16S rRNA Sequencing Research Articles

P1327 Microbial signatures associated with Inflammatory Bowel Disease in Australia: baseline data from the Australian IBD Microbiome study

Abstract Background Microbial dysbiosis is associated with Crohn’s disease (CD) and ulcerative colitis (UC) onset and disease activity, however, large-scale data pertaining to Australian patients are limited1. This study aimed to describe the differences in gut microbiota composition between patients with IBD and healthy controls within the Australian IBD Microbiome (AIM) study2. Methods Paired faecal and oral samples alongside participant demographics and disease characteristics were collected at baseline from all healthy controls (HC) and IBD patients enrolled in the Australian IBD Microbiome (AIM) study from June 2019 to November 2023. Faecal and oral samples were self-collected in DNA stabilising buffer, aliquoted and stored at -80oC until extraction. Samples underwent 16S rRNA sequencing with annotation of DNA sequences to operational taxonomic units at the genus level. Differences in alpha diversity (Chao1) between groups were assessed using Mann-Whitney U tests. Beta diversity (weighted UniFrac dissimilarity) in bacterial communities were shown using Principal Coordinate Analysis (PCoA), and significance of variance was tested using ADONIS in R. Results 751 participants (305 HC, 232 CD, 214 UC) returned baseline faecal (n = 697) and/or oral samples (n = 737) and were included in the analysis, with patient group characteristics presented in Table 1. Most IBD patients were in clinical remission (Table 1). However, CD and UC patients had comparably lower faecal alpha diversity than the HC group (Figure 1A). Faecal beta diversity differed between CD, UC, and HC groups (Figure 1B). Five phyla were significantly different between the three groups in faecal samples (Figure 1C). No significant inter-group differences were seen with oral microbial analysis. Conclusion Compared to healthy adults, patients with IBD in Australia have distinct gut microbial profiles. Faecal rather than oral microbial sampling demonstrated a difference in community structure between IBD and healthy groups. Incorporating longitudinal microbial sampling and increasing sequencing resolution may elucidate a pathogenic relationship between gut microbiota and IBD.

P1345 Association of gut microbiota changes and disease activity in patients with Crohn’s disease and ulcerative colitis: baseline data from the Australian IBD Microbiome study

Abstract Background Identifying microbial changes associated with active inflammation and inflammatory bowel disease (IBD) phenotype may improve understanding of drivers of disease activity1. This study aimed to characterise differences in gut microbial signatures according to inflammatory activity amongst patients enrolled in the Australian IBD Microbiome (AIM) study2. Methods Paired faecal and oral samples alongside participant and disease characteristics were collected at baseline from all patients with Crohn’s disease (CD) and ulcerative colitis (UC) enrolled in the AIM study from June 2019 to November 2023. Clinically active disease was defined as Crohn’s disease activity index (CDAI) score >150 or partial Mayo score >1. Biochemical activity was defined as faecal calprotectin (FCP) ≥150 μg/g. Faecal and oral microbial samples were collected in DNA stabilising buffer and stored at -80oC. Samples underwent 16S rRNA sequencing with annotation of DNA sequences to operational taxonomic units at the genus level. Differences in alpha diversity (Shannon index) and relative abundance of identified genera between the groups were assessed using Mann-Whitney U tests. Beta diversity (Bray-Curtis dissimilarity) between bacterial communities were shown using the Principal Coordinate Analysis (PCoA), and significance of variance tested using ADONIS within R. Results 446 participants (232 CD, 214 UC) returned baseline faecal (n = 403) and/or oral samples (n = 436). The majority of patients were in clinical and biochemical remission with patient and disease characteristics presented in Table 1. Oral and faecal microbial analyses showed no statistical differences in alpha or beta diversity between CD and UC patients with clinical or biochemical activity vs. those in remission. In CD, lower faecal alpha diversity was observed in patients with a stricturing phenotype (p = 0.017) and isolated ileal disease (p = 0.043) in comparison to an inflammatory phenotype and colonic CD, respectively. No differences were observed according to UC extent. There were 17 and 39 genera with significantly different relative abundances between FCP activity vs. FCP remission in CD and UC patients, respectively (Figure 1). Conclusion There were no differences in broad measures of oral or faecal microbial community structure between IBD patients in clinical or biochemical remission compared to those with active disease. However, relative abundances at the genus-level distinguished IBD patients according to biochemical activity. Increasing the sequencing depth, as well as analysing serial biological sampling and their relationship to longitudinal changes in disease activity may allow identification of microbial signatures associated with both flare and pre-flare states.

