 commonly used antibiotics, and endowed with good cell surface hydrophobicity, auto-aggregation property, and anti-oxidant activities. Results of in vitro experiments indicated that the bacteriostatic effects of this strain were related to the production of proteinaceous substances that depend on acidic conditions. Whole-genome sequencing of L. salivarius YZU37 was performed to elucidate the genetic basis underlying its probiotic potential. Pangenome analysis of L. salivarius YZU37 and other 212 L. salivarius strains available on NCBI database revealed a pigeon-unique gene coding choloylglycine hydrolase (CGH), which had higher enzyme-substrate binding affinity than that of the common CGH shared by L. salivarius strains of other sources. Annotation of the functional genes in the genome of L. salivarius YZU37 revealed genes involved in responses to acid, bile salt, heat, cold, heavy metal, and oxidative stresses. The whole genome analysis also revealed the absence of virulence and toxin genes and the presence of 65 genes distributed under 4 CAZymes classes, 2 CRISPR-cas regions, and 3 enterolysin A clusters which may confer the acid-dependent antimicrobial potential of L. salivarius YZU37. Altogether, our results highlighted the probiotic potential of L. salivarius YZU37. Further in vivo investigations are required to elucidate its beneficial effects on pigeons.

Evaluating Enterococcus faecium9 N-2 as a probiotic candidate from traditional village white cheese

In this study, various functional and probiotic attributes of the Enterococcus faecium 9 N-2 strain isolated from village-style white cheese were characterized, while also assessing its safety. To achieve this, we conducted an in vitro analysis of several key probiotic properties exhibited by the 9 N-2 strain. Notably, this strain demonstrated robust resilience to low pH, high bile salt concentrations, lysozyme, pepsin, pancreatin, and phenol. Furthermore, this strain displayed exceptional auto-aggregation capabilities and moderate co-aggregation tendencies when interacting with Escherichia coli. The cell-free supernatant derived from strain 9 N-2 exhibited significant antimicrobial activity against the tested pathogens. The strain exhibited resistance to gentamicin, meropenem, and bacitracin, while remaining susceptible to vancomycin and various other antibiotics. Furthermore, it was found that E. faecium 9 N-2 possessed the capacity to produce the phytase enzyme. When all the results of this study are evaluated, it is thought that 9 N-2 strain has superior probiotic properties, and therefore it can be used as probiotic in food, medicine, and animal feed in the future. In addition, further in vivo tests should be performed to fully understand its effects and mechanisms of action and to confirm its safety and probiotic effects. Further research and clinical trials are also needed to identify new strains with potential probiotic properties.

In-silico analysis of probiotic attributes and safety assessment of probiotic strain Bacillus coagulans BCP92 for human application

The whole genome sequence (WGS) of Bacillus coagulans BCP92 is reported along with its genomic analysis of probiotics and safety features. The identification of bacterial strain was carried out using the 16S rDNA sequencing method. Furthermore, gene-related probiotic features, safety assessment (by in vitro and in silico), and genome stability were also studied using the WGS analysis for the possible use of the bacterial strain as a probiotic. From the BLAST analysis, bacterial strain was identified as Bacillus (Heyndrickxia) coagulans. WGS analysis indicated that the genome consists of a 3 475 658 bp and a GC-content of 46.35%. Genome mining of BCP92 revealed that the strain is consist of coding sequences for d-lactate dehydrogenase and l-lactate dehydrogenases, 36 genes involved in fermentation activities, 29 stress-responsive as well as many adhesions related genes. The genome, also possessing genes, is encoded for the synthesis of novel circular bacteriocin. Using an in-silico approach for the bacterial genome study, it was possible to determine that the Bacillus (Heyndrickxia) coagulans strain BCP92 contains genes that are encoded for the probiotic abilities and did not harbour genes that are risk associated, thus confirming the strain's safety and suitability as a probiotic to be used for human application.

Complete Genome Sequence and Probiotic Properties of Pediococcus acidilactici CLP03 Isolated from Healthy Felis catus

Probiotics are available from various sources, including the gastrointestinal tract of healthy animals. In this study, Pediococcus acidilactici was isolated for the first time from Felis catus and evaluated for its functionality. The findings revealed that P. acidilactici CLP03 exhibited inhibitory properties against pathogenic bacteria (E. coli, Salmonella, S. aureus, P. aeruginosa, and L. monocytogenes). Then, survival of strains exposed to pH 2.5, 0.3% bile salts, 0.5% bile salts, and gastrointestinal fluids was 63.97%, 98.84%, 87.95%, and 52.45%, respectively. Also, P. acidilactici CLP03 demonstrated high hydrophobicity (69.63-82.03%) and self-aggregation (73.51-81.44%), negative for hemolytic, and was susceptible to clindamycin. Finally, the scavenging rates of DPPH, ABTS, and O2- were 53.55%, 54.81%, and 85.13%, respectively, which demonstrated that the strain CLP03 has good oxidation resistance. All these characteristics contribute to the survival, colonization, and functionality of the strain in the gastrointestinal tract, indicating their excellent probiotic potential. On the other hand, animal experiments (KM mice, randomly assigned to four groups) showed that the gavage of CLP03 had no toxic effects on mice, increased the serum SOD content, and decreased the MDA and BUN contents, which revealed gavage of CLP03 significantly increased the antioxidant capacity of mice in vivo. In addition, complete genome annotation showed that P. acidilactici CLP03 had 1976 CDS genes, and the numbers of CRISPR, gene islands, and phages were 8, 3, and 6, respectively. In conclusion, P. acidilactici CLP03 could be a candidate functional cat probiotic to enhance animal health and welfare.

