Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean.
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.
Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, CL 8380453, Chile.
Roberto
R
Vidal
Department of Gastroenterology and Palma Health Research Institute, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
Daniel
D
Ginard
Department of Gastroenterology and Palma Health Research Institute, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
Sam
S
Khorrami
Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), 07190 Illes Balears, Spain.
Merit
M
Mora-Ruiz
Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), 07190 Illes Balears, Spain.
Raul
R
Munoz
Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, CL 8380453, Chile.
Marcela
M
Hermoso
Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), 07190 Illes Balears, Spain.
Sara
S
Díaz
Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), 07190 Illes Balears, Spain.
Ana
A
Cifuentes
Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), 07190 Illes Balears, Spain.
Alejandro
A
Orfila
Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), 07190 Illes Balears, Spain. Electronic address: rossello-mora@uib.es.
Ramon
R
Rosselló-Móra
D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001706:Biopsy; D058448:Biota; D016000:Cluster Analysis; D003106:Colon / Q000382:microbiology*; D003424:Crohn Disease / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology*; D019083:Mediterranean Region; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
Crohn disease; Faecalibacterium prausnitzii; Firmicutes; Gut microbiome; Operational phylogenetic units; Pyrotagging