Gut Microbiota as Early Predictor of Infectious Complications before Cardiac Surgery: A Prospective Pilot Study

Cardiac surgery remains a field of medicine with a high percentage of postoperative complications, including infectious ones. Modern data indicate a close relationship of infectious disorders with pathological changes in the composition of the gut microbiome; however, the extent of such changes in cardiac surgery patients is not fully clarified. In this prospective, observational, single center, pilot study, 72 patients were included, 12 among them with the infectious complications. We analyzed the features of the fecal microbiota before and in the early postoperative period, as one of the markers for predicting the occurrence of bacterial infection. We also discovered the significant change in microbial composition in the group of patients with infectious complications compared to the non-infectious group before and after cardiac surgery, despite the intra-individual variation in composition of gut microbiome. Our study demonstrated that the group of patients that had a bacterial infection in the early postoperative period already had an altered microbial composition even before the surgery. Further studies will evaluate the clinical significance of the identified proportions of individual taxa of the intestinal microbiota and consider the microbiota as a novel target for reducing the risk of infectious complications

Yogurt fortified with vitamins and probiotics impacts the frequency of upper respiratory tract infections but not gut microbiome: A multicenter double-blind placebo controlled randomized study

Probiotics and vitamins can impact immune responses and modulate gut microbiome. We evaluated the effects of consuming a yogurt fortified with vitamins and probiotic Lacticaseibacillus casei and rhamnosus on upper respiratory tract infections frequency and gut microbiome during a 3-month intervention. The study included 2 case groups (consuming different flavours) and a placebo group of healthy adults (n = 158–160 in each group). The effects on URTI-related parameters in both case groups were gender-specific. The female subjects had lower URTI incidence and frequency, while for the males no significant differences were found. The URTI duration was shorter in one of the probiotic groups for females and in both such groups - for males. The observed changes in microbiome composition, blood and stool parameters were not different from those observed in the placebo group. Consumption of fortified fermented dairy foods is promising for improving immunity status within the general population

Knomics-Biota - a system for exploratory analysis of human gut microbiota data

Abstract Background Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers. Results Knomics-Biota is a web-based resource for exploratory analysis of human gut metagenomes. Users can generate and share analytical reports corresponding to common experimental schemes (like case-control study or paired comparison). Interactive visualizations and statistical analysis are provided in association with the external factors and in the context of thousands of publicly available datasets arranged into thematic collections. The web-service is available at https://biota.knomics.ru. Conclusions Knomics-Biota web service is a comprehensive tool for interactive metagenomic data analysis

Data on gut metagenomes of the patients with alcoholic dependence syndrome and alcoholic liver cirrhosis

Alcoholism is associated with significant changes in gut microbiota composition. Metagenomic sequencing allows to assess the altered abundance levels of bacterial taxa and genes in a culture-independent way. We collected 99 stool samples from the patients with alcoholic dependence syndrome (n=72) and alcoholic liver cirrhosis (n=27). Each of the samples was surveyed using “shotgun” (whole-genome) sequencing on SOLiD platform. The reads are deposited in the ENA (project ID: PRJEB18041)

Additional file 13: Table S11. of Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

Associations between the levels of gut microbial genera and clinical factors. The table contains the coefficients of linear model obtained by applying MaAsLin method to the reference-mapping based taxonomic composition vectors (adjusted p-value < 0.05). Positive values denote direct association between the factor and the relative abundance of the respective taxon, while negative values denote reverse association. Each empty cell denotes that no significant association was detected between the respective factor and taxon. (XLSX 8 kb

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

Abstract Background Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative “shotgun” metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts—with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group. Results Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis—with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus—but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation. Conclusions Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics

Additional file 18: Table S16. of Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

Virulence factors genes with increased abundance in ALC patients in comparison with the control group. (XLSX 12 kb

Additional file 16: Table S14. of Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

Metabolic pathways differentially abundant in ADS patients in comparison with the control group. (XLSX 8 kb

Additional file 15:Table S13. of Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

Metabolic pathways differentially abundant in ALC patients in comparison with the control group. (XLSX 8 kb