Modulation of faecal metagenome in Crohn's disease:Role of microRNAs as biomarkers

BACKGROUND The gut microbiota plays a key role in the maintenance of intestinal homeostasis and the development and activation of the host immune system. It has been shown that commensal bacterial species can regulate the expression of host genes. 16 S rRNA gene sequencing has shown that the microbiota in inflammatory bowel disease(IBD) is abnormal and characterized by reduced diversity. Micro RNAs(miRNAs) have been explored as biomarkers and therapeutic targets, since they are able to regulate specific genes associated with Crohn's disease(CD). In this work, we aim to investigate the composition of gut microbiota of active treatment-na?ve adult CD patients, with miRNA profile from gut microbiota.AIM To investigate the composition of gut microbiota of active treatment-na?ve adult CD patients, with miRNA profile from gut microbiota.METHODS Patients attending the outpatient clinics at Valme University Hospital without relevant co-morbidities were matched according to age and gender. Faecal samples of newonset CD patients, free of treatment, and healthy controls were collected. Faecal samples were homogenized, and DNA was amplified by PCR using primers directed to the 16 S bacterial rRNA gene. Pyrosequencing was performed using GS-Junior platform. For sequence analysis, MGRAST server with the database Ribosomal Project was used. MiRNA profile and their relative abundance were analyzed by quantitative PCR.RESULTS Microbial community was characterized using 16 S rRNA gene sequencing in 29 samples(n = 13 CD patients, and n = 16 healthy controls). The mean Shannon diversity was higher in the healthy control population compared to CD group(5.5 vs 3.7). A reduction in Firmicutes and an increase in Bacteroidetes were found. Clostridia class was also significantly reduced in CD. Principal components analysis showed a grouping pattern, identified in most of the subjects in both groups, showing a marked difference between control and CD groups. A functional metabolic study showed that a lower metabolism of carbohydrates(P = 0.000) was found in CD group, while the metabolism of lipids was increased. In CD patients, three miRNAs were induced in affected mucosa: mir-144(6.2 ± 1.3 fold), mir-519(21.8 ± 3.1) and mir-211(2.3 ± 0.4). CONCLUSION Changes in microbial function in active non-treated CD subjects and three miRNAs in affected vs non-affected mucosa have been found. miRNAs profile may serve as a biomarker.

Gut microbiome composition can predict the response to nivolumab in advanced hepatocellular carcinoma patients

BACKGROUND Immunotherapy has revolutionized the clinical outcomes of intractable cancer patients.Little is known about the intestinal nonpathogenic bacterial composition of hepatocellular carcinoma(HCC)patients treated by immunotherapy.AIM To determine whether there is a correlation between gut bacterial composition and prognosis in HCC patients.METHODS From September 2019 to March 2020,we prospectively collected fecal samples and examined the gut microbiome of 8 advanced HCC patients treated with nivolumab as a second-or third-line systemic treatment.Fecal samples were collected before the start of immunotherapy.Fecal samples of patients with progression during treatment were collected at the time of progression,and fecal samples of patients who showed good response to nivolumab were collected after 5-7 mo as follow-up.Metagenomic data from 16S ribosomal RNA sequencing were analyzed using CLC Genomics Workbench.Microbiome data were analyzed according to therapeutic response.RESULTS All 8 patients were male,of which 6 had underlying chronic hepatitis B.A higher Shannon index was found in the responders than in the non-responders after nivolumab therapy(P=0.036).The unweighted beta diversity analysis also showed that the overall bacterial community structure and phylogenetic diversity were clearly distinguished according to therapeutic response.There was no significant difference in the diversity or composition of the patient gut microbiome according to the immunotherapy used.Several taxa specific to therapeutic response were designated as follows:Dialister pneumosintes,Escherichia coli,Lactobacillus reteri,Streptococcus mutans,Enterococcus faecium,Streptococcus gordonii,Veillonella atypica,Granulicatella sp.,and Trchuris trichiura for the nonresponders;Citrobacter freundii,Azospirillum sp.and Enterococcus durans for the responders.Of note,a skewed Firmicutes/Bacteroidetes ratio and a low Prevotella/Bacteroides ratio can serve as predictive markers of non-response,whereas the presence of Akkermansia species predicts a good response.CONCLUSION The current presumptive study suggests a potential role for the gut microbiome as a prognostic marker for the response to nivolumab in treatment of HCC patients.

Characteristics of gut microbiota in representative mice strains:Implications for biological research

Background:Experimental animals are used to study physiological phenomena,pathological mechanisms,and disease prevention.The gut microbiome is known as a potential confounding factor for inconsistent data from preclinical studies.Although many gut microbiome studies have been conducted in recent decades,few have focused on gut microbiota fluctuation among representative mouse strains.Methods:A range of frequently used mouse strains were selected from 34 isolation packages representing disease-related animal(DRA),immunity defect animal(IDA),or gene-editing animal(GEA)from the BALB/c and C57BL/6J backgrounds together with normal mice,and their microbial genomic DNA were isolated from mouse feces to sequence for the exploration of gut microbiota.Results:Mouse background strain,classification,introduced source,introduced year,and reproduction type significantly affected the gut microbiota structure(p<0.001 for all parameters),with background strain contributing the greatest influence(R^(2)=0.237).In normal groups,distinct gut microbiota types existed in different mouse strains.Sixty-four core operational taxonomic units were obtained from normal mice,and 12 belonged to Lactobacillus.Interestingly,the gut microbiota in C57BL/6J was more stable than that in BALB/c mice.Furthermore,the gut microbiota in the IDA,GEA,and DRA groups significantly differed from that in normal groups(p<0.001 for all).Compared with the normal group,there was a significantly higher Chao 1 and Shannon index(p<0.001 for all)in the IDA,GEA,and DRA groups.Markedly changed classes occurred with Firmicutes and Bacteroidetes.The abundances of Helicobacter,Blautia,Enterobacter,Bacillus,Clostridioides,Paenibacillus,and Clostridiales all significantly decreased in the IDA,GEA,and DRA groups,whereas those of Saccharimonas,Rikenella,and Odoribacter all significantly increased.

