Gut Microbiota Patterns Associated with Colonization of Different Clostridium difficile Ribotypes

Abstract

C. difficile infection is associated with disturbed gut microbiota and changes in relative frequencies and abundance of individual bacterial taxons have been described. In this study we have analysed bacterial, fungal and archaeal microbiota by denaturing high pressure liquid chromatography (DHPLC) and with machine learning methods in 208 faecal samples from healthy volunteers and in routine samples with requested C. difficile testing. The latter were further divided according to stool consistency, C. difficile presence or absence and C. difficile ribotype (027 or non-027). Lower microbiota diversity was a common trait of all routine samples and not necessarily connected only to C. difficile colonisation. Differences between the healthy donors and C. difficile positive routine samples were detected in bacterial, fungal and archaeal components. Bifidobacterium longum was the single most important species associated with C. difficile negative samples. However, by machine learning approaches we have identified patterns of microbiota composition predictive for C. difficile colonization. Those patterns also differed between samples with C. difficile ribotype 027 and other C. difficile ribotypes. The results indicate that not only the presence of a single species/group is important but that certain combinations of gut microbes are associated with C. difficile carriage and that some ribotypes (027) might be associated with more disturbed microbiota than the others.

Alteration of the Murine Gastrointestinal Microbiota by Tigecycline Leads to Increased Susceptibility to Clostridium difficile Infection

“…Murine gut microbial structures that allow for C. difficile colonization are commonly associated with an increase in members from the Proteobacteria phylum (Enterobacteriaceae family) and a decrease in overall diversity (6,7,33). This is consistent with human studies in which high levels of Proteobacteria and low levels of Bacteroidetes in the gut microbiota were associated with C. difficile colonization (34)(35)(36)(37)(38)(39).…”

Microbial and metabolic interactions between the gastrointestinal tract andClostridium difficileinfection

“…[83][84][85][86][87] Only a handful of studies have detailed the structure of the human gut microbiota after C. difficile infection, and human samples prior to CDI are limited ( Table 2). [88][89][90][91][92][93] The most recent study comes from Antharam et al 2013 who compared the fecal microbiota of healthy subjects (n = 40) to those with antibiotic-associated diarrhea (AAD, n = 36) and C. difficile infection (CDI, n = 39). 88 Decreased microbial diversity and species richness was observed in the fecal microbiota of AAD and CDI cases compared with healthy controls.…”

Preclinical Studies of Amixicile, a Systemic Therapeutic Developed for Treatment of Clostridium difficile Infections That Also Shows Efficacy against Helicobacter pylori

“…In contrast, many of these bacteria are susceptible to fidaxomicin and vancomycin (21). Several studies found a greater abundance of members of the genus Bifidobacterium in the feces of individuals considered resistant to CDI infection than in the feces of those susceptible to recurrence (22,23). Many of these human microbiome studies of CDI and controls reveal substantial changes in the complex gut microflora but have yet to correlate these changes with specific antibiotic therapy.…”