16S RNA Research Articles

Comprehensive transcriptomic, proteomic, and intestinal microbiota analyses of largemouth bass (Micropterus salmoides) intestines reveal new insights into immune responses to Aeromonas hydrophila infection

This study investigates the immune responses of largemouth bass (Micropterus salmoides) to infection by Aeromonas hydrophila, a pathogen responsible for significant economic losses in freshwater aquaculture due to bacterial enteritis. We employed transcriptomic sequencing, label-free LC-MS/MS quantitative proteomics, and 16S RNA sequencing to evaluate the transcriptomic, proteomic, and intestinal microbiota changes in infected fish compared to healthycontrols. Each fish (approximately 60 g) in the infection group was injected with 0.5 ml of an A. hydrophila suspension (1.0 × 108 CFU/mL), while the control group received 0.5 ml of phosphate buffer. Samples were collected 72 h post-injection, with three biological replicates made from an equal mix of tissue samples from six fish each. A total of 1666 differentially expressed genes (DEGs) and 2477 differentially expressed proteins (DEPs) were identified. Integrated analysis revealed that the up-regulated DEGs/DEPs in the intestines of infected largemouth bass were primarily associated with immune-related pathways including "antigen processing and presentation", "MAPK signaling pathway", "ECM-receptor interaction", and "leukocyte transendothelial migration". Notable upregulated immune-related proteins included complement or antigen-presenting proteins like complement C1, complement C3, complement C6, ɑ-2-macroglobulin, laminin, serotransferrin, leukocyte cell-derived chemotaxin-2, immunoglobulin C1-set domain-containing protein, and the MHC class I alpha antigen. 16S RNA sequencing indicated a significant increase in Proteobacteria and a decrease in Fusobacteria in the intestines of infected fish compared to controls. Collectively, these findings demonstrate that A. hydrophila infection significantly alters gene and protein expression as well as intestinal microbiota in largemouth bass, providing insights into their immune defense mechanisms against infection.

Nano fish bone prepared by high-energy media milling extends the shelf life of tofu during cold storage: Unlocking the restriction on water mobility

Nano fish bone (NFB) was produced by high-energy media milling. The NFB was composed of circular crystals (approximately 110 nm) and fibrous collagen/peptide. Effects of NFB on the quality and microorganisms of glucono-d-lactone (GDL)-induced tofu stored at 4 °C were investigated. Water activity, syneresis, whiteness, and total bacterial counts of the tofu without NFB increased continuously, reaching 0.977, 41.66 %, 80.28, and 4.55 log CFU/g over 7 days, respectively. Breaking force and penetration distance decreased by 12.93 and 21.79 %, respectively. Adding NFB significantly increased GDL tofu's breaking force and penetration distance during storage (p < 0.05) while decreasing water activity, syneresis, whiteness, and total bacterial counts (p < 0.05). With NFB, nuclear magnetic resonance (NMR) analysis showed reduced free water and increased immobilized water. 16S RNA sequencing revealed lower bacterial diversity and Pseudomonas abundance in NFB-treated tofu. By restraining water mobility, NFB effectively extends GDL tofu's shelf life by 2 days.

Isolation and Molecular Characterization of Corynebacterium pseudotuberculosis from Goats in Andaman and Nicobar Islands, India

Caseous lymphadenitis (CLA), caused by the bacteria Corynebacterium pseudotuberculosis, is a highly contagious disease of small ruminants, especially of goats and sheep. Here, we report an outbreak of the disease in goats for the first time from the Andaman and Nicobar Islands along with isolation and molecular characterization of the pathogen. A total of 22 goats were affected, with an attack rate of 12.02%, and six isolates were identified from the clinical samples. Molecular characterization of the pathogen was carried out based on the sequence information of 16S rRNA and RNA polymerase β subunit (rpoB) gene fragments. rpoB-based phylogenetic analysis indicated that the isolates belonged to Corynebacterium pseudotuberculosis biovar ovis. The antimicrobial resistance study revealed that the isolates were 100% resistant against erythromycin and rifampicin. Fifty percent resistance was found against amoxicillin/clavulanic acid, ciprofloxacin, penicillin, and vancomycin. All the isolates were sensitive to tetracycline, chloramphenicol, cotrimoxazole, sulphafurazole, ampicillin/cloxacillin, and oxytetracycline. In conclusion, the present study reports the occurrence of CLA in goats for the first time from an isolated archipelago of India and unveils the molecular signature and antibiotic resistance patten of the pathogen. The findings of this study will be helpful to control or eradicate the disease from the Andaman and Nicobar Islands.

