Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11,497 to 34,483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.

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The microbial content of air has as yet been little described, despite its public health implications, and there remains a lack of environmental microbial data on airborne microflora in enclosed spaces. In this context, the aim of this study was to characterize the diversity and dynamics of airborne microorganisms in the Louvre Museum using high-throughput molecular tools and to underline the microbial signature of indoor air in this human-occupied environment. This microbial community was monitored for 6 month during occupied time. The quantitative results revealed variations in the concentrations of less than one logarithm, with average values of 10(3) and 10(4) Escherichia coli/Aspergillus fumigatus genome equivalent per m(3) for bacteria and fungi, respectively. Our observations highlight the stability of the indoor airborne bacterial diversity over time, while the corresponding eukaryote community was less stable. Bacterial diversity characterized by pyrosequencing 454 showed high diversity dominated by the Proteobacteria which represented 51.1%, 46.9%, and 38.4% of sequences, for each of the three air samples sequenced. A common bacterial diversity was underlined, corresponding to 58.4% of the sequences. The core species were belonging mostly to the Proteobacteria and Actinobacteria, and to the genus Paracoccus spp., Acinetobacter sp., Pseudomonas sp., Enhydrobacter sp., Sphingomonas sp., Staphylococcus sp., and Streptococcus sp.

We report the first complete genome sequence of a Vitreoscilla filiformis strain (ATCC 15551) that is used in the cosmetic industry as Vitreoscilla ferment. The assembled genome consisted of one chromosome and two plasmids. These data will provide valuable information and important insights into the physiology of this filamentous organism.T he nonpathogenic aerobic Gram-negative Vitreoscilla filiformis bacterium was named on the basis of its colorless gliding filamentous morphology (1). In the Pyrénées mountains, V. filiformis was spotted in spa muds used for skin cures and subsequently fermented at an industrial scale for more than 20 years to generate a bacterial lysate introduced into emollients. Studies have shown that this V. filiformis extract improved atopic dermatitis (2-5) by increasing keratinocyte antioxidant manganese superoxide dismutase (MnSOD) mitochondrial content (6) through a still-unknown mechanism. Currently, only two Vitreoscilla scaffold genomes are available (Vitreoscilla stercoraria and Vitreoscilla massiliensis). Here, we present the first complete genome sequence of a V. filiformis strain (ATCC 15551).Genomic DNA was isolated using the Gentra Puregene kit (Qiagen) following the manufacturer's guidelines. Sequencing was performed by Genoscreen on a PacBio RS II system (Pacific Biosciences), following construction of a 10-kb SMRTbell library, and on a HiSeq 2500 system (Illumina), following construction of a 2-kb Nextera XT library. The generated long-read sequences (1,842,560,472 nucleotides; 116,681 reads) were de novo assembled using the single-molecule real-time (SMRT) analysis software version 2.3.0 followed by Circlator version 1.4.1 for circularization (7). The assembly quality was checked using 250-base paired-end short-read sequences (595,503,983 nucleotides; 1,250,485 reads) with BOWTIE2 version 2.1.0. The assembled genome comprised 3,765,551 bp, consisting of one chromosome (3,484,895 bp) and two plasmids, pVF1 (240,640 bp) and pVF2 (40,016 bp). Structural and functional annotations carried out by Genostar using a proprietary pipeline identified 6 rRNAs (5S, 16S, and 23S), 61 tRNAs, and 3,588 protein-coding sequences, of which 2,409 (67%) were annotated with known biological functions and 1,179 (33%) encode hypothetical proteins or uncharacterized proteins.The overall genome GC content (63.5%) fits that of a previous determination, ranging from 59 to 63% (1). The V. filiformis genome size (3.77 Mb) differs from those of the Vitreoscilla stercoraria (5.16 Mb, 43.9% GC) and Vitreoscilla massiliensis (7.43 Mb, 49.4% GC) genomes sequenced to date. The Vitreoscilla hemoglobin gene used in biotechnology processes is not present in the V. filiformis genome (8, 9). The V. filiformis bacterium is known to produce poly-␤-hydroxybutyrate (PHB) granules that can accumulate to greater than half of its dry weight (1). Genome analysis confirmed the presence of the PHB operon (phbA, phbB, and phbC) as well as its regulator phaR.

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