P1340 Gut microbiota changes are associated with type of advanced therapy in patients with Inflammatory Bowel Disease: baseline data from the Australian IBD Microbiome study

Abstract Background Gut microbiota are associated with both disease course and treatment outcomes in inflammatory bowel disease (IBD)1. This study aimed to characterise differences in gut microbial signatures according to medication use in the Australian IBD Microbiome (AIM) study2. Methods Faecal and oral samples alongside participant characteristics were collected at baseline from all patients with IBD enrolled in the AIM study from June 2019 to November 2023. Faecal and oral microbial samples were collected in DNA stabilising buffer, aliquoted and stored at -80oC. Samples underwent 16S rRNA sequencing with annotation of DNA sequences to operational taxonomic units at the genus level. Differences in alpha diversity (Shannon index) and relative abundance of observed genera between medication groups were assessed using Mann-Whitney U and Kruskal-Wallis tests. Beta diversity (Bray-Curtis dissimilarity) between bacterial communities were shown using the Principal Coordinate Analysis (PCoA), and significance of variance tested using ADONIS within R. Results 446 participants (232 CD, 214 UC) returned baseline faecal (n = 403) and/or oral samples (n = 436) with patient and disease characteristics presented in Table 1. No differences in faecal calprotectin were observed between patients on advanced therapy vs. patients who were not, nor between each advanced therapy class. Patients on advanced therapy had lower alpha diversity (p = 0.003) and distinct beta diversity (R2 0.64, p = 0.002) than those not on advanced therapy. Patients on anti-TNF therapy had lower alpha (p < 0.001) and distinct beta diversity (R2 1.75, p = 0.008) compared to patients on no advanced therapy (Figure 1AB). Alpha diversity remained lower when comparing those on either infliximab (p = 0.008) or adalimumab (p = 0.012) to patients on no therapy. There were no differences in alpha or beta diversity between other advanced therapy classes, between types of immunomodulator and between patients on 5-ASA compared to patients who were not. Pairwise comparisons between patients on no therapy and each class of advanced therapy demonstrated significantly different relative abundances of multiple genera observed in faecal samples (Figure 1C). No differences were observed in oral samples. Conclusion Distinct differences in both community structure and the relative abundance of multiple genera were observed in IBD patients according to type of advanced therapy despite no significant difference in biochemical activity. No microbiota differences were observed according to conventional 5-ASA or immunomodulator use. Future analysis including longitudinal samples and treatment outcomes may allow identification of unique microbial signatures predictive of treatment response.

P1317 Oral microbiota is linked to the propensity for mucosal healing: A prospective oral-gut-stool microbiome analysis in IBD

Abstract Background The oral cavity is the second most complex human microbial niche and is the conduit through which initial gut microbial colonisation occurs during early life. While the gut microbiome is implicated in the pathogenesis of inflammatory bowel disease (IBD), the role of the oral microbiome remains underexplored. We aimed to characterise the oral-gut microbiome in IBD and its association with disease activity and complete mucosal healing (CMH), a key prognostic marker for long-term remission. Methods All patients with Crohn’s disease (CD) and Ulcerative Colitis (UC) were prospectively recruited via www.musicstudy.uk. We conducted a 3-stage experimental approach. (1) We profiled the oral microbiota in IBD vs healthy controls (HC) (CD = 34, UC = 24 and HC = 25). (2) We carried out trans-anatomical oral-ileal-stool microbial source tracking1 within the same patients at a single time-point (CD = 23; inflamed vs. non-inflamed mucosal samples), alongside longitudinal oral-stool sampling (CD = 32, UC = 17). (3) Our machine learning (ML) modelling integrated stool microbiota taxonomic profiles (CD = 53, UC = 11; sampled at 0, 3, and 6 months) with ~80 clinical variables to classify CMH using random forest, AdaBoost, XGBoost, logistic regression, and neural networks. Results 16S rRNA sequencing revealed significant divergence between IBD and HC oral microbiota (PCoA, Bray-Curtis; PERMANOVA, p=0.003). Active disease also differed from remission (PCoA, Bray-Curtis; PERMANOVA, p=0.01). Higher oral Veillonella abundances were associated with IBD; bacteria commonly enriched in the IBD gut. We determined within patient oral microbiota abundances in gut samples and found no difference between inflamed ileal mucosa compared to non-inflamed (p=0.52). Patients who did not achieve CMH exhibited significantly higher oral microbiota abundances in stool compared to those with CMH (β = 0.046, p=0.022, linear mixed-effects model). Oral microbiota abundances in stool correlated with clinical markers of disease activity, calprotectin (r = 0.23, p=0.009) and albumin (r = –0.28, p=0.002; Benjamini-Hochberg adjusted). ML models integrating stool microbiota taxonomic profiles and clinical variables outperformed clinical markers alone in predicting CMH (AUC: 0.79 vs. 0.55), indicating that the inclusion of stool microbiota features could be valuable in predicting CMH in the clinical setting. Conclusion Our data show distinct oral microbiota taxonomic profiles in IBD and active disease, with higher oral microbiota abundances in stool associated with lack of CMH. These findings highlight the oral microbiome as a potential upstream regulator of microbial-immune crosstalk from the site of IBD-inflammation.