Facial disbiosis and UV filters.

Acne is a multifactorial inflammatory disease with a robust microbial component and numerous correlations with dysbiosis states. Furthermore, various factors are recognized as triggers for skin dysbiosis, including the use of certain cosmetics. Based on these arguments, we hypothesized that using photoprotective formulations could trigger dysbiosis and the occurrence of acne manifestations. To verify this assumption, six volunteers between 19 and 23 years of age, meeting all the inclusion criteria, received two applications a day of a non-commercial sunscreen formulation developed with the sun filters ethylhexyl methoxycinnamate, ethylhexyl salicylate, methyl anthranilate, and octocrylene dispersed in a base gel, with an estimated protection factor of 28.8. The pure base gel was used as a control. The samples were applied to an area delimited by a standard template (15 cm2) in an amount corresponding to 30mg (2mg cm2) for ten days. At two points in time, pre- and post-sample applications, the facial skin surface was swabbed to collect extracted DNA and processed to verify divergent degrees of 16S RNA coding sequences. The data obtained allowed us to determine the abundance of different bacterial entities at the genus and species levels. The results showed that critical species of the acne process, such as Cutibacterium acnes and Staphylococcus epidermidis, seem to tolerate the evaluated formulation well and are not significantly affected by the formulation, suggesting no interference of its use concerning dysbiosis induction. These findings refute the idea that photoprotectors may cause skin dysbiosis in men.

Sea Buckthorn Flavonoid Extracted with High Hydrostatic Pressure Alleviated Shrimp Allergy in Mice through the Microbiota and Metabolism.

Sea buckthorn (Hippophaë rhamnoides L.) known as the deciduous shrub has been reported to have effects of antioxidant, anti-inflammatory, and immunomodulatory activities. Tropomyosin (TM) induced a regulatory immune response associated with food allergy. In this study, a mouse model of food allergy sensitized to tropomyosin (TM) was established to assess the antiallergic properties of sea buckthorn flavonoid extract (SBF). SBF alleviated mice's allergic symptoms and exhibited a significant reduction in the levels of IgE and histamine. Meanwhile, SBF repaired the allergic Th2 cell overpolarization generated by TM, via downregulating the IL-4 production and upregulating IFN-γ production to restore the balance of Th1/Th2 cells. Furthermore, the 16S RNA analysis showed that SBF primarily restored the gut microbiota via increasing the abundance in Chitinophilidae and decreasing in Burkholderiaceae, Pneumatobacteriaceae, and Sphingomonadaceae. Gut metabolomes determined by liquid chromatography-mass spectrometry (LC-MS) suggested that TM upregulated PE (14:0/22:1(13Z)) and SBF decreased formimino-l-glutamic acid and urocanic acid levels. According to the KEGG pathway analysis, SBF treatment has been shown to modulate glycerophospholipid and histidine metabolism to improve allergic reactions. SBF holds great promise as a novel potential agent for the treatment of food allergies.

Anti-cariogenic effect of experimental resin cement containing ursolic acid using dental microcosm biofilm

ObjectiveThis study aimed to assess the anticariogenic effects of resin cement containing varying ursolic acid (UA) concentrations and to determine the optimal UA concentrations in the microcosm biofilm model. Materials and methodsExperimental resin cements with UA concentrations of 0, 0.1, 0.5, 1.0, and 2.0 wt% were prepared. Class I cavities were prepared on 50 extracted human molars and restored with composite inlays and experimental resin cements. Tooth samples were subjected to artificial caries induction for 10 days in a microcosm biofilm model using human saliva as an inoculum, and then mineral changes were evaluated using quantitative light-induced fluorescence (ΔF and ΔQ) and micro-computed tomography (CT). The bacterial composition of the human saliva was analyzed by 16 s RNA microbiome profiling. One-way analysis of variance with Tukey and Duncan post-hoc tests was employed for statistical analysis (p < 0.05). ResultsAs the UA concentration increased, resin cement decreased ΔF and ΔQ before and after caries induction but showed a significant difference only in ΔQ at UA concentration ≥ 1.0 % (p < 0.05). The gray value analysis result of micro CT also showed a significant difference at UA concentration ≥ 1.0 % (p < 0.05). In the human saliva analysis, bacterial composition remained within normal oral microbiota ranges. ConclusionResin cements containing at least 1.0 % of UA exhibited an anticariogenic effect on dental microcosm biofilms. Clinical relevanceTo reduce the failure of restorations, it is essential to prevent the occurrence of secondary caries. The application of UA in resin cement can be utilized to prevent the formation of secondary caries due to the anticariogenic effect of UA.

