SEQanswers: an open access community for collaboratively decoding genomes

Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers

Can molecular DNA-based techniques unravel the truth about diabetic foot infections?

Diabetes foot infections (DFI) are a common condition and a major causal pathway to lower extremity amputation. Identification of causative pathogens is vital in directing antimicrobial therapy. Historically, clinicians have relied upon culture-dependent techniques that are now acknowledged as both being selective for microorganisms that thrive under the physiological and nutritional constraints of the microbiology laboratory, and that grossly underestimate the microbial diversity of a sample. The amplification and sequence analysis of the 16S rRNA gene has revealed a diversity of microorganisms in DFIs, extending the view of the diabetic foot microbiome. The interpretation of these findings and their relevance to clinical care remains largely unexplored. The advent of molecular methods that are culture-independent and employ massively parallel DNA sequencing technology represent a potential “game changer”. Metagenomics and its shotgun approach to surveying all DNA within a sample (whole genome sequencing, WGS) affords the possibility to characterize not only the microbial diversity within a DFI (i.e., “which microorganisms are present”) but the biological functions of the community such as virulence and pathogenicity (i.e., “what are the microorganisms capable of doing”), moving the focus from single species as pathogens to groups of species