P0203 Unique faecal & oral microbiota signatures in first degree relatives of inflammatory bowel disease patients

Abstract Background While the aetiology of IBD is unknown, a range of genetic and environmental risk factors have been described. First-degree relatives (FDRs; siblings, parents and children) of IBD patients share many of these factors. To better understand the interplay between environmental and genetic risk factors, we evaluated the gut microbial profiles of an FDR cohort, their IBD probands and healthy controls (HC). The aim was to identify whether FDRs of IBD patients have healthy or IBD-like microbial features. Methods All participants were recruited as part of the Australian IBD Microbiome (AIM) study. Participants were selected based on self-reported first-degree relative status (n=68) and, where possible, affected IBD relatives (n=24) were included for comparison. All participants were antibiotic free for 3-months prior to baseline sampling. Oral and faecal samples underwent 16S rRNA sequencing. The Microbiome Research Centre 16S analysis pipeline and R studio were used for statistical analysis and data visualisation. Results The FDR group was predominantly female (63%) with a mean age of 49.7 years and BMI of 25.5 kg/m2. The IBD cohort was significantly different in age to FDR (mean 36.7; p < 0.05) but not controls (mean 40.4 years) and BMI was comparable between groups. European Australians were the most represented ethnic group (47.6%) and 98.6% of participants were non-smokers. Oral microbiota profiles showed no significant difference in alpha diversity across FDR, IBD and HC groups. Differential abundance analysis of the oral microbiota revealed FDRs had increased abundance of Oribacterium, Granulicatella, Lachnoanaerobaculum and Rothia compared to HC, and increased levels of Capnocytophaga, Tannerella and Abiotrophia compared to the IBD group. In agreement with other studies, faecal microbial profiles in the IBD group had significantly reduced alpha diversity compared to both FDR and HC groups. All groups were compositionally different by Bray-Curtis beta dissimilarity analysis (p<0.018). FDRs had higher abundance of Akkermansia, Alistipes and Monoglobus compared to IBD and HC groups. FDRs and IBD shared similar abundance of Butyricicoccus which was lower than the HCs. Conclusion FDR oral microbiome signatures had greater variance from HC than IBD groups. Faecal microbial analysis showed distinct differences with enrichment of key beneficial genera in the FDR group. FDR profiles however still shared significant gut microbial features with the IBD group, remaining distinct from healthy controls. FDRs oral microbiome was higher in opportunistic pathogens and IBD-like whereas faecal composition was protective, rich in beneficial metabolite producing genera.

Taurochenodeoxycholic Acid Improves Growth, Physiology, Intestinal Microbiota, and Muscle Development in Red Swamp Crayfish (Procambarus clarkii)

Taurochenodeoxycholic acid (TCDCA), one of the bile acids, is thought to be involved in the regulation of muscle nutrient metabolism and gut microbial homeostasis. However, the effect of dietary addition of TCDCA on Procambarus clarkii is unclear. Therefore, in this study, an 8-week feeding experiment was conducted to explore the potential regulatory mechanisms of TCDCA on P. clarkii growth, physiology, muscle quality and gut microbes. The results indicated that dietary addition of TCDCA not only improved growth performance (final weight; weight gain; and specific growth rate) but also increased muscle elasticity and protein content. In addition, dietary TCDCA promotes muscle growth and development by increasing myofiber length, which is consistent with the activation of the expression of genes related to protein utilization (TOR and AKT) and muscle proliferation and differentiation (MyHC, MLC1, MEF2A, MEF2B). Importantly, 16s rRNA sequencing demonstrated that dietary TCDCA had no significant effect on gut microbial composition (alpha diversity) but significantly increased microbial abundance at the genus level. Functional prediction analysis of differential microbes revealed that dietary TCDCA may promote metabolism by altering gut microbes, thereby promoting muscle quality. In conclusion, our study demonstrates that the dietary addition of TCDCA promotes P. clarkii growth and muscle quality and protein deposition by altering gut microbes.