Use of an Ethinyl Estradiol/Etonogestrel Vaginal Ring Alters Vaginal Microbial Communities in Women with HIV.

HIV-1 antiretroviral therapy (ART) alters hormonal contraceptive levels delivered via intravaginal ring (IVR) in a regimen specific manner. We explored the role of the IVR on vaginal microbial communities, vaginal short chain fatty acids (SCFAs), vaginal HIV shedding, and the effect of vaginal microbes on hormone concentrations in cisgender women with HIV (WWH). Vaginal microbes were assessed by 16S RNA sequencing of weekly vaginal swabs, vaginal SCFA by mass spectrometry, HIV-1 shedding by nucleic acid amplification on vaginal aspirates, and bacterial vaginosis by Nugent scoring from 74 participants receiving an etonorgestrel/ethinyl estradiol (ENG/EE) intravaginal ring while on no ART (N=25), efavirenz-based ART (N=25), or atazanavir-based ART (N=24). At baseline, microbial communities of the 64 substudy eligible participants robustly classified as Lactobacillus crispatus--dominant (n=8), L. gasseri-dominant (n=2), L. iners-dominant (n=17), or mixed anaerobic communities (n=37). During IVR therapy, there was an increased probability of Lactobacillus-dominant community state types (CSTs) (odds-ratio=1.61, p=0.04). Vaginal CSTs were associated with Nugent scores. Bacterial vaginosis-associated bacteria were associated with significantly higher and L. iners with lower Nugent Scores (all p adj <0.1). Lactic acid levels were correlated with the relative abundance of Lactobacillus species (r2=0.574; p<0.001). Vaginal shedding of HIV-1 was less common in women with L. crispatus-dominant microbiomes (p=0.04). Mixed anaerobic vaginal communities modulated EE concentrations in a regimen-specific manner. Combined ENG/EE IVR therapy was associated with an increase in Lactobacillus-dominant vaginal microbial communities in WWH and may benefit those with bacterial vaginosis. EE levels were altered by the vaginal microbiota.

Basal Expression Profile of Seven Glutathione-S-Transferases (GSTs) Genes in Six Tissues of Tilapia (Oreochromis niloticus) for Polymerase Chain Reaction Array

Study’s Excerpt The differential expression patterns of Glutathione-S-transferase (GST) isoforms in six tissues of Nile tilapia are investigated. Seven specific GST genes are examined across six tissues, and it is determined that the liver, spleen, and intestines are key sites of significant gene expression. GST isoforms could be potentially used as biomarkers for assessing xenobiotic stress in aquatic environments. Full Abstract Because aquatic habitats are being destroyed and biodiversity is declining, xenobiotic pollution of water is a critical environmental problem that has garnered a lot of attention in the past few decades. This study looked at the expression patterns of Glutathione-S-transferases isoforms (GSTMA, GSTO1LA, GSTA, GSTR1, GSTK, GSTT1, and MGST), which are genes involved in xenobiotic metabolism, in Nile tilapia. From adult Nile tilapia, six tissues—liver, spleen, intestines, gills, heart, and muscle—were chosen, and seven genes that were optimised via quantitative polymerase chain reaction (qPCR) were used for validation. Gene expressions were assessed using a PCR array that included duplicate tissues in 96-well qPCR plates, with each gene/plate being assayed six times. Water is used in the remaining wells as no template control (NTC). As reference genes, Pan Ribosomal Protein L3 (RPL3) and Pan 18S ribosomal RNA (18S RNA) were employed. The genes’ basal tissue mRNA expression was measured in each tissue. The muscle was utilised to renormalise the expression levels of all genes throughout the remaining tissues since, under assay’s circumstances the muscle showed very low signal for most of the genes. Using quantitative real-time PCR (qPCR), the result demonstrated widespread differential expression patterns of the seven GST mRNA in the liver, spleen, intestine, gills, heart, and muscle of an untreated fish. However, it was clear that the highest significant expression level of most genes (different GST’s isoforms) was in the liver, followed by the spleen and gut, then the heart and gills compared to muscle (P&lt;0.05). The findings demonstrated widespread differential expression of the GST’s isoforms at basal level and highlighted their utility as biomarkers for xenobiotic stress in aquatic environments.