Phylogenetic Analysis of Anaerobic Co-Digestion of Animal Manure and Corn Stover Reveals Linkages between Bacterial Communities and Digestion Performance

Over 3 million tons of manures are produced annually in the United States and pose environmental and health risks if not remediated. Anaerobic digestion is an effective method in treating organic wastes to reduce environmental impacts and produce methane as an alternative energy. Previous studies suggested that optimization of feed composition, hydraulic retention time, and other operational conditions can greatly improve total solids removal and increase methane productivity. These environmental factors improve functionality by altering the microbial community structure but explicit details of how the bacterial community shifts are poorly understood. Our investigations were conducted to investigate the relationship between environmental factors, microbial community structure and bioreactor efficiency by using metagenomic analysis of the microbial communities. Our results indicated that the bioreactor with the greatest methane production, digestion efficiency and reduced levels of E. coli/Shigella had a distinctive community structure at the genus level with unique and abundant uncultivated strains of Bacteroidetes. Moreover the same bioreactor was enriched in Aminomonas paucivorans and Clostridia populations that can utilize secondary metabolites produced during cellulose/hemicellulose degradation to generate hydrogen and acetate. Hence specific digestion conditions that enrich for these populations may provide a route to the optimization of co-digestion systems and control the variability in reactor performance.

Electro-acupuncture promotes gut motility and alleviates functional constipation by regulating gut microbiota and increasing butyric acid generation in mice

Objective:Abnormalities in the gut microbiota and intestinal short-chain fatty acid(SCFA)levels are implicated in the pathogenesis of functional constipation(FC).Electro-acupuncture(EA)has been shown to improve constipation-related symptoms and rebalance the gut microbiota.However,it is currently unknown whether the gut microbiota is a key mechanistic target for EA or how EA promotes gut motility by regulating the gut microbiota and SCFAs.Therefore,we assessed the effects of EA in FC mice and pseudo-germfree(PGF)mice to address these questions.Methods:Forty female Kunming mice were randomly separated into a normal control group(n=8),an FC group(n=8),an FC+EA group(n=8),a PGF group(n=8)and a PGF+EA group(n=8).The FC group and FC+EA group were treated with diphenoxylate to establish the FC model;the PGF group and PGF+EA group were given an antibiotic cocktail to initiate the PGF model.After maintaining the model for 14 d,mice in the FC+EA and PGF+EA groups received EA stimulation at the ST25 and ST37 acupoints,once a day,5 times per week,for 2 weeks.Fecal parameters and intestinal transit rate were calculated to assess the efficacy of EA on constipation and gastrointestinal motility.Colonic contents were used to quantify gut microbial diversity using 16S rRNA sequencing,and measure SCFA concentrations using gas chromatography-mass spectrometry.Results:EA significantly shortened the first black stool defecation time(P<0.05)and increased the intestinal transit rate(P<0.01),and fecal pellet number(P<0.05),wet weight(P<0.05)and water content(P<0.01)over 8 h,compared with the FC group,showing that EA promoted gut motility and alleviated constipation.However,EA treatment did not reverse slow-transit colonic motility in PGF mice(P>0.05),demonstrating that the gut microbiota may play a mechanistic role in the EA treatment of constipation.In addition,EA treatment restored the Firmicutes to Bacteroidetes ratio and significantly increased butyric acid generation in FC mice(P<0.05),most likely due to the upregulation of Staphylococcaceae microorganisms(P<0.01).Conclusion:EA-mediated resolution of constipation occurs through rebalancing the gut microbiota and promoting butyric acid generation.

Exercise and gut microbiota: clinical implications for the feasibility of Tai Chi

Recent studies have shown exercise is associated with changes in the gut microbiota in humans as well as in experimental animals. Tai Chi is an exercise that integrates a martial art, deep breathing and mediation, and has various beneficial effects for health. This review summarizes current knowledge and recent literature on the association between exercise and gut microbiota, and explores the feasibility of Tai Chi for improving gut microbiota composition and function. PubMed/MEDLINE was used to search the English literature for the keywords exercise and gut microbiota. Fourteen relevant studies were identified. In humans, exercise increases the gut microbial diversity. However, the evidence for this association is weak, as previous studies were small-scale, non-controlled studies of short duration or cross-sectional design. In animals, exercise alters the composition of gut microbiota, with some studies suggesting exercise increases the Bacteroidetes/ Firmicutes ratio. However, these results are controversial, partly because host genetics and physical fitness also influence gut microbiota. Furthermore, the intensity of exercise may play a key role in how exercise affects gut microbiota. Tai Chi is a moderate-intensity exercise that improves immune function and inflammation of the gut. Tai Chi may also affect gut microbiota through vagal modulation and mediating the hypothalamic-pituitary-adrenal axis. However, no studies have investigated the association between Tai Chi and gut microbiota. Well designed studies exploring the effects of Tai Chi on gut microbiota are needed.