From whole genomes to probiotic candidates: A study of potential lactobacilli strains selection for vaginitis treatment.

Vaginitis, characterized by pathogenic invasion and a deficiency in beneficial lactobacilli, has recognized lactobacilli supplementation as a novel therapeutic strategy. However, due to individual differences in vaginal microbiota, identifying universally effective Lactobacillus strains is challenging. Traditional methodologies for probiotic selection, which heavily depend on extensive in vitro experiments, are both time-intensive and laborious. The aim of this study was to pinpoint possible vaginal probiotic candidates based on whole-genome screening. We sequenced the genomes of 98 previously isolated Lactobacillus strains, annotating their genes involved in probiotic metabolite biosynthesis, adherence, acid/bile tolerance, and antibiotic resistance. A scoring system was used to assess the strains based on their genomic profiles. The highest-scoring strains underwent further in vitro evaluation. Consequently, two strains, Lactobacillus crispatus LG55-27 and Lactobacillus gasseri TM13-16, displayed an outstanding ability to produce d-lactate and adhere to human vaginal epithelial cells. They also showed higher antimicrobial activity against Gardnerella vaginalis, Escherichia coli, Candida albicans, Staphylococcus aureus, and Pseudomonas aeruginosa compared to reference Lactobacillus strains. Their resilience to acid and bile environments highlights the potential for oral supplementation. Oral and vaginal administration of these two strains were tested in a bacterial vaginosis (BV) rat model at various doses. Results indicated that combined vaginal administration of these strains at 1 × 106 CFU/day significantly mitigated BV in rats. This research offers a probiotic dosage guideline for vaginitis therapy, underscoring an efficient screening process for probiotics using genome sequencing, in vitro testing, and in vivo BV model experimentation.

Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota.

The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.

Randomized controlled trial comparing the impacts of Saccharomyces boulardii and Lactobacillus rhamnosus OF44 on intestinal flora in cerebral palsy rats: insights into inflammation biomarkers and depression-like behaviors.

Background: Cerebral palsy (CP) is a unique neurological disorder which adversely affects motion. Cytokines and gut microbial composition contribute to CP and other diseases, such as reproductive tract inflammation and bone loss. Importantly, Saccharomyces boulardii (S. boulardii) reduces the degree of inflammation and improves overall health status. As our previous study showed that Lactobacillus rhamnosus (L. rhamnosus) OF44, a selected strain of gut bacteria originally used to treat reproductive tract inflammation and bone loss, has effects similar to that of S. boulardii, we decided to use L. rhamnosus OF44 on CP rats. Validation of the effects of L. rhamnosus OF44 on CP adds to its confirmed effects in treating osteoporosis and reproductive tract microbiota disorders, increasing its potential as a probiotic. The purpose of this was to ascertain whether L. rhamnosus OF44 can alleviate the symptoms of CP. Methods: CP rat models were created through left carotid artery ligation. Following this, 100-day old CP rats were exposed to L. rhamnosus OF44, S. boulardii, or normal saline gastric gavage daily for 28 days. Grouping of the rats is determined randomly. Before and after the gavage, behavioral experiments were conducted and the inflammation levels assessed via measurements of interleukin (IL)-1ß, IL-6, IL-8, and tumor necrosis factor alpha (TNF-α) inflammatory markers. The efficacy of the outcome is measured by performing statistical analysis like the t-test on the data to see its significance. Additionally, variations inside gut microbiome were evaluated via 16S ribosomal RNA sequencing. Results: Before intervention, CP rats failed to exhibit depression-like behavior (P=0.6). L. rhamnosus OF44 treatment significantly reduced the level of IL-6 (P=4.8e-05), S. boulardii treatment significantly reduced the level of TNF-α (P=0.04). In addition, both treatments altered the composition and complexity of the gut microbiome. Conclusions: Our results indicated that L. rhamnosus OF44 has potential in alleviating inflammation and altering the gut microbial composition in CP, and that it has the potential to clinically treat CP. There are some limitations of this study. For example, dietary differences and their effects on gastrointestinal dysfunction are not considered in this study, and only two behavioral experiments were used.