Oral microbiota among treatment-naïve adolescents with depression: A case-control study.

Adolescent depression has profound impacts on physical, cognitive, and emotional development. While gut microbiota changes have been linked to depression, the relationship between oral microbiota and depression remains elusive. Our study aims to investigate the oral microbiota in treatment-naïve adolescents experiencing depression and examine their potential associations with cognitive function. Our case-control study comprised two groups of adolescents aged 12-17: the depression group, including treatment-naïve individuals diagnosed with DSM-5 major depressive disorder (MDD), and a healthy control group of non-depressed individuals (HC). Participants underwent structured neuropsychiatric assessments, and fasting morning saliva samples were collected for the 16S rRNA sequencing to investigate the oral microbiota. Significant differences were identified in the α- and β-diversities of the oral microbiota between MDD and HC groups. Specific bacterial taxa, including genera Streptococcus, Neisseria, Hemophilus, Fusobacterium, and g_norank_f_norank_o_Absconditabacteriales_SR1, were significantly associated with MDD. The association extends to cognitive functions, where correlations were observed between certain oral bacteria and cognitive scores, including instant and delayed memory, visual breadth, and speech features for the combined MDD and HC individuals (p<0.05). Random forest analysis identified ten genera of oral microbes with the highest predictive values for MDD. The area under the curve (AUC) is 0.78 in the receiver operating characteristic (ROC) curve analysis. Our results highlight the oral microbiota's role as a biomarker for adolescent depression and its impact on cognitive functions. These insights underscore the need for further research into the links between oral health, mental health, and cognitive functions.

P1330 The gut microbiome at the onset of inflammatory bowel disease: A systematic review of the literature and unified bioinformatic synthesis of sequencing data from &amp;gt;1000 treatment naïve patients

Abstract Background There are few studies of the gut microbiome in new-onset IBD. We present a novel secondary bioinformatic re-analysis (BA) of sequence outputs mapped to latest microbial taxonomy derived from systematic review. Methods MEDLINE and Embase searches were performed for microbiome studies in pre-treatment IBD. Appraisal was completed with ROBINS-E. Available 16S rRNA sequence datasets were downloaded and missing datasets requested. Integrated datasets were run through a unified pipeline based in QIIME2 supplemented by phyloseq and DESeq2. Results From 12,264 studies, 10,804 abstracts and 217 full texts were screened. 31 studies were eligible; 18 met the requirements for BA. Most were low risk for bias, except uncontrolled confounding. Methodology varied extensively. Considering only amplicon data; samples originated from 1,743 unique individuals (including 678 Crohn’s disease (CD), 399 ulcerative colitis (UC), 123 ‘other’ IBD, 130 healthy, 405 symptomatic, and 8 familial controls) derived from 15 countries. DNA was extracted using 15 different kits, sequencing performed on 4 separate platforms targeting 10 different 16S rRNA hypervariable regions. There was a paucity of adult data, particularly mucosal biopsies. Bacterial alpha diversity was reduced: in faeces in paediatric UC vs symptomatic controls (SC), in adult CD and UC vs HC and in paediatric SC vs HC (Figure 1). In paediatric biopsies in CD vs SC, CD vs UC, SC vs UC (Figure 2). Beta-diversity BA by Bray-Curtis demonstrated clear distinctions between faecal and mucosal biopsy communities, least evident in UC. Faecal communities separated by geography, though less evidently in biopsies. Differential abundance analysis revealed enrichment of oral genera across sample types (Fusobacterium, Peptostreptococcus, Neisseria in CD; Haemophilus, Aggregatibacter, Peptostreptococcus, Porphyromonas, Neisseria, Gemella in UC). Short-chain fatty acid (SCFA) producers were diminished but less consistently across IBD phenotype and sample type. Conclusion This work demonstrates the utility of a combined systematic review/secondary data analysis approach to published microbiome datasets. Whilst synthesis remains challenging due to the methodological inconsistencies within these studies, this approach better accounts for these variations and presents a new way to consider this data. A reduction in bacterial diversity remains core to the IBD microbiome, though with more complexity than previously considered (SC&amp;lt;UC in paediatric biopsies). Microbial community structure changes by sample type and geography. Enrichment of oral bacteria is consistent across IBD subtypes and sample types suggesting their importance in the disease. A deficit in SCFA producers may also be important.

