As a pivotal defense system within the female lower genital tract, the healthy vaginal microecosystem, dominated by Lactobacillus, safeguards against pathogenic microorganisms and maintains overall reproductive health through producing antimicrobial substances and sustaining an acidic environment. However, this intricate ecosystem is susceptible to a variety of adverse factors that trigger vaginal microbiota (VMB) dysbiosis, which further precipitate vaginal infections and gynecological disorders. Based on rigorous clinical evidence, this review systematically summarizes current mechanistic understanding of Lactobacillus-mediated VMB homeostasis. It evaluates the therapeutic potential of probiotics in both pharmaceutical and dietary supplement forms, and discusses the clinical necessity and existing challenges in developing live biotherapeutic products (LBPs) targeting the vaginal microecology. By integrating perspectives from both basic research and translational medicine, this work provides a theoretical foundation for developing targeted microbiota modulation strategies, thereby advancing precision medicine approaches for the management of vaginal dysbiosis.

Three-Strain Probiotic Combination (Golden Bifid), a probiotic formulation composed of Bifidobacterium longum, Lactobacillus bulgaricus, and Streptococcus thermophilus, is widely used to modulate gut microbiota homeostasis and treat various gastrointestinal disorders. However, the specific molecular mechanisms underlying its therapeutic effects in slow transit constipation (STC) remain incompletely understood. In this study, we demonstrated that Golden Bifid alleviates loperamide-induced constipation by coordinately modulating host transcriptomic profiles, particularly the MAPK and serotonin signaling pathways, and restoring gut microbiota composition and diversity. These multi-omics findings provide novel mechanistic insights into the clinical efficacy of this probiotic combination, which have not been previously elucidated. Using a loperamide (LOP)-induced STC rat model, Golden Bifid was shown significantly increase defecation frequency, fecal water content, and intestinal motility, while improving the pathological damage of colonic tissues. It also elevated the protein expression of c-kit, 5-HT, 5-HT3R, and 5-HT4R in colonic tissue. RNA sequencing identified 1,998 differentially expressed transcripts in Golden Bifid group compared with the LOP group, with 899 upregulated and 1,099 downregulated. These transcripts were enriched in pathways, such as the mitogen-activated protein kinase (MAPK), tumor necrosis factor (TNF) and estrogen signaling pathway. Additionally, 16S rDNA sequencing demonstrated that the Golden Bifid partially restored gut microbiota structure, increased microbial diversity, and reversed the dysbiosis induced by LOP, notably reducing the abundance of Patescibacteria and modulating microbial taxa at both the phylum and genus levels to resemble the gut microbiota composition of the control group. These findings suggest that Golden Bifid alleviate STC by enhancing c-kit and 5-HT signaling, modulating the MAPK signaling pathway and pathway and restoring gut microbiota balance, offering promising therapeutic potential for STC treatment.

The evaluation of pathobiome strains should be conducted at the strain level, involving the identification of the functional genes, while considering the impact of ecological niche and drug interactions. The safety, efficacy, and quality management of live biotherapeutic products (LBPs), especially pathobiome strains, have certain peculiarities. Promising development methods include the recombinant LBP and active metabolites.

The iMeta Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals. Social media plays a crucial role in engaging the public and facilitating scientific communication, thus amplifying the impact of research. Together, these elements create a self-sustaining loop that fosters continuous innovation and collaboration in the field of bioinformatics, biotechnology and microbiome research.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

Modulation of gut microbiota by FMT from donors has been applied to the treatment of UC and yielded variable effectiveness in clinical trials. One possibility is that this variable effectiveness was related to donor selection, as a patient’s response to FMT may rely on the capability of the used donor’s microbiota to restore the specific gut disturbances of the patient.

