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Biology Dec 2022Background: The vaginal microbiome is closely associated with the onset and recurrence of bacterial vaginosis (BV). In the present study, the state of vaginal microbiota...
Background: The vaginal microbiome is closely associated with the onset and recurrence of bacterial vaginosis (BV). In the present study, the state of vaginal microbiota during the onset and post-treatment asymptomatic stages of BV were compared to that of a healthy population to evaluate the changes in different characteristic bacteria during the onset, progression, and remission of BV. Methods: A case−control study was performed to explore these changes. Women with clinical symptoms of BV were divided into the disease group (M) and case−control group (C) based on the Nugent score. Subjects in the disease group whose symptoms were resolved after the treatment were assigned to the treated group (T) and healthy subjects were recruited into the normal control (N) group. The V3−V4 hypervariable regions of bacterial 16S rRNA genes were sequenced on the Illumina MiSeq platform. Results: The N harbored the highest number of detected species and a higher abundance of microbiota; they had a significantly higher abundance of Lactobacillus and different bacterial community composition compared to the other three groups. In group M, Gardnerella vaginalis was the dominant species, whereas Lactobacillus iners was predominant in the other three groups. While Lactobacillus was more commonly present in Group C compared to group M. it was significantly increased in group T. Alpha diversity analysis of bacterial communities revealed significant differences in community richness and diversity among all four groups (p < 0.05). Significant differences in the distribution of various bacterial communities among the different groups were also observed (p < 0.05). Specifically, the abundance of eight bacterial taxa (Megasphaera, Aerococcus christensenii, Clostridiales, Gardnerella, Peptostreptococcus, Veillonellaceae, Akkermansia, Coriobacteriales) differed significantly among the four groups (p < 0.05). Conclusion: Significant differences in the composition and alpha diversity of the vaginal microbiota at different stages of BV and the distribution of bacterial communities were observed among the investigated groups. In addition to Gardnerella, Sneathia sanguinegens and Prevotella timonensis play an important role in the pathogenesis of BV. The appearance of BV-like clinical symptoms was closely associated with the decrease in Prevotella and Atopobium vaginae populations.
PubMed: 36552306
DOI: 10.3390/biology11121797 -
Applied and Environmental Microbiology May 2023d--hydroxyphenylglycine (d-HPG) is an important intermediate in the pharmaceutical industry. In this study, a tri-enzyme cascade for the production of d-HPG from l-HPG...
d--hydroxyphenylglycine (d-HPG) is an important intermediate in the pharmaceutical industry. In this study, a tri-enzyme cascade for the production of d-HPG from l-HPG was designed. However, the amination activity of Prevotella timonensis -diaminopimelate dehydrogenase (DAPDH) toward 4-hydroxyphenylglyoxylate (HPGA) was identified as the rate-limiting step. To overcome this issue, the crystal structure of DAPDH was solved, and a "binding pocket and conformation remodeling" strategy was developed to improve the catalytic activity toward HPGA. The best variant obtained, DAPDH, exhibited a catalytic efficiency (/) that was 26.75-fold higher than that of the wild type. This improvement was due to the enlarged substrate-binding pocket and enhanced hydrogen bond networks around the active center; meanwhile, the increased number of interdomain residue interactions drove the conformation distribution toward the closed state. Under optimal transformation conditions, DAPDH produced 19.8 g/L d-HPG from 40 g/L racemate DL-HPG in a 3 L fermenter within 10 h, with 49.5% conversion and >99% enantiomeric excess. Our study provides an efficient three-enzyme cascade pathway for the industrial production of d-HPG from racemate DL-HPG. d--hydroxyphenylglycine (d-HPG) is an important intermediate in the synthesis of antimicrobial compounds. d-HPG is mainly produced via chemical and enzymatic approaches, and enzymatic asymmetric amination employing diaminopimelate dehydrogenase (DAPDH) is considered an attractive method. However, the low catalytic activity of DAPDH toward bulky 2-keto acids limits its applications. In this study, we identified a DAPDH from Prevotella timonensis and created a mutant, DAPDH, which exhibited a catalytic efficiency (/) toward 4-hydroxyphenylglyoxylate that was 26.75-fold higher than that of the wild type. The novel strategy developed in this study has practical value for the production of d-HPG from inexpensive racemate DL-HPG.