DOP022 Shared and Distinct Features of the Gut Microbiome in Immune-mediated Inflammatory Diseases: Initial Analysis from the INTEGRATE Cohort Study

Abstract Background Inflammatory bowel disease (IBD) and ankylosing spondylitis (AS) share overlapping pathophysiological mechanisms as immune-mediated inflammatory diseases. While gut microbial dysbiosis has been implicated in both conditions, the shared and distinct features of the oral-gut microbiome axis remain poorly understood. This study aims to characterize the oral and gut microbial signatures and their relationship with environmental factors in IBD and AS to identify common pathogenic pathways and disease-specific patterns. Methods The INTEGRATE study is a nationwide prospective observational study in Korea targeting recruitment of 1,100 IBD patients, 700 AS patients, and 2,244 healthy controls over five years (Table 1). Systematic collection includes clinical data and biological samples (saliva, stool, blood, intestinal tissues) for multi-omics analyses. Microbial characterization employs full-length 16S rRNA gene sequencing and shotgun metagenomics for saliva and stool samples, complemented by metabolomic analyses of saliva, stool, and plasma. This initial analysis includes gut microbiome data from 254 IBD patients, 156 AS patients, and 194 healthy controls. Results Alpha diversity analysis revealed a gradient pattern, with IBD patients showing lowest gut microbiome diversity, AS patients intermediate, and healthy controls highest (p&amp;lt;1.0e-12 for all indices, Fig. 1). In IBD patients, alpha diversity significantly correlated with disease activity indices (Harvey-Bradshaw Index score in Crohn's disease, total Mayo score in ulcerative colitis) and inflammatory markers (CRP, r=-0.13, p=0.042). Blood urea nitrogen levels showed positive correlation with alpha diversity in both IBD (r=0.21, p=0.00062) and AS cohorts (r=0.20, p=0.015). Beta diversity analysis demonstrated distinct clustering patterns (UniFrac distance), with AS patients positioned intermediately between IBD patients and healthy controls (Healthy vs IBD: R²=0.0502, Healthy vs AS: R²=0.0148, IBD vs AS: R²=0.0198; all p=0.001). Species-level analysis through full-length 16S rRNA sequencing identified specific taxa (Clostridium bolteae, Blautia hansenii) significantly enriched in both IBD and AS patients compared to controls. Conclusion Our initial analysis demonstrates distinct gut microbiome signatures across IMIDs, with a clear diversity gradient and shared taxonomic features between IBD and AS. These findings, coupled with specific clinical correlations, provide a foundation for understanding common pathogenic pathways. Ongoing multi-omics analyses and quantitative microbiome profiling will further elucidate the role of the oral-gut microbiome axis in these IMIDs, potentially identifying novel microbial biomarkers for precision medicine.

Potential roles of cigarette smoking on gut microbiota profile among Chinese men

BackgroundCigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.MethodsHere, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total = 3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.ResultsActinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum γ-glutamylcysteine (γ-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.ConclusionsWe characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.

Gut-Derived Ursodeoxycholic Acid from Saponins of Quinoa Regulated Colitis via Inhibiting the TLR4/NF-κB Pathway.

Alteration of the gut microbiota and its metabolites plays a key role in the development of inflammatory bowel disease (IBD). Here, we investigated the mechanism of saponins, a byproduct from quinoa (SQ) processing, in regulating IBD. SQ ameliorated gut microbiota dysbiosis revealed by 16S rRNA sequencing and improved colonic antioxidant activities and barrier integrity in dextran sulfate sodium (DSS)-treated mice. Broad-spectrum antibiotics further proved that the gut-protective effects of SQ were mediated by gut microbiota. Next, fecal microbiota transplantation (FMT) of SQ-induced gut microbiota/metabolites to inoculate DSS-treated mice alleviated colitis significantly. Untargeted metabolomics and lipidomics revealed that ursodeoxycholic acid (UDCA) was enriched as a microbial metabolite after SQ supplementation. UDCA was then found to attenuate DSS-induced colitis in vivo by targeting the TLR4/NF-κB pathway, which was also verified in a Caco-2 cell model treated with a TLR4 agonist/antagonist. Overall, our findings established that gut microbiota-UDCA-TLR4/NF-κB signaling plays a key role in mediating the protective effects of SQ.

Antibacterial Potential of Crude Extracts from Cylindrospermum alatosporum NR125682 and Loriellopsis cavernicola NR117881.