IDDF2018-ABS-0162 Figure 1 PCA ordination of the gut microbiota communities, fitted with serum and liver tissue biochemistry assays (*** P<0.001, ** P<0.01) Results Histological scores showed that MCD induced the severest steatohepatitis, followed by HF and CD-HF diets. Based on operational taxonomic units (OTUs) at cutoff of 97% similarity, there were significant (PERMANOVA, p=0.001) differences in overall gut bacterial communities among MCD, HF, CD-HFD, and the Control, forming three major clusters in PCA ordination with HF and CD-HF groups more similar (figure 1). Furthermore, a-diversity of HF and CD-HF groups, including observed OTU numbers, Shannon index, and Pielou evenness were significantly (ANOVA, p<0.05) higher than the Control and MCD group. Overall, Abstracts A8 Gut 2018;67(Suppl 2):A1–A118 on S etem er 5, 2023 by gest. P rocted by coright. http/gut.bm jcom / G t: frst pulished as 10.113utjnl-2018-ID D F absacts.18 on 8 Jne 218. D ow nladed fom

EDITORIAL article Front. Cell. Infect. Microbiol., 18 October 2023Sec. Clinical Microbiology Volume 13 - 2023 | https://doi.org/10.3389/fcimb.2023.1292815

Objective Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes. Design This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing. Results According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota . However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii , Pyricularia grisea , Lachancea thermotolerans , and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii , were associated with remission in patients receiving capsulized FMT. Conclusion In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).

Background The role of the gut microbiome in developing chronic hepatitis B has received more and more attention in recent years. However, the relationship between gut fungi and chronic hepatitis B (CHB) has not been fully explored. Here, we aim to characterize the fungal microbiome in the progression of hepatitis B virus (HBV) infection. Methods We collected stools from 20 healthy people, 20 HBV carriers, 20 CHB patients, and 20 patients with HBV-related cirrhosis for ITS sequencing. Another cohort including 28 healthy people, 34 HBV carriers, 78 CHB patients, and 60 patients with HBV-related cirrhosis was enrolled for the serum anti-Saccharomyces cerevisiae antibody (ASCA) test. Results ITS sequencing results showed a significant gut fungal imbalance in the progression of chronic hepatitis B. HBV related cirrhosis group showed a lower abundance than the healthy group. At the genus level, the abundance of Saccharomyces cerevisiae (P<0.05) and Candida albicans (P<0.05) increased significantly with the progression of HBV infection. Additionally, patients with HBV-related cirrhosis had a significantly higher level of serum ASCA IgG (P<0.05) and IgA (P<0.01). Conclusions These observations will pave the way to understanding the relationship between gut fungal disorders and the development of hepatitis B infection. Saccharomyces cerevisiae and serum anti-Saccharomyces cerevisiae antibodies, can be used as predictive biomarkers in HBV-related cirrhosis.

Fecal microbiota transplantation has been successfully used in patients. Recently, capsulized FMT was reported to induce a response in patients with UC.

Abstract BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is a therapy that can induce clinical remission in ulcerative colitis. FMT through enema or colonoscopy brings pain to patients. In this study, we aimed to assess the efficiency of FMT via capsules in UC and determine the specific factors related to the response to clinical remission. METHODS We conducted a single-blind trial in Zhongshan Hospital of Xiamen University, China. 21 patients were randomized to accept FMT, and 4 were assigned to the placebo. Patients in the FMT group received capsules filled with healthy donor fecal material and those in the placebo group received capsules filled with glycerol. We performed 16s ribosomal RNA gene sequencing and shotgun metagenomics in fecal samples and analyzed serum samples for metabolome features. RESULTS FMT via capsules could receive favorable levels of therapeutic success in UC. 3 FMTs in 1 week induced clinical remission in 57.1% (12 of 21) and clinical response in 76.2% (16 of 21). Gut bacterial richness after FMT was increased in the patients who achieved remission. The increased relative abundance of Alistipes sp, O. splanchnicus, and F. prausnitzii was the strongest predictor of clinical remission. Patients in remission after FMT had enrichment of Alistipes sp, O. splanchnicus and had increased levels of indolelactic acid. Patients who did not achieve remission had enrichment of Escherichia coli and Klebsiella and increased levels of 12,13-DiHOME and lipopolysaccharide biosynthesis. CONCLUSIONS We had demonstrated the efficacy of FMT via capsules in active UC. We found that FMT could promote gut microbiome reconstruction, reduce the invasion of harmful bacteria and the synthesis of LPS, and accelerate the metabolism of indoleacetic acid by increasing the abundance of specific bacteria to alleviate intestinal inflammation. These findings may raise a new way in the design of FMT therapy for UC. ClinicalTrails.gov (NCT03426683).

