sRNA Sequencing Research Articles

SRNAdeep: a novel tool for bacterial sRNA prediction based on DistilBERT encoding mode and deep learning algorithms

BackgroundBacterial small regulatory RNA (sRNA) plays a crucial role in cell metabolism and could be used as a new potential drug target in the treatment of pathogen-induced disease. However, experimental methods for identifying sRNAs still require a large investment of human and material resources.MethodsIn this study, we propose a novel sRNA prediction model called sRNAdeep based on the DistilBERT feature extraction and TextCNN methods. The sRNA and non-sRNA sequences of bacteria were considered as sentences and then fed into a composite model consisting of deep learning models to evaluate classification performance.ResultsBy filtering sRNAs from BSRD database, we obtained a validation dataset comprised of 2438 positive and 4730 negative samples. The benchmark experiments showed that sRNAdeep displayed better performance in the various indexes compared to previous sRNA prediction tools. By applying our tool to Mycobacterium tuberculosis (MTB) genome, we have identified 21 sRNAs within the intergenic and intron regions. A set of 272 targeted genes regulated by these sRNAs were also captured in MTB. The coding proteins of two genes (lysX and icd1) are implicated in drug response, with significant active sites related to drug resistance mechanisms of MTB.ConclusionIn conclusion, our newly developed sRNAdeep can help researchers identify bacterial sRNAs more precisely and can be freely available from https://github.com/pyajagod/sRNAdeep.git.

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.

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

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.

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.

Metabolome and Metagenome Integration Unveiled Synthesis Pathways of Novel Antioxidant Peptides in Fermented Lignocellulosic Biomass of Palm Kernel Meal.

Approximately one-third of the entire world's food resources are deemed to be wasted. Palm kernel meal (PKM), a product that is extensively generated by the palm oil industry, exhibits a unique nutrient-rich composition. However, its recycling is seldom prioritized due to numerous factors. To evaluate the impact of enzymatic pretreatment and Lactobacillus plantarum and Lactobacillus reuteri fermentation upon the antioxidant activity of PKM, we implemented integrated metagenomics and metabolomics approaches. The substantially enhanced (p < 0.05) property of free radicals scavenging, as well as total flavonoids and polyphenols, demonstrated that the biotreated PKM exhibited superior antioxidant capacity. Non-targeted metabolomics disclosed that the Lactobacillus fermentation resulted in substantial (p < 0.05) biosynthesis of 25 unique antioxidant biopeptides, along with the increased (p < 0.05) enrichment ratio of the isoflavonoids and secondary metabolites biosynthesis pathways. The 16sRNA sequencing and correlation analysis revealed that Limosilactobacillus reuteri, Pediococcus acidilactici, Lacticaseibacillus paracasei, Pediococcus pentosaceus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and polysaccharide lyases had significantly dominated (p < 0.05) proportions in PMEL, and these bacterial species were strongly (p < 0.05) positively interrelated with antioxidants peptides. Fermented PKM improves nutritional value by enhancing beneficial probiotics, enzymes, and antioxidants and minimizing anti-nutritional factors, rendering it an invaluable feed ingredient and gut health promoter for animals, multifunctional food elements, or as an ingredient in sustainable plant-based diets for human utilization, and functioning as a culture substrate in the food sector.

Akkermansia muciniphila alleviates abdominal aortic aneurysms via restoring CITED2 activated by EPAS1.

Abdominal aortic aneurysm (AAA) is a life-threatening cardiovascular disease that has been linked to gut microbiome dysbiosis. Therefore, this study aims to investigate the effects of Akkermansia muciniphila (Am) on AAA mice and the biomolecules involved. AAA mice were generated using angiotensin II (Ang II), and 16sRNA sequencing was used to identify an altered abundance of microbiota in the feces of AAA mice. Vascular smooth muscle cell (VSMC) markers and apoptosis, and macrophage infiltration in mouse aortic tissues were examined. The abundance of Am was reduced in AAA mouse feces, and endothelial PAS domain-containing protein 1 (EPAS1) was downregulated in AAA mice and VSMC induced with Ang II. Am delayed AAA progression in mice, which was blunted by knockdown of EPAS1. EPAS1 was bound to the Cbp/p300-interacting transactivator 2 (CITED2) promoter and promoted CITED2 transcription. CITED2 reduced VSMC apoptosis and delayed AAA progression. Moreover, EPAS1 inhibited macrophage inflammatory response by promoting CITED2 transcription. In conclusion, gut microbiome dysbiosis in AAA induces EPAS1-mediated dysregulation of CITED2 to promote macrophage inflammatory response and VSMC apoptosis.

