Table of Contents Author Guidelines Submit a Manuscript
Gastroenterology Research and Practice
Volume 2013, Article ID 636785, 13 pages
http://dx.doi.org/10.1155/2013/636785
Research Article

Dominant Fecal Microbiota in Newly Diagnosed Untreated Inflammatory Bowel Disease Patients

1Hedmark University College, 2306 Hamar, Norway
2Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, 1432 Ås, Norway
3Department of Gastroenterology, Akershus University Hospital, 1478 Lørenskog, Norway
4Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Division of Medicine, Akershus University Hospital, University of Oslo, 0316 Oslo, Norway
5Pediatric Department, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
6Medical Clinic, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway

Received 30 April 2013; Revised 15 August 2013; Accepted 29 August 2013

Academic Editor: Akira Andoh

Copyright © 2013 Lill Therese Thorkildsen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Suppl Table 1: R2 values illustrating the correlation between the two replicates of PCR amplification, direct sequencing and MCR analysis for one hundred stool samples.

Suppl Table 2. R2 values illustrating the correlation between the two replicates of the direct sequencing and MCR analysis for ten random PCR products.

Suppl Table 3: Composition of the clone library. The table summarizes the classification obtained in the Ribosomal Database Project II Classifier for all diagnosis groups. The classifications shown here are at the phylum, order and genus level with the confidence threshold set at 80%.

Suppl Figure 1: Graphical illustration of the reproducibility of the method. PCR amplification of the same extracted DNA from stool samples, direct sequencing and subsequent MCR analysis was performed in replicates for all hundred stool samples. The amount of the components in replicate 1 and 2 are plotted against each other for every one of the components in separate graphs. The R2 values are shown for all components.

Suppl Figure 2: Graphical illustration of the reproducibility of the direct sequencing and MCR analysis. Direct sequencing and MCR analysis were repeated on the same PCR product for ten samples. The amount of the components in replicate 1 and 2 are plotted against each other for every one of the components in separate graphs. The R2 values are shown for all components.

Suppl Figure 3: Phylogenetic distribution of the clone library. Neighbor joining tree showing clusters of five phyla; Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. Multiple alignment was performed using the MUSCLE algorithm in CLC. The tree was constructed using the online tool BioNJ at Phylogeny.fr, and further visualized and edited using Dendroscope. Bootstrap values are based on 1000 replications. Sequences marked in red are covered by probes. The sequences are named according to hits from the Ribosomal Database Project Classifier, with a confidence threshold of 80%. In addition, the diagnoses CD (Crohn’s disease), UC (Ulcerative colitis) and Con (control) as well as the ID of the samples from which the clones originated are indicated.

Suppl Figure 4: Comparison between the MCR-predicted relative amount of each component in the cloned samples and the relative amount of colonies were the component was detected. Amplified 16S rRNA gene sequences from 15 stool samples were selected for cloning based on high relative amounts of each of the five MCR predicted components.

  1. Supplementary Materials