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Gut microbiota patterns associated with colonization of different Clostridium difficile ribotypes.

Skraban J, Dzeroski S, Zenko B, Mongus D, Gangl S, Rupnik M - PLoS ONE (2013)

Bottom Line: Bifidobacterium longum was the single most important species associated with C. difficile negative samples.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.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Medicine, University of Maribor, Maribor, Slovenia.

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.

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Related in: MedlinePlus

Bacterial DHPLC profiles of all seven sets of samples.Bacterial microbiota in healthy individuals is composed of a large number of species, hence the peaks are numerous but the area below each peak is small. The presence of C. difficile correlates with decreased diversity reflected by a lower number of peaks which are, however, more prominent.
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pone-0058005-g003: Bacterial DHPLC profiles of all seven sets of samples.Bacterial microbiota in healthy individuals is composed of a large number of species, hence the peaks are numerous but the area below each peak is small. The presence of C. difficile correlates with decreased diversity reflected by a lower number of peaks which are, however, more prominent.

Mentions: Bacterial microbiota was most complex (Fig. 1c, Fig. 3). Altogether we have identified 23 different bacterial groups. Some chromatographic peaks were assigned to more than one genus because they either contained mixed sequences, or because the short sequences used in the DHPLC analysis did not allow distinction between them (e.g. Clostridium difficile/Sporacetigenium sp.; Citrobacter freundii/Enterobacter sp.; Streptococcus sp./Enterococcus sp. 1 and 2). Bacterial groups that were identified to the same genus or family but had different retention times were designated by a number (Enterobacteriaceae 1, 2 and 3; Bacteroides sp. 1 and 2, Streptococcus sp./Enterococcus sp. 1 and 2). Because short fragments are used in the DHPLC analysis further identification of particular amplified fraction was not possible. The remaining identified groups were Clostridium sp., Peptostreptococcaceae, Blautia sp., Ruminococcus bromii, Ruminococcus sp., Faecalibacterium sp., Klebsiella pneumonia; Escherichia/Shigella sp., Prevotella sp., Alistipes sp., Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium longum and Bifidobacterium sp.


Gut microbiota patterns associated with colonization of different Clostridium difficile ribotypes.

Skraban J, Dzeroski S, Zenko B, Mongus D, Gangl S, Rupnik M - PLoS ONE (2013)

Bacterial DHPLC profiles of all seven sets of samples.Bacterial microbiota in healthy individuals is composed of a large number of species, hence the peaks are numerous but the area below each peak is small. The presence of C. difficile correlates with decreased diversity reflected by a lower number of peaks which are, however, more prominent.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585249&req=5

pone-0058005-g003: Bacterial DHPLC profiles of all seven sets of samples.Bacterial microbiota in healthy individuals is composed of a large number of species, hence the peaks are numerous but the area below each peak is small. The presence of C. difficile correlates with decreased diversity reflected by a lower number of peaks which are, however, more prominent.
Mentions: Bacterial microbiota was most complex (Fig. 1c, Fig. 3). Altogether we have identified 23 different bacterial groups. Some chromatographic peaks were assigned to more than one genus because they either contained mixed sequences, or because the short sequences used in the DHPLC analysis did not allow distinction between them (e.g. Clostridium difficile/Sporacetigenium sp.; Citrobacter freundii/Enterobacter sp.; Streptococcus sp./Enterococcus sp. 1 and 2). Bacterial groups that were identified to the same genus or family but had different retention times were designated by a number (Enterobacteriaceae 1, 2 and 3; Bacteroides sp. 1 and 2, Streptococcus sp./Enterococcus sp. 1 and 2). Because short fragments are used in the DHPLC analysis further identification of particular amplified fraction was not possible. The remaining identified groups were Clostridium sp., Peptostreptococcaceae, Blautia sp., Ruminococcus bromii, Ruminococcus sp., Faecalibacterium sp., Klebsiella pneumonia; Escherichia/Shigella sp., Prevotella sp., Alistipes sp., Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium longum and Bifidobacterium sp.

Bottom Line: Bifidobacterium longum was the single most important species associated with C. difficile negative samples.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.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Medicine, University of Maribor, Maribor, Slovenia.

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.

Show MeSH
Related in: MedlinePlus