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.

Clinical Identification of Two Novel C. kroppenstedtii-like Species Isolated as Pathogens of Granulomatous Lobular Mastitis.

Granulomatous lobular mastitis (GLM) is a rare benign breast inflammatory disease that affects women of childbearing age. Corynebacterium species, especially Corynebacterium kroppenstedtii, was reported as the pathogen of GLM. A recent study showed that the C. kroppenstedtii complex is composed of C. kroppenstedtii and two novel species, C. parakroppenstedtii and C. pseudokroppenstedtii. The study presents seven C. kroppenstedtii-like strains isolated from GLM patients. However, they turned out to be six strains of C. parakroppenstedtii and one strain of C. pseudokroppenstedtii according to 16sRNA sequencing. In order to conduct a phylogenetic study, we further sequenced the fusA and rpoB genes, which were frequently employed in studies of Corynebacterium species. Novel Mass Spectral Peaks (MSPs) for C. parakroppenstedtii were created with Bruker MALDI-TOF MS. Then, the identification power of the MSPs was tested by C. parakroppenstedtii strains and remotely related Corynebacterum spp. The antibiotic sensitivity tests were performed according to the CLSI M45 guidelines. All of the strains were not resistant to β-lactams, vancomycin or linezolid. However, applying erythromycin and clindamycin could be fruitless. Phenotypic identification using a Vitek2 ANC ID card proved all of the C. parakroppenstedtii strains were identified as Actinomycete naeslundii. The test of Ala-Phe-Pro arylamidase and urease could be employed as the characteristics to distinguish C. pseudokroppenstedtii from C. parakroppenstedtii. Here, we present the identification, antibiotic sensitivity tests (ASTs) and epidemiological investigation of two novel C. kroppenstedtii-like species with the purpose of improving the understanding of C. kroppenstedtii-like species and related diseases.

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.

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.

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.

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.

Small RNAs in plasma extracellular vesicles define biomarkers of premanifest changes in Huntington's disease.

Despite the advances in the understanding of Huntington's disease (HD), there is a need for molecular biomarkers to categorize mutation carriers during the preclinical stage of the disease preceding functional decline. Small RNAs (sRNAs) are a promising source of biomarkers since their expression levels are highly sensitive to pathobiological processes. Here, using an optimized method for plasma extracellular vesicles (EVs) purification and an exhaustive analysis pipeline of sRNA sequencing data, we show that EV-sRNAs are downregulated early in mutation carriers and that this deregulation is associated with premanifest cognitive performance. Seven candidate sRNAs (tRF-Glu-CTC, tRF-Gly-GCC, miR-451a, miR-21-5p, miR-26a-5p, miR-27a-3p and let7a-5p) were validated in additional subjects, showing a significant diagnostic accuracy at premanifest stages. Of these, miR-21-5p was significantly decreased over time in a longitudinal study; and miR-21-5p and miR-26a-5p levels correlated with cognitive changes in the premanifest cohort. In summary, the present results suggest that deregulated plasma EV-sRNAs define an early biosignature in mutation carriers with specific species highlighting the progression and cognitive changes occurring at the premanifest stage.

RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions

BackgroundSmall RNA (sRNAs)- mediated RNA silencing is emerging as a key player in host-microbe interactions. However, its role in fungus-plant interactions relevant to biocontrol of plant diseases is yet to be explored. This study aimed to investigate Dicer (DCL)-mediated endogenous and cross-kingdom gene expression regulation in the biocontrol fungus Clonostachys rosea and wheat roots during interactions.ResultsC. rosea Δdcl2 strain exhibited significantly higher root colonization than the WT, whereas no significant differences were observed for Δdcl1 strains. Dual RNA-seq revealed the upregulation of CAZymes, membrane transporters, and effector coding genes in C. rosea, whereas wheat roots responded with the upregulation of stress-related genes and the downregulation of growth-related genes. The expression of many of these genes was downregulated in wheat during the interaction with DCL deletion strains, underscoring the influence of fungal DCL genes on wheat defense response. sRNA sequencing identified 18 wheat miRNAs responsive to C. rosea, and three were predicted to target the C. rosea polyketide synthase gene pks29. Two of these miRNAs (mir_17532_x1 and mir_12061_x13) were observed to enter C. rosea from wheat roots with fluorescence analyses and to downregulate the expression of pks29, showing plausible cross-kingdom RNA silencing of the C. rosea gene by wheat miRNAs.ConclusionsWe provide insights into the mechanisms underlying the interaction between biocontrol fungi and plant roots. Moreover, the study sheds light on the role of sRNA-mediated gene expression regulation in C. rosea-wheat interactions and provides preliminary evidence of cross-kingdom RNA silencing between plants and biocontrol fungi.

Fecal microbiota transplantation as a new way for OVA-induced atopic dermatitis of juvenile mice

Children all over the world suffer from atopic dermatitis (AD), a prevalent condition that impairs their health. Corticosteroids, which have long-term negative effects, are frequently used to treat AD. There has been a growing body of research on the gut microbiota’s function in AD. Nevertheless, the function and underlying mechanisms of fecal microbiota transplantation (FMT) in AD children remain to be established. Therefore, in order to assess the preventive effects of FMT treatment on AD and investigate the mechanisms, we constructed an ovalbumin (OVA)-induced juvenile mouse AD model in this investigation. This study explored the role and mechanism of FMT treatment in AD through 16S RNA sequencing, pathological histological staining, molecular biology, and Flow cytometry. Results demonstrated that the FMT treatment improved the gut microbiota’s diversity and composition, bringing it back to a level similar to that of a close donor. Following FMT treatment, OVA-specific antibodies were inhibited, immunoglobulin (Ig) E production was decreased, the quantity of mast cells and eosinophils was decreased, and specific inflammatory markers in the skin and serum were decreased. Further mechanistic studies revealed that FMT treatment induced CD103+ DCs and programmed cell death ligand 1 (PD-L1)/programmed cell death 1 (PD-1) expression in skin-draining lymph nodes and promoted Treg production to induce immune tolerance and suppress skin inflammation. Meanwhile, changes in the gut microbiota were substantially correlated with Th2 cytokines, OVA-specific antibodies, and PD-L1/PD-1. In conclusion, FMT regulates the Th1/Th2 immunological balance and the gut microbiota. It may also inhibit AD-induced allergy responses through the PD-L1/PD-1 pathway, and providing a unique idea and possibly a fresh approach to the treatment of AD.

PSLBII-13 Bioinformatics of rumen fluid from steers fed alfalfa-bermudagrass mixtures in the Deep South

Abstract When harvesting high-quality, high-water content forages like legumes, there is often a greater percentage of nutritive loss due to the drying process. Alternative feeding strategies like baleage provide a way to mitigate these losses. However, there is not much adoption of baleage in the Deep South. Therefore, our objective was to assess the influence of conserved forage type on rumen metabolomes of beef cattle systems in the Deep South. Three treatments including bermudagrass (Cynodon dactylon) hay, alfalfa (Medicago sativa) baleage, and alfalfa-bermudagrass baleage were supplied to four fistulated steers with a calculated daily forage allowance based on intake, body weight, and feed refusals. Each diet was allocated to one of three periods in which all four animals received the same diet due to potential feed spoilage. Each period had a 21-d adaptation period followed by a 5-d collection period to analyze rumen fluid, total fecal weight, feed intake, feed refusal, and total urine. This study integrated 16S RNA sequencing and LC-MS-based metabolomics to evaluate rumen bacterial diversity and metabolome of beef steers. Sequencing data from the rumen fluid samples were then analyzed using QIIME2. Bermudagrass hay had a reduced alpha diversity compared with alfalfa baleage (Shannon: H = 5.19, P = 0.02). Additionally, we saw a change in beta diversity (P &amp;lt; 0.001), measured using the unweighted UniFrac distance, between conserved forage types and distinct clustering in the PCoA analysis. The most abundant taxa in all microbial communities were from the orders Lachnospirales, Bacteroidales, and Oscillospirales. Previous analysis in this study evidenced that baleage had an increased dry matter digestibility (DMD; P = 0.02). The increase in DMD was associated with the increase in diversity of the metabolome which could influence animal health and performance. Thus, baleage can serve as a beneficial conserved forage type that mitigates the losses of high-quality forages and diversifies the gut microbiome of ruminant animals.