The challenges of antimicrobial resistance (AMR) to human health have pushed for the discovery of a new antibiotics agent from natural products. Cyanobacteria are oxygen-producing photosynthetic prokaryotes found in a variety of water habitats. Secondary metabolites are produced by cyanobacteria to survive extreme environmental stress factors, including microbial competition. This study presents the antibacterial activity and mechanism of the crude extracts from Cylindrospermum alatosporum NR125682 (A) and Loriellopsis cavernicola NR117881 (B) isolated from freshwater. The cyanobacteria were identified through 16S rRNA sequencing. Crude extracts were sequentially prepared using hexane, dichloromethane, and ethanol consistently. The minimum inhibition concentration (MIC), minimum bactericidal concentration (MBC) using the CSLI microdilution test protocol, and crude extract potential to inhibit the growth of the tested clinical bacteria strains were evaluated. The mechanism of action of the extracts including membrane damage, efflux pump, β-lactamase activity, DNA degradation, and extract-drug interaction was investigated using standard procedures. The hexane extract of B performed the best with a MIC (0.7-1.41 mg/mL) and MBC (1.41-2.81 mg/mL) range. All the crude extracts inhibited efflux pump activity against the bacteria tested. However, the extracts poorly inhibited β-lactamase. The ethanol extract of B exhibited the most appreciable antibacterial activity. The dichloromethane extract of B showed the highest significant DNA degradation potential, when compared with other samples. The extracts exhibited synergism when combined with erythromycin against some test bacteria, indicating primary microbial activity through membrane interactions. Hence, this study demonstrates the significance of cyanobacteria for antibiotic development.

Acer tegmeutosum Maxim extract alleviates acute alcohol-induced liver disease and regulates gut microbiota dysbiosis in mice.

Acer tegmentosum Maxim (AT) has a variety of pharmacological activities, however, the effects of AT on liver injury and gut microbiota in alcoholic liver disease (ALD) mice is still unclear. This study aimed to evaluate the preventive effect of AT extract on acute alcoholic liver disease. Six-week-old male C57BL/6J mice were randomly divided into 6 groups. Each group was intragastrically treated saline or different concentration of AT extract solution for 5 weeks continuously. After the last gavage, except for the NC group, all the other groups were gavaged twice with 56% alcohol to establish the acute ALD model and biochemical indexes, histopathological, and gut microbiota were analyzed. Established an acute ALD mouse model and detected serum, liver oxidation levels, and alcohol metabolism-related gene expressions. Through 16S rRNA sequencing, analyzed gut microbiota, explored the relationship between gut microbiota and liver indicators. AT extract significantly decreased lipid levels, promoted ADH, ALDH, and increased the antioxidant activities. Meanwhile, AT extract significantly downregulated the expression of lipid oxidation and inflammatory factors, upregulated alcohol metabolism genes. In addition, 16S rRNA sequencing and analysis showed that AT extract effectively regulated the gut microbiota diversity of ALD mice, significantly improved the structural disturbance of intestinal microflora. AT extract regulated gut microbiota and had a strong correlation with serum, liver-related indexes, and gene expression levels. All these results showed that AT can alleviate alcohol induced liver injury by regulating oxidative stress, inflammatory response, alcohol metabolism, and gut microbiota disorder.

Fecal metabolomic analysis of the role of gut microbiota and short-chain fatty acids in the therapeutic mechanism of Timosaponin AIII in Sjögren's syndrome.

Sjogren's syndrome (SS) is a chronic inflammatory and difficult-to-treat autoimmune disease. Timosaponin AIII (TAIII), a plant-derived steroidal saponin, effectively inhibits cell proliferation, induces apoptosis, and exhibits anti-inflammatory properties. This study explored the mechanisms of action of TAIII in SS treatment by studying gut microbiota and short-chain fatty acids (SCFAs) using fecal metabolomics. The model group used non-obese diabetic (NOD) mice. The treatment group was classified into TAIII and hydroxychloroquine groups. The gut microbiota, SCFAs, and metabolites were analyzed using 16S rRNA sequencing, gas chromatography-mass spectrometry analysis, and liquid chromatography-mass spectrometry, respectively. TAIII effectively alleviated dry mouth in NOD mice, slowed the progression of salivary gland tissue injury, reduced inflammatory factor expression, and increased the levels of aquaporins 1 and 5. TAIII regulated SCFA content and tryptophan metabolism by altering the abundance of the Rikenellaceae_RC9_gut_group, thereby reducing the inflammatory response. TAIII can improve imbalances in the gut microbiota and the metabolic levels of related SCFAs and tryptophan, thereby reducing the level of inflammation. The significant differences observed in the abundance of the Rikenellaceae_RC9_gut_group between the treatment and control groups indicated the potential relationship between bacteria and metabolites in SS. Key Points • The safe and effective treatment of SS with traditional Chinese medicine • Multi-means study on intestinal flora, short-chain fatty acids, and metabonomics.

