Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease

Alessandra Lo Presti, Francesca Zorzi, Federica Del Chierico, Annamaria Altomare, Silvia Cocca, Alessandra Avola, Fabiola De Biasio, Alessandra Russo, Eleonora Cella, Sofia Reddel, Emma Calabrese, Livia Biancone, Giovanni Monteleone, Michele Cicala, Silvia Angeletti, Massimo Ciccozzi, Lorenza Putignani, Michele Pier Luca Guarino

Research output: Contribution to journalArticle

Abstract

An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.

Original languageEnglish
Pages (from-to)1655
JournalFrontiers in Microbiology
Volume10
DOIs
Publication statusPublished - 2019

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Irritable Bowel Syndrome
Microbiota
Inflammatory Bowel Diseases
Biomarkers
Discriminant Analysis
rRNA Genes
Enterococcaceae
Mucous Membrane
Gammaproteobacteria
Enterococcus
Homeostasis
Prospective Studies
Bacteria

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Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease. / Lo Presti, Alessandra; Zorzi, Francesca; Del Chierico, Federica; Altomare, Annamaria; Cocca, Silvia; Avola, Alessandra; De Biasio, Fabiola; Russo, Alessandra; Cella, Eleonora; Reddel, Sofia; Calabrese, Emma; Biancone, Livia; Monteleone, Giovanni; Cicala, Michele; Angeletti, Silvia; Ciccozzi, Massimo; Putignani, Lorenza; Guarino, Michele Pier Luca.

In: Frontiers in Microbiology, Vol. 10, 2019, p. 1655.

Research output: Contribution to journalArticle

Lo Presti, A, Zorzi, F, Del Chierico, F, Altomare, A, Cocca, S, Avola, A, De Biasio, F, Russo, A, Cella, E, Reddel, S, Calabrese, E, Biancone, L, Monteleone, G, Cicala, M, Angeletti, S, Ciccozzi, M, Putignani, L & Guarino, MPL 2019, 'Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease', Frontiers in Microbiology, vol. 10, pp. 1655. https://doi.org/10.3389/fmicb.2019.01655
Lo Presti, Alessandra ; Zorzi, Francesca ; Del Chierico, Federica ; Altomare, Annamaria ; Cocca, Silvia ; Avola, Alessandra ; De Biasio, Fabiola ; Russo, Alessandra ; Cella, Eleonora ; Reddel, Sofia ; Calabrese, Emma ; Biancone, Livia ; Monteleone, Giovanni ; Cicala, Michele ; Angeletti, Silvia ; Ciccozzi, Massimo ; Putignani, Lorenza ; Guarino, Michele Pier Luca. / Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease. In: Frontiers in Microbiology. 2019 ; Vol. 10. pp. 1655.
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AU - Zorzi, Francesca

AU - Del Chierico, Federica

AU - Altomare, Annamaria

AU - Cocca, Silvia

AU - Avola, Alessandra

AU - De Biasio, Fabiola

AU - Russo, Alessandra

AU - Cella, Eleonora

AU - Reddel, Sofia

AU - Calabrese, Emma

AU - Biancone, Livia

AU - Monteleone, Giovanni

AU - Cicala, Michele

AU - Angeletti, Silvia

AU - Ciccozzi, Massimo

AU - Putignani, Lorenza

AU - Guarino, Michele Pier Luca

PY - 2019

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N2 - An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.

AB - An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.

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