500 Effect of different iron sources on growth performance, gut health, and microbiota in nursery pigs

Abstract This study evaluated the effect of different iron sources, including iron polysaccharide complexes (SQM iron) and ferrous sulfate (FS) on growth performance, gut health, pathogenic bacteria load, colon fecal microbiota, and fecal iron concentration in nursery pigs. Nursery pigs (n = 320, TN70 cross, Topigs Norsvin Canada) weaned at 21 ± 2 d were randomly assigned to four treatments arranged in 2 x 2 factorial, with the factors being sanitation conditions (clean vs. dirty) and iron sources (SQM iron vs. FS, each at 100 mg iron/kg) to give 8 pens (10 piglets per pen) per treatment. Pigs were fed their respective diets in two phases over a 28-d period. Fecal scores, body weight (BW) and feed intake were recorded weekly. Iron content, gene expression of butyryl-CoA:acetate CoA-transferase and bisulfite reductase, and pathogenic bacteria counts were determined in fresh fecal samples collected on d 0, d 14, and d 21. On d 28, one pig randomly selected from each pen was euthanized to sample colon digesta for microbiota analysis and jejunal tissue and serum for gut integrity and permeability analysis. Data were analyzed using PROC MIXED of SAS followed by Tukey’s multiple comparison test except for raw 16s sRNA sequences, which were processed using QIIME2 and analyzed with Kruskal-Wallis test. Overall, from d 0 to14 SQM iron resulted in higher average daily gain (ADG) and average daily feed intake (ADFI; P &amp;lt; 0.05). SQM iron resulted in higher fecal iron at d 21 and improved fecal scores at d 27 (P &amp;lt; 0.05). SQM iron increased the relative abundance of fecal Campylobacter jejuni when comparing d 21 to d 0, and O157 E. Coli when comparing d 14 to d 0 (P &amp;lt; 0.05). Ferrous sulfate resulted in greater changes in relative abundance of butyryl-CoA:acetate CoA-transferase and bisulfate reductase than the SQM iron treatment under clean conditions when comparing d 21 to d 0 (P &amp;lt; 0.05). Dietary iron treatments did not significantly affect gastrointestinal integrity and permeability in jejunum and did not alter fecal microbiota composition on d 28. In conclusion, substituting 100 mg/kg added iron as FS with equal concentration of SQM iron improved ADG in the initial 2 wk and overall ADFI and promoted gut health indicators.

Plastic Debris in the Aquatic Environment: An Emerging Substratum for Antimicrobial Resistant (AMR) Biofilms.

Plastic pollution has quadrupled over the past years and has become a global concern due to its direct impact on life forms. The present study analysed whether the plastic debris in aquatic environments could act as the substratum for the antimicrobial-resistant (AMR) bacteria to form biofilm for survival. We have collected various plastic debris (n = 32) from six sites of the Periyar River, the drinking water source for the entire city and one of the most polluted rivers in Kerala (India). The chemical composition of plastics was screened via FTIR analysis and found that they comprised two types, viz., polyethylene and polypropylene. Bacteria isolated from the samples were screened for the AMR characteristics towards eight different classes of antibiotics. All isolates showed 100% resistance towards colistin and obtained the MAR index value of 0.1-0.4 range. Six representative bacterial isolates with high multiple antibiotic resistance (MAR) index were selected and identified by 16sRNA sequencing as Lysinibacillus mangiferihumi, Bacillus pumilus, Bacillus safensis, Bacillus cereus, Bacillus altitudins and Bacillus pumilus. In vitro biofilm formation was experimented on the purchased plastic samples in artificial media and river water using two selected strains, Bacillus pumilus and Bacillus cereus. Significant variations were observed in biofilm growth in different media (P < 0.05) regardless of plastic types (P > 0.05). The extracellular polymeric substances (EPS) and the characteristic holes on the surface morphology were visualized in SEM analysis, thus indicating the conditioning of the plastics by the isolates for biofilm formation.