Safety assessment of potential probiotic Lactobacillus acidophilus AM13-1 with high cholesterol-lowering capability isolated from human gut.

An important risk factor for cardiovascular disease is dyslipidemia, especially abnormal cholesterol levels. The relation between probiotics and cholesterol-lowering capability has been extensively studied. Lactobacillus acidophilus plays a significant role in affecting host health, and produces multitudinous metabolites, which have prohibitory functions against pathogenic microorganisms. In this study, we identified a cholesterol-lowering strain AM13-1, isolated from a fecal sample obtained from a healthy adult male, and performed comprehensive function analysis by whole-genome analysis and in vitro experiments. Genome analyses of L. acidophilus AM13-1 revealed that carbohydrate and amino acid transport, metabolism, translation, ribosomal structure, and biogenesis are abundant categories of functional genes. No virulence factors or toxin genes with experimentally verified were found in the genome of strain AM13-1. Besides, plenty of probiotic-related genes were predicted from the L. acidophilus AM13-1 genome, such as cbh, atpA-D, and dltD, with functions related to cholesterol-lowering and acid resistance. And strain AM13-1 showed high-efficiency of bile salt hydrolase activity and the capacity for removing cholesterol with efficiency rates of 70%. These function properties indicate that strain AM13-1 can be considered as a probiotic candidate for use in food and health care products.

Orally administrated Lactobacillus gasseri TM13 and Lactobacillus crispatus LG55 can restore the vaginal health of patients recovering from bacterial vaginosis.

Bacterial vaginosis (BV) is a common infection of the lower genital tract with a vaginal microbiome dysbiosis caused by decreasing of lactobacilli. Previous studies suggested that supplementation with live Lactobacillus may benefit the recovery of BV, however, the outcomes vary in people from different regions. Herein, we aim to evaluate the effectiveness of oral Chinese-origin Lactobacillus with adjuvant metronidazole (MET) on treating Chinese BV patients. In total, 67 Chinese women with BV were enrolled in this parallel controlled trial and randomly assigned to two study groups: a control group treated with MET vaginal suppositories for 7 days and a probiotic group treated with oral Lactobacillus gasseri TM13 and Lactobacillus crispatus LG55 as an adjuvant to MET for 30 days. By comparing the participants with Nugent Scores ≥ 7 and < 7 on days 14, 30, and 90, we found that oral administration of probiotics did not improve BV cure rates (72.73% and 84.00% at day 14, 57.14% and 60.00% at day 30, 32.14% and 48.39% at day 90 for probiotic and control group respectively). However, the probiotics were effective in restoring vaginal health after cure by showing higher proportion of participants with Nugent Scores < 4 in the probiotic group compared to the control group (87.50% and 71.43% on day 14, 93.75% and 88.89% on day 30, and 77.78% and 66.67% on day 90). The relative abundance of the probiotic strains was significantly increased in the intestinal microbiome of the probiotic group compared to the control group at day 14, but no significance was detected after 30 and 90 days. Also, the probiotics were not detected in vaginal microbiome, suggesting that L. gasseri TM13 and L. crispatus LG55 mainly acted through the intestine. A higher abundance of Prevotella timonensis at baseline was significantly associated with long-term cure failure of BV and greatly contributed to the enrichment of the lipid IVA synthesis pathway, which could aggravate inflammation response. To sum up, L. gasseri TM13 and L. crispatus LG55 can restore the vaginal health of patients recovering from BV, and individualized intervention mode should be developed to restore the vaginal health of patients recovering from BV. Clinical trial registration: https://classic.clinicaltrials.gov/ct2/show/, identifier NCT04771728.

Probiotic characteristics of Lactobacillus gasseri TF08-1: A cholesterol-lowering bacterium, isolated from human gut.

