The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain)

<div><p>We have analysed oral wash samples from 72 healthy young adults in Valencia (Spain) for a metagenomic analysis through the construction of shotgun libraries and high-throughput-sequencing. The oral viral communities have been taxonomically characterised as well as and the gene content from the latter. The majority of viruses are found in few individuals, with single occurrences being the most widespread ones, whereas universally distributed viruses, while present, are relatively rare, with bacteriophages from families <i>Siphoviridae</i> and <i>Myoviridae</i>, and <i>Streptococcus</i> phages, as well as the eukaryotic viral family <i>Herpesviridae</i> amongst the most widespread viruses. No significant differences were found between females and males for either viruses and bacteria in abundance and alpha and beta diversity. The virome show similarities with other oral viromes previously reported for healthy individuals, suggesting the existence of a universal core of oral viruses, at least in the Western society, regardless of the geographical location.</p></div

InterProScan annotation overview.

<p>Total number of matches and total number of unique protein names assigned by different annotation tools provided by InterProScan. This table summarizes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047654#pone.0047654.s003" target="_blank">Table S1</a>, which contains the whole list of protein matches in our assembly. The number of matches is higher than the number of unique protein names because one type of protein could be found in several contigs or one ORF could contain several matches to the same protein.</p

Results of reductive evolution simulations under nutrient-limited and nutrient-rich conditions.

<p>Results of reductive evolution simulations under nutrient-limited and nutrient-rich conditions.</p

Network reconstruction protocol.

<p>Schematic representation of the reconstruction of ancestral and extant genome-scale metabolic networks of <i>S. glossinidius</i>. For a detailed explanation of the protocol, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030652#pone.0030652.s009" target="_blank">Methods S1</a>.</p

ORFs with potential industrial or medical applications.

<p>Columns describe ORF annotations, contig identifiers and ORFs identifier.</p

<i>S. symbiotica</i> COG profile modification from FLS and between them.

<p><i>S. symbiotica</i> COG profile modification from FLS and between them.</p

Hybrid Sequencing Approach Applied to Human Fecal Metagenomic Clone Libraries Revealed Clones with Potential Biotechnological Applications

<div><p>Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be “domesticated” for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7–15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning <em>ad-hoc</em> biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.</p> </div

Pan-genome of <i>Serratia</i> spp.

<p>Euler diagram displaying the number of clusters found on each subspace of the pan-genome. The pan-genome defined here as the total collection of CDS clusters found in <i>S. symbiotica</i> SCc, <i>S. symbiotica</i> SAp, <i>S. proteamaculans</i> 568, <i>S. odorifera</i> 4R×13 and <i>S. marcescens</i> Db11 (first two obligate and facultative endosymbiont respectively and the rest free-living).</p

Species, accession numbers and genomic features comparison of <i>Serratia</i> spp. and selected <i>B. aphidicola</i> genomes.

<p>Species, accession numbers and genomic features comparison of <i>Serratia</i> spp. and selected <i>B. aphidicola</i> genomes.</p

Comparison of the genome characteristics and <i>in silico</i> metabolic networks of <i>S. glossinidius</i>, <i>B. aphidicola</i> APS and <i>E. coli</i> K12.

<p>Comparison of the genome characteristics and <i>in silico</i> metabolic networks of <i>S. glossinidius</i>, <i>B. aphidicola</i> APS and <i>E. coli</i> K12.</p