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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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Principal component analysis of DHPLC profiles of dominant bacterial, fungal and archaeal species.Individual samples (represented by black dots) were clustered into sets according to C. difficile presence and type, origin and consistency (elipses) and the centre of gravity computed for each set of samples. All sets of samples show large dispersion and overlap (elipses). Figure 4a compares the samples sent for routine C.difficile testing (pat) and healthy donors (hea). Particularly the former set shows a great dispersion. Figures 4b, c and d compare different sets of samples from the patients. Figure 4b shows comparison of six different sets of routine samples; a greater shift in the centre of gravity between the formed and the diarrhoeal C. difficile negative samples (FNP/DNP), compared to the C. difficile positive samples (FOS/DOS, F027/D027). Fig 4c shows only the subset of different routine diarrheic samples. Fig 4d shows only the subset of different routine formed samples DNP - diarrhoeal/C. difficile negative samples, D27 - diarrhoeal/C. difficile ribotype 027 positive samples, DOS–diarrhoeal/C. difficile other ribotypes positive samples, FNP - formed stool/C. difficile negative samples, F27 - formed stool/C. difficile ribotype 027 positive samples, FOS - formed stool/C. difficile other ribotypes positive samples, pat - samples sent for routine C. difficile testing, hea - healthy donors).
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pone-0058005-g004: Principal component analysis of DHPLC profiles of dominant bacterial, fungal and archaeal species.Individual samples (represented by black dots) were clustered into sets according to C. difficile presence and type, origin and consistency (elipses) and the centre of gravity computed for each set of samples. All sets of samples show large dispersion and overlap (elipses). Figure 4a compares the samples sent for routine C.difficile testing (pat) and healthy donors (hea). Particularly the former set shows a great dispersion. Figures 4b, c and d compare different sets of samples from the patients. Figure 4b shows comparison of six different sets of routine samples; a greater shift in the centre of gravity between the formed and the diarrhoeal C. difficile negative samples (FNP/DNP), compared to the C. difficile positive samples (FOS/DOS, F027/D027). Fig 4c shows only the subset of different routine diarrheic samples. Fig 4d shows only the subset of different routine formed samples DNP - diarrhoeal/C. difficile negative samples, D27 - diarrhoeal/C. difficile ribotype 027 positive samples, DOS–diarrhoeal/C. difficile other ribotypes positive samples, FNP - formed stool/C. difficile negative samples, F27 - formed stool/C. difficile ribotype 027 positive samples, FOS - formed stool/C. difficile other ribotypes positive samples, pat - samples sent for routine C. difficile testing, hea - healthy donors).

Mentions: To compare the faecal profiles of the dominant microbiota in the seven sets of samples, we first used PCA to calculate the spatial coordinates of each sample (Fig. 4). All sets of samples showed a large dispersion, particularly samples sent for routine C. difficile testing (Fig. 4a). Although the centres of gravity were different for samples from healthy persons and for routine samples, they also substantially overlapped (Fig. 4a). The result was similar when we compared the samples based on appearance (diarrhoea/formed) and C. difficile colonisation status (Fig. 4b, c and d).


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)

Principal component analysis of DHPLC profiles of dominant bacterial, fungal and archaeal species.Individual samples (represented by black dots) were clustered into sets according to C. difficile presence and type, origin and consistency (elipses) and the centre of gravity computed for each set of samples. All sets of samples show large dispersion and overlap (elipses). Figure 4a compares the samples sent for routine C.difficile testing (pat) and healthy donors (hea). Particularly the former set shows a great dispersion. Figures 4b, c and d compare different sets of samples from the patients. Figure 4b shows comparison of six different sets of routine samples; a greater shift in the centre of gravity between the formed and the diarrhoeal C. difficile negative samples (FNP/DNP), compared to the C. difficile positive samples (FOS/DOS, F027/D027). Fig 4c shows only the subset of different routine diarrheic samples. Fig 4d shows only the subset of different routine formed samples DNP - diarrhoeal/C. difficile negative samples, D27 - diarrhoeal/C. difficile ribotype 027 positive samples, DOS–diarrhoeal/C. difficile other ribotypes positive samples, FNP - formed stool/C. difficile negative samples, F27 - formed stool/C. difficile ribotype 027 positive samples, FOS - formed stool/C. difficile other ribotypes positive samples, pat - samples sent for routine C. difficile testing, hea - healthy donors).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585249&req=5

pone-0058005-g004: Principal component analysis of DHPLC profiles of dominant bacterial, fungal and archaeal species.Individual samples (represented by black dots) were clustered into sets according to C. difficile presence and type, origin and consistency (elipses) and the centre of gravity computed for each set of samples. All sets of samples show large dispersion and overlap (elipses). Figure 4a compares the samples sent for routine C.difficile testing (pat) and healthy donors (hea). Particularly the former set shows a great dispersion. Figures 4b, c and d compare different sets of samples from the patients. Figure 4b shows comparison of six different sets of routine samples; a greater shift in the centre of gravity between the formed and the diarrhoeal C. difficile negative samples (FNP/DNP), compared to the C. difficile positive samples (FOS/DOS, F027/D027). Fig 4c shows only the subset of different routine diarrheic samples. Fig 4d shows only the subset of different routine formed samples DNP - diarrhoeal/C. difficile negative samples, D27 - diarrhoeal/C. difficile ribotype 027 positive samples, DOS–diarrhoeal/C. difficile other ribotypes positive samples, FNP - formed stool/C. difficile negative samples, F27 - formed stool/C. difficile ribotype 027 positive samples, FOS - formed stool/C. difficile other ribotypes positive samples, pat - samples sent for routine C. difficile testing, hea - healthy donors).
Mentions: To compare the faecal profiles of the dominant microbiota in the seven sets of samples, we first used PCA to calculate the spatial coordinates of each sample (Fig. 4). All sets of samples showed a large dispersion, particularly samples sent for routine C. difficile testing (Fig. 4a). Although the centres of gravity were different for samples from healthy persons and for routine samples, they also substantially overlapped (Fig. 4a). The result was similar when we compared the samples based on appearance (diarrhoea/formed) and C. difficile colonisation status (Fig. 4b, c and d).

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