Aspirin inhibits atherosclerosis through macrophage pyroptosis by interacting with Lactobacillus johnsonii and its metabolite butyrate

Abstract Introduction Atherosclerotic cardiovascular disease (ASCVD) is a chronic progressive disease closely related to metabolism and inflammation. Aspirin inhibits cyclooxygenase (COX) and has antiplatelet aggregation effects, considered as the cornerstone of ASCVD treatment. Numerous studies have shown that gut microbiota (GM) and its metabolites affects host metabolism. Studies have also shown that people taking aspirin exhibit specific changes in the microbiota profile. However, whether the interaction of aspirin with GM and its metabolites affects the therapeutic efficacy of aspirin in treating atherosclerosis (AS) have not been reported. Purpose This study aimed to explore the interaction of aspirin with the GM and its metabolites in the treatment of AS, to reveal the specific mechanism of the GM-metabolite axis and provide potential new targets for the combined treatment of AS. Methods To establish the mouse model of atherosclerosis by high-fat diet, and the atherosclerotic plaque burden and composition were analyzed. The role of GM in aspirin anti-atherosclerosis was explored by antibiotics and fecal microbiota transplantation (FMT). The third generation 16S RNA sequencing was used to explore the effects of aspirin on species diversity and abundance of GM, and to screen differential microorganisms for intervention of AS mice. UHPLC-MS and GC-MS were used to explore the changes of intestinal metabolites induced by aspirin. The correlation between gut microbiota and metabolites was also investigated. Finally, in vitro and in vivo experiments were performed to confirm the effects and mechanisms of metabolites on macrophage pyroptosis and atherosclerosis. Results Aspirin has anti-atherosclerosis effect. After removing gut microbiota, the therapeutic effect of aspirin on atherosclerosis was decreased. Three generations of 16S rRNA gene sequencing results showed that aspirin supplementation alters the diversity of gut microbiota, and increased the relative abundance of Lactobacillus johnsonii(L.johnsonii) and Ligilactobacillus murinus(L.murinus). After gavage of L.johnsonii and L.murinus, the plaque burden and macrophage pyroptosis were significantly reduced in AS mice. Colonization with L.johnsonii and L.murinus significantly increased the abundance of probiotics and butyrate level in the feces of AS mice and L.johnsonii and L.murinus were positively correlated with butyrate. Supplementation of butyrate inhibited macrophage pyroptosis and atherosclerosis in vivo. In vitro, butyrate could inhibit the expression of NLRP3/Caspase-1/IL-1β and pyroptosome production, and this process mainly by activating butyrate receptors GPR41, GPR43 and GPR109A. Conclusions The gut microbiota may mediate the anti-AS effect of aspirin by promoting an increase in the abundance of L.johnsonii and L.murinus. Butyrate produced by Lactobacillus may mediate the anti-AS effect of aspirin, and inhibiting macrophage pyroptosis and the progression of AS.

Alterations of gut microbiome profiles as potential markers in patients developing acute coronary syndrome

Abstract Background Imbalanced gut microbiota or gut dysbiosis leads to systemic inflammation, one of key contributors to the development and progression of atherosclerosis. A recent study revealed the association of the gut microbiota and the severity of coronary artery lesions in patients with acute coronary syndrome (ACS). However, the gut microbiota profile in ACS patients in comparison with patients with high-risk cardiovascular disease (CVD) has not been thoroughly investigated. Purpose We aimed to compare the profiles of gut microbiome between patients with ACS and patients with high-risk CVD, as well as to determine the association between gut microbiota and CVD risk factors. Methods This cross-sectional study enrolled 24 stabilized ACS patients within 24 hrs of hospitalization and 59 outpatients in CVD clinics, as a control group. Echocardiography was done in those patients. Blood was collected for biochemical analysis, and fecal samples were collected for gut microbiome analysis via 16S RNA sequencing. Results The demographic data showed no significant differences between groups in CVD risk factors (age, levels of systolic and diastolic blood pressure, fasting glucose, high- and low-density cholesterol, and triglycerides). However, patients with ACS had greater cigarette use and alcohol consumption than the control group. For gut microbiome, both alpha and beta diversity levels of ACS group were significantly higher than those in a control group (Figure 1A-B). Differential abundance analysis by ANCOM-BC revealed significantly increased level of bacteria in the Atopobiaceae family in ACS patients, compared to controls (Figure 1C). Since Atopobiaceae was reported to be positively associated with percent atheroma volume (PAV), a marker of plaque deposit in the arteries, we found an increased number of Atopobiaceae which was positively associated with serum Troponin T level (Figure 1D), systemic inflammation (Figure 1E), and a trend to negatively correlated with LV ejection fraction. Conclusion Our findings suggested that alterations of gut microbiota occurred in ACS patients, and an increase in gut Atopobiaceae level could potentially be the predictive marker of the development of ACS in CVD patients.Figure 1