2021年8月～9月,通过三家开展肠菌移植的单位进行了电子问卷调查,旨在从捐献者的角度,探究我国文化语境下他们对于捐献肠菌的特殊感受和对相关伦理问题的认知态度.结果显示,多数捐献者(80.0%)出于利他的目的进行捐献;超半数捐献者(53.0%)认识到捐献肠菌的风险;61.0%的捐献者同意自己的样本用于未来开放的研究,且后续研究都无需再次同意;与纯粹的捐献相比,具有经济目的的捐献者更加重视肠菌的所有权(χ2=5.73,P＜0.05)和利益分享(χ2=10.13,P＜0.05).捐献肠菌会引发污名化、隐私权等道德风险,需要提高研究人员的伦理意识,提升民众对生物科学研究的知情权与参与能力,保护公众和个体的利益不被侵犯.

Autoimmune diseases (ADs) represent a type of disease that causes damage to the body due to the disorder of autoantigen immune tolerance and host immune responses to autoantigens. Such defects could affect any part of the body, i.e. weakening bodily function and even turning life-threatening consequences. The incidence of ADs has increased over the past decade, affecting 5% to 8% of the world population and posing great challenge to the healthcare system. Up to now, more than eighty types of autoimmune diseases have been clinically identified. In addition to protect the host against infections, cancers and other diseases, the immune system also produces elevated levels of inflammatory cytokines and auto-antibodies that could induce complex autoimmune disorders (AIDs), such as Type I diabetes ( T1D), primary biliary cirrhosis (PBC), rheumatoid arthritis (RA), multiple sclerosis (MS), autoimmune liver disease (ALD), systemic lupus erythematosus (SLE), ankylosing spondylitis (AS), Sjogren syndrome (SS), and polymyositis/dermatomyositis, etc. However, the pathogenesis of ADs and many other diseases, especially certain types of cancers, still remains elusive and needs to be illuminated systematically.

Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China, 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States, Department of Teaching Support, Army Medical University, Chongqing, China, Geneis (Beijing) Co., Ltd., Beijing, China, College of Environmental Science and Engineering, Nankai University, Tianjin, China, 6 Inner Mongolia Shuangqi Pharmaceutical Co., Ltd., Huhhot, China, 7 Shenzhen Wedge Microbiology Research Co., Ltd., Shenzhen, China

To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella . Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.

Aeromonas veronii can cause severe aquaculture-related diseases through the production of virulence factors, which are mediated by quorum sensing, but little is known about the impact of quorum-sensing systems on intestinal colonization by A. veronii. Therefore, in this study, an acyl-homoserine-lactones (AHLs) synthase gene (ahyI) mutant strain was constructed to investigate its intestinal colonization and damage on zebrafish intestine. The mutant strain reduced the production of biofilm and exogenous C4-HSL could increase its biofilm production. The intestinal colonization of mutant strain was significantly (P < 0.05) lower than that of wild strain and the addition of C4-HSL, but the intestinal colonization of the mutant strain was significantly (P < 0.05) increased in the ampicillin pretreated zebrafish with less colonization resistance, which indicated that AHLs-mediated quorum sensing can enhance defense against colonization resistance. Meanwhile, histopathological analysis and 16S rRNA gene sequencing confirmed that AHLs-mediated quorum sensing promotes the damage caused by A. veronii to intestinal structures and the disruption of the commensal bacterial community. Therefore, our study determined the effect of AHLs-mediated quorum sensing on intestinal colonization by A. veronii as well as its defense against colonization resistance, which provides a basis for further study on intestinal colonization by pathogens.

For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.