Vibrio cholerae Gut Colonization of Zebrafish Larvae Induces a Dampened Sensorimotor Response.

Background: Cholera is a diarrheal disease prevalent in populations without access to clean water. Cholera is caused by Vibrio cholerae, which colonizes the upper small intestine in humans once ingested. A growing number of studies suggest that the gut microbiome composition modulates animal behavior. Zebrafish are an established cholera model that can maintain a complex, mature gut microbiome during infection. Larval zebrafish, which have immature gut microbiomes, provide the advantage of high-throughput analyses for established behavioral models. Methods: We identified the effects of V. cholerae O1 El Tor C6706 colonization at 5 days post-fertilization (dpf) on larval zebrafish behavior by tracking startle responses at 10 dpf. We also characterized the larval gut microbiome using 16S rRNA sequencing. V. cholerae-infected or uninfected control groups were exposed to either an alternating light/dark stimuli or a single-tap stimulus, and average distance and velocity were tracked. Results: While there was no significant difference in the light/dark trial, we report a significant decrease in distance moved for C6706-colonized larvae during the single-tap trial. Conclusion: This suggests that early V. cholerae colonization of the larval gut microbiome has a dampening effect on sensorimotor function, supporting the idea of a link between the gut microbiome and behavior.

Quinazolinone Derivative MR2938 Protects DSS-Induced Barrier Dysfunction in Mice Through Regulating Gut Microbiota.

Background/Objectives: Ulcerative colitis (UC), a chronic inflammatory bowel disease (IBD), is characterized by colorectal immune infiltration and significant microbiota compositional changes. Gut microbiota homeostasis is necessary to maintain the healthy state of humans. MR2938, a quinazolin-4(3H)-one derivative derived from the marine natural product penipanoid C, alleviated DSS-induced colitis in a dose-dependent manner. Herein, we aimed to investigate the impact of MR2938 on the gut microbiota in dextran sodium sulfate (DSS)-induced colitis in mice and to elucidate the role of the gut microbiota in the therapeutic mechanism of MR2938 for alleviating colitis. Methods: Acute colitis was induced with DSS in mice. Mice were administered with 100 mg/kg or 50 mg/kg of MR2938. Cecal content was also preserved in liquid nitrogen and subsequently analyzed following 16S RNA sequencing. Antibiotic cocktail-induced microbiome depletion was performed to further investigate the relationship between MR2938 and gut microbiota. The inflammatory factor levels were performed by quantitative polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assay (ELISA). Alcian blue staining and immunofluorescence were used to estimate the intestinal barrier. Results: The 16S rRNA sequencing revealed microbiota modulation by MR2938. Compared with the model group, the 100 mg/kg MR2938 group was associated with higher abundances of Entercoccus and a lower abundance of Staphylococcus, while the 50 mg/kg MR2938 group was associated with higher abundances of Lactobacillus and a lower abundance of Staphylococcus. The antibiotic-mediated microbiota depletion experiments demonstrated that the gut microbiota primarily contributed to barrier function protection, with little impact on inflammatory factor levels during the MR2938 treatment. Conclusions: These findings suggest that intestinal flora play a crucial role in MR2938's therapeutic mechanism for alleviating colitis.

Interactions between live attenuated influenza vaccine and nasopharyngeal microbiota among children aged 24-59months in The Gambia: a phase 4, open-label, randomised controlled trial.