Evaluating the efficacy of endophytic bacteria in controlling rice sheath blight: In vitro and In vivo studies

Rice production is highly susceptible to various pathogens, including Rhizoctonia solani, Curvularia lunata, and Epicoccum rostratum, which are major threats in Asia. Exploring biological control methods using endophytic bacteria offers promising opportunities to enhance rice resilience against these lethal diseases. Using 16S RNA sequencing, we identified four endophytic isolates of Bacillus spp. from rice roots, stems, and leaves. We evaluated the antagonistic activity of these endophytic bacterial isolates against rice pathogens both in vitro and in vivo. These isolates inhibited the growth of C. lunata by 82 %, R. solani by 79 %, and E. rostratum by 88 % in vitro. The detached leaf assay for sheath blight (ShB) disease severity in strains ranged from 10.4 % to 73.3 %. In vivo results showed that B. amyloliquefaciens (R-19) exhibited the lowest disease intensity at 7.2 % and the highest disease suppression at 78.8 %. The fungicide propiconazole at 0.1 % treatment showed the lowest disease intensity of 7.7 % and the highest disease suppression of 73.4 %, compared to the infected control. Besides biocontrol efficacy, endophytic isolates enhance plant growth parameters, including shoot height, root length, fresh and dry weights, number of tillers, and grains per tiller. Plant hormones abscisic acid (ABA) and gibberellic acids (GA3) increased by 35 % and 53 %, respectively, due to B. subtilis (R-20) and B. amyloliquefaciens (R-19), while flavonoid and indole acetic acid (IAA) concentrations surged by 30%–80 %. Similarly, chlorophyll (a, b), carotenoids, antioxidant enzymatic activity, phenolic content, carbohydrates, and proline contents were higher compared to the control. This study provides a foundation for future studies on novel and eco-friendly biocontrol agents. In addition, our study recommends the integration of endophytic bacteria into sustainable agriculture for enhancing rice production and reducing disease impacts.

Toxic Effect of Heavy Metal Poisoning on Living Organisms in Water and Health Risk: A Central India Study

The main causes of this environmental catastrophe are pollutants such as iron, zinc, lead, nickel, and chromium that have entered the water system as a result of uncontrolled industrial effluent discharge in the area. This study finds resistant bacteria and shows the toxicity of heavy metals in industrial effluent near the steel industry. Five separate locations were used for water sampling, and 16s RNA sequencing of the microorganisms that were found was done along with physicochemical parameter analysis and atomic absorption spectrophotometer use. Different water samples’ conductivity, TDS, salinity, DO, turbidity, and pH levels indicate changes in the quality of the water. In addition to having higher values for each of these characteristics, Sample D3’s water samples had greater concentrations of heavy metals, suggesting contamination. Aspergillus niger and Aspergillus terreus were identified in all samples. Both Gram-negative and Gram-positive Bacilli’s resistance to heavy metals has been found to be a sign of microbial adaptation to exposure to heavy metals. 16s rRNA sequencing of microorganisms revealed their roles in heavy metal bioremediation processes. The delicate balance between the flora and fauna in the affected water bodies has been upset by the devastating losses in aquatic life. In this study, we presented the biological methods for eliminating heavy metals, which comprised both metabolically dependent and independent techniques.

Microbial and Transcriptomic Landscape Associated With Neutrophil Extracellular Traps in Perianal Fistulizing Crohn's Disease.

