Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.

Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.

A clinical evaluation of a sensor to detect blockage due to crystalline biofilm formation on indwelling urinary catheters.

OBJECTIVE: To test the performance and acceptability of an early warning sensor to predict encrustation and blockage of long-term indwelling urinary catheters. PATIENTS AND METHODS: In all, 17 long-term indwelling catheter users, 15 'blockers' and two 'non-blockers' (controls) were recruited; 11 participants were followed prospectively until catheter change, three withdrew early and three did not start. Two sensors were placed in series between the catheter and the urine bag at catheter change. The sensor nearest the bag was changed at the same time as the bag change (weekly); the sensor nearest the catheter remained in situ for the duration of the catheter's life. Bacteriology and pH determinations were performed on urine samples at each bag, sensor and catheter change. The colour of the sensors was recorded daily. On removal, each sensor and the catheter were examined for visible evidence of encrustation and blockage. Participants were asked to keep a daily diary to record colour change and any other relevant observations and to complete a psychosocial impact of assistive devices tool at the end of the study. Participants and carers/healthcare professionals (when involved in urine bag or catheter change) were asked to complete a questionnaire about the sensor. RESULTS: Urease-producing bacteria were isolated from seven of the 14 patients (including early withdrawals; P. mirabilis in four, Morganella or Providencia in three). In six of the seven patients the sensors turned blue-black; two of these were early withdrawals, two went to planned catheter change (one of these was recruited as a 'non-blocker') and three had catheter blockage. The number of days of catheterisation before blockage was 22, 23 and 25 days, and the sensor changed colour within 24-48 h after insertion. The urine mean (range) pH of the sensors that turned blue-black was 7.6 (5.5-9.0) and of the sensors that remained yellow 6.1 (5.1-7.5). The sensor was generally well-received and was positive in the psychosocial assessment. CONCLUSIONS: The sensor is a useful indicator of urine pH and of the conditions that lead to catheter blockage. It may be particularly useful for new indwelling catheter users. To be a universally acceptable predictor of catheter blockage, the time from sensor colour change to blockage needs to be reduced.

Exoproducts of the Escherichia coli strain H22 inhibiting some enteric pathogens both in vitro and in vivo.

AIMS: The antagonistic activity of the Escherichia coli strain H22 against enteric bacteria was studied both in vitro and in vivo. METHODS AND RESULTS: In vitro, bacterial strains belonging to seven of nine genera of the family Enterobacteriaceae (Enterobacter, Escherichia, Klebsiella, Morganella, Salmonella, Shigella and Yersinia) were inhibited by the strain H22. Six days after simultaneous oral inoculation in germ-free mice, E. coli strain H22 reduced the faecal population of Shigella flexneri 4 to undetectable levels (P < 0.05). In ex vivo assay, inhibitory zones against Sh. flexneri 4 were observed around faecal samples from mice inoculated with E. coli strain H22. The in vitro inhibition of Sh. flexneri 4 was shown to be mediated by microcin C7. In addition to microcin C7, strain H22 was shown to produce aerobactin, new variants of colicins E1 and Ib, and bacteriophage particles with morphology similar to the phages of the family Myoviridae. CONCLUSIONS: Altogether, the properties of E. coli H22, observed both under in vitro and in vivo conditions, suggest its potential use as a probiotic strain for livestock and humans. SIGNIFICANCE AND IMPACT OF THE STUDY: The strain H22 was shown to produce several antimicrobial compounds with inhibitory capabilities against pathogenic or potentially pathogenic enterobacteria.