Topics: Amination; Substrate Specificity
PubMed: 37070978
DOI: 10.1128/aem.00109-23 -
Biomedicine & Pharmacotherapy =... May 2022New means to stabilize the microbial balance during pregnancy could benefit maternal health. Our objectives were to investigate in overweight/obese pregnant women 1) the... (Randomized Controlled Trial)
Randomized Controlled Trial
New means to stabilize the microbial balance during pregnancy could benefit maternal health. Our objectives were to investigate in overweight/obese pregnant women 1) the impact of long-chain polyunsaturated fatty acids (fish oil) and/or probiotics on the vaginal microbiota, 2) its relation to gestational diabetes mellitus (GDM) and 3) its interaction with vaginal active matrix metalloproteinase-8 (aMMP-8) and serum high sensitivity C-reactive protein (hsCRP) and phosphorylated insulin-like growth factor-binding protein-1 (phIGFBP-1), IGFBP-1 and aMMP-8. The women were allocated to fish oil + placebo, probiotics + placebo, fish oil + probiotics and placebo + placebo-groups, from early pregnancy onwards (fish oil: 1.9 g docosahexaenoic acid and 0.22 g eicosapentaenoic acid; probiotics: Lacticaseibacillus rhamnosus HN001 (formerly Lactobacillus rhamnosus HN001) and Bifidobacterium animalis ssp. lactis 420, 10 colony-forming units each). Vaginal and serum samples (early pregnancy, n = 112; late pregnancy, n = 116), were analyzed for vaginal microbiota using 16S rRNA gene amplicon sequencing and vaginal aMMP-8 and serum hsCRP, aMMP-8, phIGFBP-1 and IGFBP-1 by immunoassays. GDM was diagnosed from a 2-h 75 g OGTT. ClinicalTrials.gov, NCT01922791. The intervention exerted effects on many low-abundant bacteria. Compared to the placebo-group, there was a lower abundance of potential pathobionts, namely Ureaplasma urealyticum in the fish oil-group, Ureaplasma, U. urealyticum and Prevotella disiens in the probiotics-group, Dialister invisus and Prevotella timonensis in the fish oil + probiotics-group. Moreover, probiotics decreased the abundance of a few potential pathobionts during pregnancy. Many bacteria were related to GDM. The vaginal aMMP-8 level correlated significantly with α-diversity and inversely with two Lactobacillus species. Dietary interventions, especially probiotics, may have beneficial effects on the vaginal microbiota during pregnancy.
Topics: Bifidobacterium animalis; C-Reactive Protein; Diabetes, Gestational; Female; Fish Oils; Humans; Insulin-Like Growth Factor Binding Protein 1; Lacticaseibacillus rhamnosus; Microbiota; Obesity; Overweight; Pregnancy; Pregnant Women; Probiotics; RNA, Ribosomal, 16S
PubMed: 35344737
DOI: 10.1016/j.biopha.2022.112841 -
Genes Apr 2023Microbial Dysbiosis is associated with the etiology and pathogenesis of diseases. The studies on the vaginal microbiome in cervical cancer are essential to discern the...
Microbial Dysbiosis is associated with the etiology and pathogenesis of diseases. The studies on the vaginal microbiome in cervical cancer are essential to discern the cause and effect of the condition. The present study characterizes the microbial pathogenesis involved in developing cervical cancer. Relative species abundance assessment identified , , and dominating the phylum level. A significant increase in and at the species level revealed its pathogenic influence on cervical cancer progression. The diversity, richness, and dominance analysis divulges a substantial decline in cervical cancer compared to control samples. The β diversity index proves the homogeneity in the subgroups' microbial composition. The association between enriched at the species level, , , and genera with cervical cancer is identified by Linear discriminant analysis Effect Size (LEfSe) prediction. The functional enrichment corroborates the microbial disease association with pathogenic infections such as aerobic vaginitis, bacterial vaginosis, and chlamydia. The dataset is trained and validated with repeated k-fold cross-validation technique using a random forest algorithm to determine the discriminative pattern from the samples. SHapley Additive exPlanations (SHAP), a game theoretic approach, is employed to analyze the results predicted by the model. Interestingly, SHAP identified that the increase in Ralstonia has a higher probability of predicting the sample as cervical cancer. New evidential microbiomes identified in the experiment confirm the presence of pathogenic microbiomes in cervical cancer vaginal samples and their mutuality with microbial imbalance.
Topics: Humans; Female; Uterine Cervical Neoplasms; Dysbiosis; Microbiota; Artificial Intelligence
PubMed: 37107694
DOI: 10.3390/genes14040936 -
BMJ Open Respiratory Research Feb 2023Invasive pulmonary aspergillosis (IPA) remains underestimated in patients with community-acquired pneumonia (CAP). This study aims to describe clinical features and...