Perianal fistulizing Crohn's disease (pfCD) poses significant healing challenges, closely associated with neutrophil extracellular traps (NETs). This study aimed to investigate the microbe-host interactions influencing NETs in pfCD. From January 2019 to July 2022, patients with pfCD were screened at Ren Ji Hospital. Patients in remission following comprehensive treatment were recruited. We documented clinical characteristics, medication regimens, healing outcomes, and infliximab levels in fistula tissues. NET positivity was confirmed by positive results in citrullinated histone H3 (CitH3) enzyme-linked immunosorbent assay (ELISA) and dual immunofluorescence staining for myeloperoxidase and CitH3. Microbial and transcriptomic profiles from fistula tissues, obtained during surgery, were analyzed using 16S rRNA gene sequencing and RNA sequencing. Differences in microbiome and transcriptomic profiles were evaluated, and their relationships were assessed using Mantel's and Spearman's coefficients. Significant differences in microbial communities were found between groups (P = .007). Representatively differential microbes such as Prevotella bivia, Streptococcus gordonii, and Bacteroides dorei were enriched in NETs-positive fistulas (P < .05). Functional analysis of microbes revealed reduced ubiquinol biosynthesis and butanoate production in NETs-negative fistulas (P < .05). Transcriptomic analysis indicated increased neutrophil and monocyte infiltration in NETs-positive fistulas, associated with pathways involving bacterial response, neutrophil chemotaxis, secretory processes, and peptidase activity (P < .05). Species prevalent in NETs-positive fistulas correlated positively with immune responses and wound healing pathways, whereas bacteria in NETs-negative fistulas correlated negatively. NETs were negatively associated with tissue infliximab levels (P = .001) and healing outcomes (P = .025). Our findings reveal unique microbial and transcriptomic signatures associated with NETs in pfCD, highlighting their profound influence on clinical outcomes.

Developing Robust Probiotic Consortia: A Methodological Optimization Approach.

Developing effective probiotic consortia requires a comprehensive understanding of strain interactions. While traditional methods focus on direct interactions of the participating microbes, the role of microbial metabolites remains largely unexplored. Present study introduces a novel approach of evaluating the impact of strains as well as their secondary metabolites on compatibility during co-culture by assessing the antagonistic and synergistic attributes for multi-strain probiotic formulation. Assessment of antagonistic activity by spot method indicated suppressive nature of PIG1FD and PIG1IR on other strain's growth, hence not appropriate for consortia formulation. Findings of synergistic attribute demonstrated growth promoting role of cell supernatants from isolates PIG6IR and PIG5CI significantly, as it accelerated the entry of all other isolates into the log phase by 5-6h and 0-2h, respectively. By employing this methodology, we identified PIG5CI and PIG6IR (isolates identified as Bacillus spizizenii BAB 7915 and Bacillus subtilis BAB 7918 by 16S RNA sequencing method) as promising candidates for consortium formation due to their ability to enhance the growth of other strains through metabolite production. By attempting to elucidate the microbial interactions and metabolite-mediated effects, this research contributes to a more comprehensive understanding of probiotic consortia dynamics and offers valuable insights for future translational studies.

Screening for contamination with genetically modified organisms in food, feed and their additives obtained in retail and online shops in Latvia

The aim of the study was to screen for contamination of food and feed products with genetically modified organisms (GMO) in several sample groups obtained from retail and online shops. The total number of samples was 171, including 67 of food, 26 feed, 27 additive, and 51 samples of dried pollen for human consumption. Detection and quantification of GMO in food and feed was performed according to the approved quantitative real-time PCR methods. Fermentation product samples were analyzed using screening for antimicrobial resistance genes, 16S RNA and ITS1 sequencing, isolation of bacterial cultures and whole genome sequencing. In total, GMO contamination was found in 12 samples (in 10.45% of food and in 19.23% of feed samples). A lower proportion of GMO containing samples were from the European Union (10.26 %) vs. samples from outside (17.02%), but none with ingredients of both origins. Non-compliant were three food and five feed samples. Of the 27 samples of food and feed additives and food supplements, 10 samples were possibly non-compliant, as they contained live bacteria with antimicrobial resistance genes, and seven of them contained possibly recombinant DNA. The study indicates presence of GMO contamination that emphasizes the need for further monitoring.

Complete genome sequence analysis and Pks genes identification of Brevibacillus brevis FJAT-0809-GLX with a broad inhibitory spectrum against phytopathogens.

