Gut microbiota in a healthy population is shaped by various geographic, demographic and lifestyle factors. Using the amplicon sequencing approach we analyzed bacterial and fungal gut communities in a Slovenian cohort of 186 healthy volunteers. We detected 27.852 OTUs corresponding to 253 bacterial genera and a total of 2.158 OTUs corresponding to 195 fungal genera, but the majority of these showed low prevalence and are likely transient foodborne contaminations. A core microbiome analysis revealed high consistency with previous studies, most prominently showing that genera Faecalibacterium, Bacteroides and Roseburia regularly comprise the core community. We report three significant questionnaire-based host covariates associated with microbiota composition. Bacterial community was associated with age and gender. More specifically, bacterial diversity was increased with age and was higher in the female population compared to male. The analysis of fungal community showed that more time dedicated to physical activity resulted in a higher fungal diversity and lower abundance of S. cerevisiae. This is likely dependent on different diets, which were reported by participants according to the respective rates of physical activity.
COBISS.SI-ID: 512875832
While in Bacteria, a working consensus of species circumscription may have been reached also at the genetic level, bacteriophage taxonomy is just being revised to achieve similar. In this work we use model group of bacteriophages to show that by using ANI we are able to group bacteriophages similarly to current ICTV scheme and further show existence of subgroups which could represent the fundamental natural unit of bacteriophages based on additional genetic analyses and available experimental data.
COBISS.SI-ID: 4063112
Disturbance in gut microbiota is crucial for the development of Clostridioides difficile infection (CDI). Different mechanisms through which gut microbiota influences C. difficile colonization are known. However, C. difficile could also affect gut microbiota balance as previously demonstrated by cultivation of fecal microbiota in C. difficile conditioned medium. In current study, the interactions of C. difficile cells with gut microbiota were addressed. Three different strains (ribotypes 027, 014/020, and 010) were co-cultivated with two types of fecal microbiota (healthy and dysbiotic) using in vitro batch model. While all strains showed higher sporulation frequency in the presence of dysbiotic fecal microbiota, the growth was strain dependent. C. difficile either proliferated to comparable levels in the presence of dysbiotic and healthy fecal microbiota or grew better in co-culture with dysbiotic microbiota. In co-cultures with any C. difficile strain fecal microbiota showed decreased richness and diversity. Dysbiotic fecal microbiota was more affected after co-culture with C. difficile than healthy microbiota. Altogether, 62 OTUs were significantly changed in co-cultures of dysbiotic microbiota/C. difficile and 45 OTUs in co-cultures of healthy microbiota/C. difficile. However, the majority of significantly changed OTUs in both types of microbiota belonged to the phylum Firmicutes with Lachnospiraceae and Ruminococcaceae origin.
COBISS.SI-ID: 512824376
In this study the antibiotic clindamycin and polyphenol extracts from pomegranate and blueberries were used individually and in combination to modulate fecal microbial communities in minibioreactor arrays (MBRA). Modulated communities were inoculated with C. difficile (ribotype 027). Subsequent 7-day periodical monitoring included evaluation of C. difficile growth and activity of toxins TcdA and TcdB as well as analysis of MBRA bacterial community structure (V3V4 16%S metagenomics). Polyphenols affected multiple commensal bacterial groups and showed different synergistic and antagonistic effects in combination with clindamycin. Exposure to either clindamycin or polyphenols led to the loss of colonization resistance against C. difficile. The successful growth of C. difficile was most significantly correlated with the decrease in Collinsella and Lachnospiraceae. Additionally, we demonstrated that Clostridium sporogenes decreased the activity of both C. difficile toxins TcdA and TcdB. The feature was shown to be common among distinct C. sporogenes strains and could potentially be applicable as a non-antibiotic agent for the alleviation of C. difficile infection.
COBISS.SI-ID: 16205827
Typical disease associated microbiota changes are widely studied as potential diagnostic or therapeutic targets. Our aim was to analyze a hospitalized cohort including a variety gastroenterological disorders in order to fine map the gut microbiota dysbiosis and its association with the underlying disease. Bacterial (V3V4) and fungal (ITS2) communities were determined in 121 hospitalized gastrointestinal patients from a single ward and compared to 162 healthy controls. Random forest models implemented in this study indicated that the gut community structure is in most cases not sufficient to differentiate the subjects based on their underlying disease. Instead, hospitalized patients in our study formed three distinct disease non-related clusters (C1, C2 and C3). Majority of the subjects (cluster C1) closely resembled healthy controls, showing only mild signs of community disruption; most significant was the decrease in Faecalibacterium and Roseburia. The remaining two clusters (C2 and C3) were characterized by severe signs of dysbiosis; custer C2 was associated with an increase in Enterobacteriaeceae and cluster C3 by an increase in Enterococcus. According to the cluster affiliation subjects also showed different degrees of inflammation, most prominent was the positive correlation between levels of C-reactive protein and the abundance of Enterococcus. Our results show that dysbiotic microbiota in hospitalized patients show decrease of core microbiota representatives and increase of groups often associated with antibiotic resistance (ESBL, VRE).
COBISS.SI-ID: 33165351