BACKGROUND
Invasive pulmonary aspergillosis (IPA) remains underestimated in patients with community-acquired pneumonia (CAP). This study aims to describe clinical features and outcomes of IPA in CAP patients, assess diagnostic performance of metagenomic next-generation sequencing (mNGS) for IPA and analyse lung microbiome via mNGS data.
METHODS
This retrospective cohort study included CAP patients from 22 April 2019 to 30 September 2021. Clinical and microbiological data were analysed. Diagnostic performance of mNGS was compared with traditional detection methods. The lung microbiome detected by mNGS was characterised and its association with clinical features was evaluated.
MAIN RESULTS
IPA was diagnosed in 26 (23.4%) of 111 CAP patients. Patients with IPA displayed depressed immunity, higher hospital mortality (30.8% vs 11.8%) and intensive care unit mortality (42.1% vs 17.5%) compared with patients without IPA. The galactomannan (GM) antigen test had the highest sensitivity (57.7%) in detecting the spp, followed by mNGS (42.3%), culture (30.8%) and smear (7.7%). The mNGS, culture and smear had 100% specificity, while GM test had 92.9% specificity. The microbial structure of IPA significantly differed from non-IPA patients (p<0.001; Wilcoxon test). Nineteen different species were significantly correlated with clinical outcomes and laboratory biomarkers, particularly for , and .
CONCLUSIONS
Our results reveal that patients with infection tend to have a higher early mortality rate. The mNGS may be suggested as a complement to routine microbiological test in diagnosis of patients at risk of infection. The lung microbiota is associated with inflammatory, immune and metabolic conditions of IPA, and thus influences clinical outcomes.
Topics: Humans; Invasive Pulmonary Aspergillosis; Retrospective Studies; Sensitivity and Specificity; Bronchoalveolar Lavage Fluid; Aspergillosis; Lung; Pneumonia; Microbiota
PubMed: 36828645
DOI: 10.1136/bmjresp-2022-001358 -
Microorganisms Jun 2020Vaginal microbiota dysbiosis and bacterial vaginosis (BV) affect negatively women's health. Understanding vaginal microbiota fluctuations in BV during and after...
Vaginal microbiota dysbiosis and bacterial vaginosis (BV) affect negatively women's health. Understanding vaginal microbiota fluctuations in BV during and after antibiotic treatment would facilitate accurate decision-making on the treatment regimen, avoid unnecessary antibiotic use, and potentially mitigate recurrence. We investigated vaginal microbiota composition of 30 women with BV before and after 5-day metronidazole treatment and compared the results with 30 healthy women. Vaginal microbiota was assessed by Nugent score and analyzed by 16S rRNA gene sequencing in swabs on baseline Day 1, and on Day 8 and 15, after completion of antibiotic treatment by women with BV. Prior to antibiotic treatment (Day 1), BV-positive women were dominated by (25.8%), (18.0%), and (14.6%), whereas healthy women were dominated by (37.5%) and (19.2%). On Day 8, abundance increased in BV-treated women being significantly higher compared with healthy women (67.8% vs. 37.5%, = 0.049). On Day 15, the relative abundance of all microbial taxa was similar between the groups. Vaginal microbiota of women with BV shifted to resemble that of healthy controls after metronidazole. Sequencing analysis provides more in-depth understanding of changes in vaginal microbiota. The role of in vaginal health and dysbiosis requires further investigations.
PubMed: 32527048
DOI: 10.3390/microorganisms8060875 -
PloS One 2020To evaluate the changes of vaginal microbiota during cervical carcinogenesis in women with high-risk human papillomavirus infection.
OBJECTIVE
To evaluate the changes of vaginal microbiota during cervical carcinogenesis in women with high-risk human papillomavirus infection.
MATERIALS AND METHODS
Vaginal microbiota was analyzed using next-generation sequencing in women with normal, cervical intraepithelial neoplasia (CIN), or cervical cancer.
RESULTS
A marked decrease of Lactobacillus crispatus was found in the CIN/cancer groups compared with that in the normal group. The diversity of microorganisms increased in patients with CIN or cervical cancer with HPV infection. Atopobium vaginae (OR 4.33, 95% CI 1.15-16.32), Dialister invisus (OR 4.89, 95% CI 1.20-19.94), Finegoldia magna (OR 6.00, 95% CI 1.08-33.27), Gardnerella vaginalis (OR 7.43, 95% CI 1.78-31.04), Prevotella buccalis (OR 11.00, 95% CI 2.00-60.57), and Prevotella timonensis (OR 6.00, 95% CI 1.46-24.69) were significantly associated with the risk of CIN 2/3 or cervical cancer.