Brevibacillus brevis FJAT-0809-GLX has a broad spectrum of antimicrobial activity. Understanding the molecular basis of biocontrol ability of B. brevis will allow us to develop effective microbial agents for sustainable agriculture. In this study, we present the complete and annotated genome sequence of FJAT-0809-GLX. The complete genome size of B. brevis FJAT-0809-GLX was 6,137,019bp, with 5688 predicted coding sequences (CDS). The average GC content of 47.38%, and there were 44 copies of the rRNAs operon (16S, 23S and 5S RNA), and 127 tRNA genes. A total of 11,162 genes were functionally annotated with the COG, GO, and KEGG databases, and 123 genes belonged to CAZymes. Genomic secondary metabolite analysis indicated 13 clusters encoding potential new antimicrobials. FJAT-0809-GLX was designated as B. brevis according to average nucleotide polymorphism (ANI) and phylogenetic analysis. The pangenome consisted of 7141 homologous genes, and 4469 homologous genes shared by B. brevis FJAT-0809-GLX, B. brevis NBRC100599, B. brevis DSM30, and B. brevis NCTC2611. The number of unique homologous genes of B. brevis FJAT-0809-GLX (419 genes) and B. brevis NBRC100599 (480 genes) were much more than those in B. brevis DSM30 (13 genes), and B. brevis NCTC2611 (6 genes). Nine gene clusters encoding for secondary metabolite biosynthesis were compared in the genome of B. brevis FJAT-0809-GLX with those of B. brevis NBRC100599, B. brevis DSM30 and B. brevis NCTC2611, and the gene clusters encoding for lantipeptide and transatpks-otherks only existed in genome of B. brevis FJAT-0809-GLX. The 11 BbPks genes were included in the B. brevis FJAT-0809-GLX genome, which contained the conserved PS-DH domain. The relative expression of BbPksL, BbPksM2, BbPksM3, BbPksN3, BbPksN4 and BbPksN5 reached a maximum at 120h and then decreased at 144h. Our results provided detailed genomic and Pks genes information for the FJAT-0809-GLX strain, and lid a foundation for studying its biocontrol mechanisms.

Z-ligustilide alleviates atherosclerosis by reconstructing gut microbiota and sustaining gut barrier integrity through activation of cannabinoid receptor 2

BackgroundZ-Ligustilide (ZL) is an essential phthalide found in Ligusticum chuanxiong Hort, a commonly used traditional Chinese medicine for treating atherosclerosis (AS) clinically. ZL has been shown to be effective in treating AS. However, the underlying mechanism of ZL against AS and its potential targets remain elusive. PurposeThe purpose of this research was to assess the influence of ZL on AS and explore the role of the gut microbiome in mediating this effect. MethodsA well-established AS mouse model, apolipoprotein E deficient (ApoE-/-) mice was used to examine the effects of ZL on AS, inflammation, and the intestinal barrier. To analyze the changes in gut microbial community, we employed the 16S rRNA gene sequencing. Antibiotic cocktail and fecal microbiota transplantation (FMT) were employed to clarify the contribution of the gut microbiota to the anti-AS effects of ZL. The mechanism through which ZL provided protective effects on AS and the intestinal barrier was explored by untargeted metabolomics, as well as by validating the involvement of cannabinoid receptor 2 (CB2R) in mice and Caco-2 cells. ResultsOral administration of ZL inhibited the development of atherosclerotic lesions, improved plaque stability, inhibited the increase in serum and atherosclerotic inflammation, and improved intestinal barrier function. Fecal bacteria from ZL-treated mice induced similar beneficial effects on AS and the intestinal barrier. We used 16S RNA gene sequencing to reveal a significant increase in Rikenella abundance in both ZL-treated mice and ZL-FMT mice, which was associated with the beneficial effects of ZL. Further function prediction analysis of the gut microbiota and CB2R antagonist intervention experiment in mice and Caco-2 cells showed that the activation of CB2R resulted in the enhancement of the intestinal barrier by ZL. Furthermore, the analysis of metabolomic profiling revealed the enrichment of capsaicin upon ZL treatment, which induced the activation of CB2R in human colon epithelial cells. ConclusionOur study is the first to demonstrate that oral treatment with ZL has the potential to alleviate AS by reducing inflammation levels and enhancing the intestinal barrier function. This mechanism relies on the gut microbiota in a CB2R-dependent manner, suggesting promising strategies and ideas for managing AS. This study provides insights into a novel mechanism for treating AS with ZL.

A Description of the THRIVE (“The Study of Host-Bacterial Relationships in Different Vaginal Environments”) Bacterial Vaginosis Observational Study

