Comparison of the cultured fungi identified by both MALDI-TOF MS and direct ITS sequencing.

<p>Comparison of the cultured fungi identified by both MALDI-TOF MS and direct ITS sequencing.</p

The different eukaryotes previously detected by molecular methods in the human gut using universal 18S rDNA or ITS primers.

*<p>Eukaryotes detected in both healthy and patient gut.</p>†<p>Eukaryotes detected only in patient gut.</p

Comparison of our molecular results and those obtained previously for the human stool samples [<b>8]</b>, [12], [14]–[16] using various universal primers.

<p>The universal primers used previously for the analysis of the human gut are indicated by the number of the reference. * indicates primers used for the first time to describe the human eukaryotic microbiota. Green color box = species positive in our sample and negative in the former studies; blue color box = species positive in both our sample and in the former studies; red color box = species negative in our sample and positive in the former studies.</p

Comparison between phenotypic and genotypic detection and identification.

<p>The number in the box indicates the number of clones obtained for each bacterial species in each sputum. C1, C2, C3, and C4 were control analysis. Blue color box = concordant results between PCR-cloning and culture; red color box = negative PCR-cloning and positive culture; green color box = positive PCR-cloning and negative culture; yellow color box = misidentified bacteria.</p

Box plot graph representing the number of detected bacterial species in the two groups of patients.

<p>Group 1 = patients to whom 24 clones from their sputa have been sequenced; Group 2 = patients to whom 40 clones from their sputa have been sequenced.</p

The bacterial diversity detected using the genomic methods.

*<p>Species that have been detected either in normal oral flora, endodontic/peridontic infections, VAP, or CF samples using T-RFLP or cloning <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002908#pone.0002908-Rogers1" target="_blank">[4]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002908#pone.0002908-Rogers2" target="_blank">[9]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002908#pone.0002908-Harris1" target="_blank">[11]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002908#pone.0002908-Sakamoto1" target="_blank">[13]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002908#pone.0002908-Aas1" target="_blank">[20]</a>.</p>†<p>First species detection in CF samples using cloning in this study.</p

Bacteria identified by the conventional culture methods in children (A) and in adults (B).

<p>Bacteria identified by the conventional culture methods in children (A) and in adults (B).</p

Additional file 1: Table S1. of Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.

Differential phenotypic characteristics between Microbacterium gorillae sp. nov. strain G3T and others Microbacterium strains. (DOCX 14 kb

Additional file 4:Â Folder S1. of Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.

Annotation results. (RAR 1566 kb

Additional file 3: Figure S2. of Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.

Gel view comparing Microbacterium gorillae strain G3T spectra with other members of the genus Microbacterium. The gel view displays the raw spectra of all loaded spectrum files arranged in a pseudo-gel like look. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a gray-scale scheme code. The color bar and the right y-axis indicate the relation between the color a peak is displayed with and the peak intensity in arbitrary units. Displayed species are indicated on the right. (PPTX 76 kb