CONCLUSION
Women with the CIN and cervical cancer showed a high diversity in vaginal microbiota. Depletion of Lactobacillus crispatus and increased abundance of anaerobic bacteria were detected in women with cervical disease.
Topics: Bacteria; Biodiversity; Carcinogenesis; Female; Humans; Microbiota; Papillomaviridae; Papillomavirus Infections; Principal Component Analysis; Species Specificity; Vagina
PubMed: 32941440
DOI: 10.1371/journal.pone.0238705 -
Nature Communications Apr 2020Emerging evidence suggests associations between the vaginal microbiota (VMB) composition, human papillomavirus (HPV) infection, and cervical intraepithelial neoplasia...
Emerging evidence suggests associations between the vaginal microbiota (VMB) composition, human papillomavirus (HPV) infection, and cervical intraepithelial neoplasia (CIN); however, causal inference remains uncertain. Here, we use bacterial DNA sequencing from serially collected vaginal samples from a cohort of 87 adolescent and young women aged 16-26 years with histologically confirmed, untreated CIN2 lesions to determine whether VMB composition affects rates of regression over 24 months. We show that women with a Lactobacillus-dominant microbiome at baseline are more likely to have regressive disease at 12 months. Lactobacillus spp. depletion and presence of specific anaerobic taxa including Megasphaera, Prevotella timonensis and Gardnerella vaginalis are associated with CIN2 persistence and slower regression. These findings suggest that VMB composition may be a future useful biomarker in predicting disease outcome and tailoring surveillance, whilst it may offer rational targets for the development of new prevention and treatment strategies.
Topics: Adolescent; Adult; Cervix Uteri; Cohort Studies; DNA, Bacterial; Female; Follow-Up Studies; Gardnerella vaginalis; Humans; Lactobacillus; Microbiota; Neoplasm Staging; Papillomaviridae; Papillomavirus Infections; Prevotella; RNA, Ribosomal, 16S; Risk Factors; Uterine Cervical Neoplasms; Vagina; Young Adult; Uterine Cervical Dysplasia
PubMed: 32332850
DOI: 10.1038/s41467-020-15856-y -
PloS One 2022Bacterial vaginosis (BV) is associated with a state of vaginal dysbiosis typically involving depletion of otherwise dominant populations of Lactobacillus. The causes of...
Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes.
Bacterial vaginosis (BV) is associated with a state of vaginal dysbiosis typically involving depletion of otherwise dominant populations of Lactobacillus. The causes of this microbial succession are not known; there may be multiple causes. Standard treatment includes oral metronidazole, which typically restores Lactobacillus species to dominance. However, recurrence rates are high; recurrent BV patients recur 3-4 times annually and are often refractory to treatment. Our previous qPCR-based study of recurrent BV patients pointed to putatively more virulent species of Gardnerella that were associated with refractory responses to oral metronidazole, and less robust recovery of Lactobacillus species associated with recurrence after an initial period of remission. However, these associations did not account for outcomes in all patients, suggesting that other bacterial species were involved. In this follow-up study, we sequenced the V4 domain of 16S rRNA sequences of 41of these same patients pre- and posttreatment. Overall compositions among pretreatment clinical outcome groups were not different, although alpha diversity significantly decreased: refractory > recurrent > remission. Combinations of key species were associated with and prognostic for outcome. Higher pretreatment abundance of Megasphaera lornae together with lower abundance of Gardnerella Gsp07 and Finegoldia magna predicted long term remission after oral metronidazole. Furthermore, a subset of refractory patients that did not have high levels of Gardnerella Gsp07, instead had elevated levels of alternative species including Atopobium vaginae, Mageeibacillus indolicus (BVAB3), and Prevotella timonensis. Patients who recurred after transient remission had elevated abundance of species including Atopobium vaginae, Gardnerella, and Aerococcus christensenii, compared to long-term remission patients. Core bacterial species among refractory patients did not change in abundance after metronidazole, suggesting resistance or tolerance, in contrast to the loss in abundance of the same species among recurrent or remission patients. These findings have potential prognostic and therapeutic implications.
Topics: Actinobacteria; Bacteria; Female; Follow-Up Studies; Gardnerella vaginalis; Humans; Lactobacillus; Metronidazole; RNA, Ribosomal, 16S; Vagina; Vaginosis, Bacterial
PubMed: 35901180
DOI: 10.1371/journal.pone.0272012