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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

J48 decision tree describing the patterns of colonisation associated with presence or absence of C. difficile.Decision tree is showing only routine sample sets. The decision tree shows combinations of microbial groups that predict the outcome regarding C. difficile colonisation. The numbers in parentheses show the total number of samples and the number of incorrectly cassified instances, respectively.
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pone-0058005-g006: J48 decision tree describing the patterns of colonisation associated with presence or absence of C. difficile.Decision tree is showing only routine sample sets. The decision tree shows combinations of microbial groups that predict the outcome regarding C. difficile colonisation. The numbers in parentheses show the total number of samples and the number of incorrectly cassified instances, respectively.

Mentions: A decision tree was constructed by the J48 machine learning approach, based on the presence or absence of microbial groups, to predict the outcome regarding C. difficile colonisation. The resulting decision tree splits the samples by category first. We only discuss the part that refers to the routine samples, shown in Figure 6. This decision tree was built automatically from the data on the collected samples. Each internal node is labeled with a test on the presence/absence of a microbial group, while each terminal node (leaf) is labeled with the most frequent class/outcome (C. difficile 027/C.difficile other ribotypes/C. difficile negative). The numbers in parentheses provide an indication of the accuracy of the prediction made by the leaf (total number of samples in the leaf/incorrectly classified samples). The tree therefore summarizes the data on the samples and the results of their analysis, relating microbial group composition to the outcome.


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)

J48 decision tree describing the patterns of colonisation associated with presence or absence of C. difficile.Decision tree is showing only routine sample sets. The decision tree shows combinations of microbial groups that predict the outcome regarding C. difficile colonisation. The numbers in parentheses show the total number of samples and the number of incorrectly cassified instances, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0058005-g006: J48 decision tree describing the patterns of colonisation associated with presence or absence of C. difficile.Decision tree is showing only routine sample sets. The decision tree shows combinations of microbial groups that predict the outcome regarding C. difficile colonisation. The numbers in parentheses show the total number of samples and the number of incorrectly cassified instances, respectively.
Mentions: A decision tree was constructed by the J48 machine learning approach, based on the presence or absence of microbial groups, to predict the outcome regarding C. difficile colonisation. The resulting decision tree splits the samples by category first. We only discuss the part that refers to the routine samples, shown in Figure 6. This decision tree was built automatically from the data on the collected samples. Each internal node is labeled with a test on the presence/absence of a microbial group, while each terminal node (leaf) is labeled with the most frequent class/outcome (C. difficile 027/C.difficile other ribotypes/C. difficile negative). The numbers in parentheses provide an indication of the accuracy of the prediction made by the leaf (total number of samples in the leaf/incorrectly classified samples). The tree therefore summarizes the data on the samples and the results of their analysis, relating microbial group composition to the outcome.

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