ObjectivesBacterial vaginosis (BV) contributes to poor reproductive health and is characterized by a displacement of Lactobacillus in the vaginal microbiome. However, treatment for BV is limited to antibiotics and half of the women treated experience recurrence within a year. THRIVE is a prospective study in XXXXX, which is designed to capture the daily variation of the microbiome and host mucosal immunity during treatment. The objective of this study is to identify host and bacterial factors that associate with vaginal microbiome stability to better inform therapeutic interventions. MethodsWomen treated for BV, and controls, are followed for 6 months collecting daily vaginal swabs and monthly questionnaires. Comprehensive mucosal sampling, including swabs, cytobrushes, biopsies, and blood are collected at baseline, months 1 and 6 post-enrolment. ResultsWe performed analysis on the first 52 participants, (19 BV+, 33 BV–). Molecular profiling by 16s RNA sequencing showed 20 women with non-Lactobacillus-dominant microbiomes and 32 with Lactobacillus-dominant microbiomes, with increased microbial diversity in non-Lactobacillus-dominant microbiomes (P = 3.1E-05). A pilot analysis in 2 participants demonstrates that multi-omics profiling of self-collected daily swabs provides high-quality data identifying 73 bacterial species, 1773 mucosal proteins and 117 metabolites. Initial flow cytometry analysis showed an increased cluster of differentiation (CD)4+ T cells and neutrophil activation (CD11b+CD62Lneg/dim) in the positive participant at baseline, while after treatment these shifted and resembled the control participant. ConclusionsThis study provides a framework to comprehensively investigate the kinetics of vaginal mucosal microbiome alterations, providing further insight into host and molecular features predicting BV recurrence.

Variability of the Microbiota in Chronic Rhinosinusitis: A Scoping Review.

Chronic rhinosinusitis (CRS) is characterized by a persistent inflammation of the nasal and paranasal sinus mucosa that could be potentially linked to a dysregulation between the microbiota and the immune system. We aim to explore general, methodological, and microbiological aspects of microbiota research in CRS compared to disease-free individuals. Embase, Ovid MEDLINE, PubMed, Scopus, and Web of Science. All studies comparing the composition of the resident microbiota of the sinonasal cavities in 2 groups: CRS and normal participants. We conducted systematic study selection, data extraction, and analysis first using the title and abstract, and then the full texts based on predefined inclusion and exclusion criteria. Compiled and presented findings include sampling site and technique, and microbiological results such as the relative abundance and the variability of the composition of the microbiota in both groups. Twenty-seven studies, using genomic identification with 16s RNA were analyzed. Case definitions primarily followed EPOS or AAO-HNS guidelines, with endoscopic swabs (82%), and middle meatus sampling (74%) being prevalent techniques. Despite relative abundance variability, patterns emerged across studies, indicating an increase in Haemophilus (19%) and Pseudomonas (11%), and decrease in Propionibacterium (15%) and Anaerococcus (11%). Another pattern was observed, showing a decreased alpha diversity (6/19; 22%) in CRS compared to normal individuals. While variations exist among studies, analysis of CRS microbiota suggests an association with dysbiosis, potentially contributing to chronic inflammation. Future research must prioritize standardized criteria for diagnostics and patient selection, fostering a more comprehensive understanding of CRS microbiota.

Exploring the Gut Microbiota Landscape in Cow Milk Protein Allergy: Clinical Insights and Diagnostic Implications in Pediatric Patients

Cow milk protein allergy (CMPA) is a significant health concern characterized by adverse immune reactions to cow milk proteins. Biomarkers for the accurate diagnosis and prognosis of CMPA are lacking. This study analyzed the clinical features of CMPA, and 16S RNA sequencing was used to investigate potential biomarkers through fecal microbiota profiling. Children with CMPA exhibit a range of clinical symptoms, including gastrointestinal (83% of patients), skin (53% of patients), and respiratory manifestations (26% of patients), highlighting the complexity of this condition. Laboratory analysis revealed significant differences in red cell distribution width (RDW) and inflammatory markers between the CMPA and control groups, suggesting immune activation and inflammatory responses in CMPA. Microbial diversity analysis revealed higher specific diversity indices in the CMPA group compared with those in control group, with significant differences at the genus and species levels. Bacteroides were more abundant in the CMPA group, whereas Bifidobacterium, Ruminococcus, Faecalibacterium, and Parabacteroides were less abundant. The control group exhibited a balanced microbial profile, with a predominant presence of Bifidobacterium bifidum and Akkermansia muciniphila. The significant abundance of Bifidobacterium in the control group (23.19% vs 9.89% in CMPA) was associated with improved growth metrics such as height and weight, suggesting its potential as a probiotic to prevent CMPA and enhance gut health. Correlation analysis linked specific microbial taxa such as Coprococcus and Bifidobacterium to clinical parameters such as family allergy history, weight and height, providing insights into CMPA pathogenesis. Significant differences in bacterial abundance suggested diagnostic potential, with a panel of 6 bacteria achieving high predictive accuracy (area under curve (AUC) = 0.8708). This study emphasizes the complex relationship between the gut microbiota and CMPA, offering valuable insights into disease mechanisms and diagnostic strategies.