Evaluation of cholesterol transformation abilities and probiotic properties of Bacteroides dorei YGMCC0564

Hypercholesterolemia, a risk factor for cardiovascular disease (CVD), often requires therapeutic agents with varying degrees of side effects. This has created a need for safe and natural alternatives such as medications or functional foods that can improve lipid metabolism and reduce cholesterol levels. In recent years, Next-generation probiotics (NGPs) have recently emerged as a potential solution, offering distinct mechanisms compared to traditional probiotics. Among the NGPs, Bacteroides, a dominant bacterial genus in the human gut, has gained significant attention due to its prevalence, ability to break down plant polysaccharides, and production of short-chain fatty acids (SCFAs). Recent evidence has demonstrated that Bacteroides effectively reduces cholesterol levels, prevents obesity, and lowers the risk of CVD. However, research on Bacteroides is currently limited to a few species, leaving rooms for exploration of the beneficial functions of different species in this genus. In this study, we isolated 66 Bacteroides strains, including 9 distinct species, from healthy adults' fecal samples. By comparing their ability to assimilate cholesterol, we found that the transformation ability was not specific to any particular species. Notably, Bacteroides dorei YGMCC0564 revealed superior cholesterol-lowering capabilities and bile salt hydrolase (BSH) activity in vitro, surpassing that of Lactobacillus GG (LGG). YGMCC0564 exhibited favorable probiotic characteristics, including high survival rate in vitro simulation of gastrointestinal digestion, excellent adhesion ability, susceptibility to antibiotics, absence of hemolysis or virulence genes, and substantial production of SCFAs. The strain also demonstrated remarkable bile salt deconjugation activities and upregulation of the BT_416 gene associated with cholesterol, providing insights into a possible molecular mechanism underlying its cholesterol-reducing activity. These findings establish YGMCC0564 as a promising NPG candidate for improving cardiovascular health.

Assessment of the safety and probiotic characteristics of Lactobacillus salivarius CGMCC20700 based on whole-genome sequencing and phenotypic analysis

Lactic acid bacteria are generally regarded as alternatives to antibiotics in livestock and poultry farming, especially Lactobacillus strains, which are safe and have probiotic potential. Although Lactobacillus salivarius has long been proposed to be a probiotic, the understanding of the roles of this species is still in its infancy. Here, a strain of L. salivarius CGMCC20700 isolated from the intestinal mucosa of Yunnan black-bone chicken broilers was investigated in the context of its safety and probiotic characteristics by whole-genome sequencing in parallel with phenotypic analysis. Whole-genome sequencing results showed that L. salivarius CGMCC20700 has a single scaffold of 1,737,577 bp with an average guanine-to-cytosine (GC) ratio of 33.51% and 1,757 protein-coding genes. The annotation of Clusters of Orthologous Groups (COG) classified the predicted proteins from the assembled genome as possessing cellular, metabolic, and information-related functions. Sequences related to risk assessment, such as antibiotic resistance and virulence genes, were identified, and the strain was further confirmed as safe according to the results of antibiotic resistance, hemolytic, and acute oral toxicology tests. Two gene clusters of antibacterial compounds and broad-spectrum antimicrobial activity were identified using genome mining tools and antibacterial spectrum tests. Stress resistance genes, active stressor removal genes, and adhesion related genes that were identified and examined with various phenotypic assays (such as stress tolerance tests in acids and bile salts and auto aggregation and hydrophobicity assays). The strain showed a high survival rate in the presence of bile salts and under acidic conditions and exhibited significant auto aggregation capacity and hydrophobicity. Overall, L. salivarius CGMCC20700 demonstrated excellent safety and probiotic potential at both the genomic and physiological levels and can be considered an appropriate candidate probiotic for livestock and poultry farming.

