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Title

Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean

AuthorsVidal, Roberto; Ginard, Daniel; Khorrami, Sam; Mora-Ruiz, Merit del Rocio; Muñoz, Raúl; Hermoso, Marcela; Díaz, Sara; Cifuentes, Ana ; Orfila, Alejandro ; Rosselló-Mora, Ramón
KeywordsCrohn disease
Pyrotagging
Operational phylogenetic units
Gut microbiome
Firmicutes
Faecalibacterium prausnitzii
Issue Date1-Sep-2015
PublisherElsevier
CitationSystematic and Applied Microbiology 38(6): 442-452 (2015)
Abstract© 2015 Elsevier GmbH. Next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16S rRNA diversity surveys than classical methods. However, the sequences are only partial and thus lack sufficient resolution for a reliable identification. The OPU approach used here, based on a tandem combination of high quality 454 sequences (mean >500 nuc) applying strict OTU thresholds, and phylogenetic inference based on parsimony additions to preexisting trees, seemed to improve the identification yields at the species and genus levels. A total of thirteen biopsies of Crohn-diagnosed patients (CD) and seven healthy controls (HC) were studied. In most of the cases (73%), sequences were affiliated to known species or genera and distinct microbial patterns could be distinguished among the CD subjects, with a common depletion of Clostridia and either an increased presence of Bacteroidetes (CD1) or an anomalous overrepresentation of Proteobacteria (CD2). Faecalibacterium prausnitzii presence was undetectable in CD, whereas Bacteroides vulgatus-B. dorei characterized HC and some CD groups. Altogether, the results showed that a microbial composition with predominance of Clostridia followed by Bacteroidetes, with F. prausnitzii and B. vulgatus-B. dorei as major key bacteria, characterized what could be considered a balanced structure in HC. The depletion of Clostridia seemed to be a common trait in CD.
Publisher version (URL)http://dx.doi.org/10.1016/j.syapm.2015.06.008
URIhttp://hdl.handle.net/10261/123567
DOI10.1016/j.syapm.2015.06.008
Identifiersdoi: 10.1016/j.syapm.2015.06.008
issn: 1618-0984
Appears in Collections:(IMEDEA) Artículos
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