Live attenuated influenza vaccines (LAIVs) alter nasopharyngeal microbiota in adults. It is poorly understood why LAIV immunogenicity varies across populations, but it could be linked to the microbiome. We aimed to investigate the interactions between intranasal immunisation with LAIV and nasopharyngeal microbiota composition in children from The Gambia. We conducted a phase 4, open-label, randomised controlled trial in Sukuta, The Gambia. Children aged 24-59months with no underlying illness or history of respiratory illness for at least 14days before recruitment were eligible. Participants were randomly assigned (2:1) by use of a computer-generated sequence in permuted blocks of 15, stratified by sex, to receive trivalent LAIV either on day 0 (intervention group) or after active follow-up at day 21 (control group). The investigator team was initially masked to block size and randomisation sequence; however, group allocation was later revealed to the team. Microbiome profiles were characterised from nasopharyngeal samples collected from all participants on days 0, 7, and 21by use of 16S rRNA sequencing. The primary outcomes were the effect of LAIV on nasopharyngeal microbiome profiles on day 7and day 21, and the association between the nasopharyngeal microbiome at baseline and LAIV-induced mucosal IgA responses at day21, assessed with permutational ANOVA tests. Asymptomatic respiratory viral co-infection at baseline and year of recruitment (2017 or 2018) were included as covariates. This trial is registered with ClinicalTrials.gov (NCT02972957) and is closed. Between Feb 8and April 12, 2017, and Jan 15and March 28, 2018, 343children were screened for eligibility, of whom 220 (64%) children were randomly assigned to the intervention group and 110 (32%) to the control group. 213 (97%) children in the intervention group and 108 (98%) in the control group completed the study and were included in the final analysis. Although we did not observe an independent effect of LAIV on microbial community composition at days 7or 21, we found that LAIV had an effect dependent on the year of recruitment. LAIV affected microbial community composition in 2018 (R2 1·97% [95% CI 0·85-5·94]; p=0·037), but not in 2017 (1·23% [0·49-4·46]; p=0·091). We also found that viral co-infection at baseline had an effect on microbial composition at day 7, regardless of recruitment year (R21·01% [95% CI 0·28-3·01]; p=0·026). Nasopharyngeal microbial community composition at baseline had no effect on mucosal IgA responses to LAIV administration (R2 0·51% [95% CI 0·23-2·49]; p=0·46). Our findings suggest that the effect of LAIVs on nasopharyngeal microbiota composition in children is modest and temporary; therefore, LAIVs could be used as an intervention to curb influenza in children from low-income and middle-income countries, without causing long-lasting perturbations in nasopharyngeal microbiota. However, nasopharyngeal microbiota at the time of vaccination might not explain the variability observed between individuals in LAIV-induced IgA responses. The Wellcome Trust, UK National Institute for Health Research, and Chief Scientist Office Scotland.

16S rRNA amplicon sequencing of organic and conventional chickens.

We report 16S rRNA sequencing of microbiomes associated with organic and conventional retail chickens (n=31), processed via whole-carcass enrichment and rinse methodologies. Amplicon sequencing was performed targeting the V3-V4 region of the 16S rRNA gene, which resulted with Good's coverage exceeding 99.7% of the libraries.

Actinomycetes studies in Tunisia.

Tunisia, located in North Africa, has a diverse topography along the Mediterranean Sea to the Sahara Desert. These environments encompass oases, rhizosphere soils, desert deposits, saline wetlands, offshore oilrigs, and ancient monument rocks. The country's varied environments have led to the isolation of a multitude of actinomycetes. A phylogenetic analysis based on the 16S rRNA sequences of one hundred isolated actinomycetes strains revealed that the majority belong to the genus Streptomyces. Secondary metabolite studies from these actinomycetes yielded 33 natural products. Notably, compound 12, 3-O-methylviridicatin, exhibited antitumor activity and suppressed HIV expression. This showcases Tunisia's potential for natural product research.

Epicatechin protects mice against OVA-induced asthma through inhibiting airway inflammation and modulating gut microbiota.

Allergic asthma is a chronic airway inflammatory reaction that seriously affects people's quality of life and even endangers their lives. The aim of this study was to explore the role of epicatechin (EC) on asthma and its potential mechanism. A mice model of allergic asthma was established by intraperitoneal injection of ovalbumin (OVA) with aluminum hydrogen solution, and nebulized inhalation of OVA to stimulate. EC (10, 20, 40 mg/kg) was administered 30 min before nebulization for three consecutive days. The results showed that EC attenuated OVA-induced lung injury, inflammatory cell infiltration, IgE, and inflammatory cytokine production. EC also inhibited OVA-induced NF-κB activation and increased Nrf2 and HO-1 expression. 16S rRNA sequencing analysis demonstrated that at genus level, EC significantly increased the abundance of Lachnospiraceae_NK4A136_group, Ligilactobacillus, Alloprevotella. Meanwhile, EC inhibited the abundance of Clostridia UCG-014, Helicobacter, Paramuribaculum, and Escherichia-Shigella. In conclusion, EC can effectively alleviate the symptoms of asthma in mice, which may through regulating the composition of gut microbiota and inhibiting inflammatory response.