Genetic and Probiotic Characteristics of Urolithin A Producing Enterococcus faecium FUA027

Enterococcus faecium FUA027 transforms ellagic acid (EA) to urolithin A (UA), which makes it a potential application in the preparation of UA by industrial fermentation. Here, the genetic and probiotic characteristics of E. faecium FUA027 were evaluated through whole-genome sequence analysis and phenotypic assays. The chromosome size of this strain was 2,718,096 bp, with a GC content of 38.27%. The whole-genome analysis revealed that the genome contained 18 antibiotic resistance genes and seven putative virulence factor genes. E. faecium FUA027 does not contain plasmids and mobile genetic elements (MGEs), and so the transmissibility of antibiotic resistance genes or putative virulence factors should not occur. Phenotypic testing further indicated that E. faecium FUA027 is sensitive to clinically relevant antibiotics. In addition, this bacterium exhibited no hemolytic activity, no biogenic amine production, and could significantly inhibit the growth of the quality control strain. In vitro viability was >60% in all simulated gastrointestinal environments, with good antioxidant activity. The study results suggest that E. faecium FUA027 has the potential to be used in industrial fermentation for the production of urolithin A.

Assessing the Safety and Probiotic Characteristics of Lacticaseibacillus rhamnosus X253 via Complete Genome and Phenotype Analysis

Lacticaseibacillus rhamnosus is a generalist that can adapt to different ecological niches, serving as a valuable source of probiotics. The genome of L. rhamnosus X253 contains one chromosome and no plasmids, with a size of 2.99 Mb. Both single-copy orthologous gene-based phylogenetic analysis and average nucleotide identity indicated that dairy-derived L. rhamnosus X253 was most closely related to the human-intestine-derived strain L. rhamnosus LOCK908, rather than other dairy strains. The adaptation of L. rhamnosus X253 and the human-intestine-derived strain L. rhamnosus GG to different ecological niches was explained by structural variation analysis and COG annotation. Hemolytic assays, API ZYM assays, and antimicrobial susceptibility tests were performed to validate risk-related sequences such as virulence factors, toxin-encoding genes, and antibiotic-resistance genes in the genomes of L. rhamnosus X253 and GG. The results showed that L. rhamnosus GG was able to use L-fucose, had a higher tolerance to bile salt, and adhered better to CaCo-2 cells. In contrast, L. rhamnosus X253 was capable of utilizing D-lactose, withstood larger quantities of hydrogen peroxide, and possessed excellent antioxidant properties. This study confirmed the safety and probiotic properties of L. rhamnosus X253 via complete genome and phenotype analysis, suggesting its potential as a probiotic.

W D, U. M K, S.D K. Bacillus Coagulans and its Spore as Potential Probiotics in the Production of Novel Shelf- Stable Foods

The synbiotic foods with therapeutic activities have been beneficial to gut health and immunity development, including Bacillus coagulans as the probiotic microorganism. It is preferred over other lactic acid bacteria (LAB) as it can produce spores. It is grown in the pH range of 5.5 to 6.2 and releases spores at 37 °C. These microbial spores can withstand environments with high temperatures, acidic conditions, and salinity, making it a viable probiotic organism for production of novel shelf-stable foods. It has become an essential ingredient in the functional food industry due to its probiotic characteristics and great resistance to stressful conditions. For extensive commercial use and a wide range of food applications, apart from probiotic characteristics, a probiotic organism must be cost-effective, convenient and remain viable throughout the processing, storage and consumption. The non-spore- forming lactic acid bacteria can be utilized to make probiotic products and fermented dairy products under controlled processing and storage conditions. The spore- forming probiotic organism can be delivered into the human gut through novel food products derived from cereals, legumes, fruits and vegetables, confectionery products, and meat and non-dairy products. This has led to the development of convenient and shelf-stable non-dairy probiotics. These non-dairy-based probiotics are cheaper, resilient against various processing conditions, high in bioactive components, and can mitigate the risk of lifestyle diseases and reduce. Further, lactose intolerance is associated with the consumption of dairy probiotics. Therefore, this review aimed to assess the utilization of probiotic Bacillus coagulans spores in emerging shelf-stable novel non-dairy products with probiotic potential.

Assessments of Probiotic Potentials of Lactiplantibacillus plantarum Strains Isolated From Chinese Traditional Fermented Food: Phenotypic and Genomic Analysis

The lack of rapid and effective approaches to determine the health benefits of strains is one of the main challenges affecting the selection of probiotics from large numbers of candidates. In this study, the probiotic potential of 44 Lactiplantibacillus plantarum strains isolated from different Chinese traditional fermented foods was evaluated, including acid and bile salt resistance, adhesion ability, survival in simulated human gastrointestinal transit, antioxidant activity, bile salt hydrolase (BSH) activity, and antibacterial activity. All tested L. plantarum strains showed high antioxidant capacity, BSH activity, and antibacterial activity. Among the strains, B652, C232, D444, and E932 were identified as the best comprehensive performed strains, which were selected for whole-genome sequencing, in order to provide clear information and identify key genes responsible for functional characteristics in vitro. It demonstrated that the antioxidant activity, adhesion activity, and ability to survive in the simulated gastric environment were found to be closely correlated with antioxidant enzyme encoding genes, cell-surface protein-encoding genes, and stress response genes, respectively. The numbers of functional genes present in strains might decide their performance in probiotic profile evaluation. The outcome of the study could support the development of a novel approach for the screening and identification of probiotics.