Lactobacillus contribute to maintain the human healthy and use for nutritional additives as probiotics. In this study, a cholesterol-lowering bacterium, Lactobacillus gasseri TF08-1, was isolated from the feces of a healthy adolescent, and its probiotic potentials were evaluated through genomic mining and in vitro test. The assembled draft genome comprised of 1,974,590 bp and was predicted total of 1,940 CDSs. The annotation of the genome revealed that L. gasseri TF08-1 harbored abundant categories of functional genes in metabolic and information processing. Moreover, strain TF08-1 has capacity to utilize D-Glucose, Sucrose, D-Maltose, Salicin, D-Xylose, D-Cellobiose, D-Mannose, and D-Trehalose, as the carbon source. The safety assessment showed strain TF08-1 contained few antibiotic resistance genes and virulence factors and was only resistant to 2 antibiotics detected by antimicrobial susceptibility test. A high bile salt hydrolase activity was found and a cholesterol-reducing effect was determined in vitro, which the result showed a remarkable cholesterol removal capability of L. gasseri TF08-1 with an efficiency of 84.40 %. This study demonstrated that the strain showed great capability of exopolysaccharide production, and tolerance to acid and bile salt. Therefore, these results indicate that L. gasseri TF08-1 can be considered as a safe candidate for probiotic, especially its potential in biotherapeutic for metabolic diseases.

Chromosome-level de novo assembly of Coprinopsis cinerea A43mut B43mut pab1-1 #326 and genetic variant identification of mutants using Nanopore MinION sequencing.

The homokaryotic Coprinopsis cinerea strain A43mut B43mut pab1-1 #326 is a widely used experimental model for developmental studies in mushroom-forming fungi. It can grow on defined artificial media and complete the whole lifecycle within two weeks. The mutations in mating type factors A and B result in the special feature of clamp formation and fruiting without mating. This feature allows investigations and manipulations with a homokaryotic genetic background. Current genome assembly of strain #326 was based on short-read sequencing data and was highly fragmented, leading to the bias in gene annotation and downstream analyses. Here, we report a chromosome-level genome assembly of strain #326. Oxford Nanopore Technology (ONT) MinION sequencing was used to get long reads. Illumina short reads was used to polish the sequences. A combined assembly yield 13 chromosomes and a mitochondrial genome as individual scaffolds. The assembly has 15,250 annotated genes with a high synteny with the C. cinerea strain Okayama-7 #130. This assembly has great improvement on contiguity and annotations. It is a suitable reference for further genomic studies, especially for the genetic, genomic and transcriptomic analyses in ONT long reads. Single nucleotide variants and structural variants in six mutagenized and cisplatin-screened mutants could be identified and validated. A 66 bp deletion in Ras GTPase-activating protein (RasGAP) was found in all mutants. To make a better use of ONT sequencing platform, we modified a high-molecular-weight genomic DNA isolation protocol based on magnetic beads for filamentous fungi. This study showed the use of MinION to construct a fungal reference genome and to perform downstream studies in an individual laboratory. An experimental workflow was proposed, from DNA isolation and whole genome sequencing, to genome assembly and variant calling. Our results provided solutions and parameters for fungal genomic analysis on MinION sequencing platform.

Genomic and transcriptomic comparison of Aspergillus oryzae strains: a case study in soy sauce koji fermentation.

The filamentous fungus Aspergillus oryzae is used in soy sauce koji making due to its high productivity of hydrolytic enzymes. In this study, we compared the genomes and transcriptomes of an industrial strain RD2 and a strain with decreased fermentation performance TS2, aiming to explain their phenotypic differences at the molecular level. Under the regulation of conidiation and fermentation conditions, the enhanced hydrolytic enzyme production and flavor precursor formation in RD2 described a complete expression profile necessary to maintain desirable fermentation performance. By contrast, central carbon metabolism was up-regulated in TS2 for fast growth, suggesting a conflicting relationship between mycelium growth and fermentation performance. Accumulation of mutations also lowered the fermentation performance of TS2. Our study has deepened the understanding of the metabolism and related regulatory mechanisms in desirable koji fermentation. A list of potential molecular markers identified here could facilitate targeted strain maintenance and improvement for better koji fermentation.