Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load

Abstract

Data concerning the human microbiota composition during Clostridioides (Clostridium) difficile infection (CDI) using next-generation sequencing are still limited. We aimed to confirm key features indicating tcdB positive patients and compare the microbiota composition between subgroups based on toxin gene load ( tcdB gene) and presence of significant diarrhea. Ninety-nine fecal samples from 79 tcdB positive patients and 20 controls were analyzed using 16S rRNA gene sequencing. Chao1 index for alpha diversity were calculated and principal coordinate analysis was performed for beta diversity using Quantitative Insights into Microbial Ecology (QIIME) pipeline. The mean relative abundance in each group was compared at phylum, family, and genus levels. There were significant alterations in alpha and beta diversity in tcdB positive patients (both colonizer and CDI) compared with those in the control. The mean Chao1 index of tcdB positive patients was significantly lower than the control group ( P <0.001), whereas there was no significant difference between tcdB groups and between colonizer and CDI. There were significant differences in microbiota compositions between tcdB positive patients and the control at phylum, family, and genus levels. Several genera such as Phascolarctobacterium , Lachnospira , Butyricimonas , Catenibacterium , Paraprevotella , Odoribacter , and Anaerostipes were not detected in most CDI cases. We identified several changes in the microbiota of CDI that could be further evaluated as predictive markers. Microbiota differences between clinical subgroups of CDI need to be further studied in larger controlled studies.

A unique and reliable fecal DNA extraction method for 16S rRNA gene and shotgun metagenomic sequencing in the analysis of the human gut microbiome

“…We observed a lower microbial diversity for CDI + patients compared to healthy volunteers (Data not shown), con rming the results of previous studies [74]. As a considerable variability was found within each group of individuals, we corrected the individual effect in the statistical model to emphasize differences between extraction protocols.…”

Gut microbiome features associated withClostridium difficilecolonization in puppies

“…We found C. difficile -positive samples to be enriched with members of the Escherichia, Bacteroides, Enterococcus and Parabacteroides genera, and C. difficile -negative samples with members of the Prevotella, Megamonas , and Streptococcus genera. Almost identical trends were found for taxa of the Escherichia, Parabacteroides, Enterococcus, Prevotella and Megamonas genera in one study comparing C. difficile non-colonized, asymptomatically colonized and infected human adults (19), and for taxa of the Parabacteroides, Prevotella, Paraprevotella and Enterococcus genera in another study of non-colonized and colonized adults (38). Similar findings were found for the Bacteroides genera in a study of human infants (39) .…”

“…Asymptomatic carriage of C. difficile is common in young animals of many species, including humans, dogs, pigs, and horses. In people, colonization with C. difficile has been shown to be associated with altered gut microbial diversity (17, 19, 36–38), but no studies have examined this association in dogs. We found that the association between lower bacterial community diversity and C. difficile colonization was statistically significant even when accounting for age, and certain bacterial taxa were preferentially associated with C. difficile colonization.…”

“…Similar findings were found for the Bacteroides genera in a study of human infants (39) . In particular, increased relative abundances of taxa from the Parabacteroides and Enterococcus genera are thought to be the result of a blooming phenomenon associated with reduced ecological niche competition in people with CDI (38, 43, 44).…”

Le transfert de microbiote fécal : quel potentiel thérapeutique dans le traitement des maladies métaboliques ?

“…Le nombre d'espèces présentes dans le microbiote des patients atteins d'infection récidivante à Cd est diminuée d'environ 40 % par rapport aux individus sains(35). L'abondance de plusieurs genres bactériens constitutifs du "core microbiome", c'est-àdire l'ensemble des espèces présentes chez tous les individus sains, est considérablement diminuée(36). La TMF restaure la diversité du microbiote intestinal ainsi que son effet barrière contre la colonisation par des pathogènes et permet ainsi une amélioration clinique dans 80 à 90 % des cas et une rémission complète un mois après l'intervention dans 60 % des cas(37- 39).…”