Biology subjects

Singer, S. W.

Publications and source records attributed to Singer, S. W..

2 recordsLinked to original sources

bioRxiv2017

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes

Native plasmids constitute a major category of extrachromosomal DNA elements responsible for harboring and transferring genes important in survival and fitness. A focused evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We examined the plasmid DNA from two pristine wells at the Oak Ridge Field Research Center. Using a cultivation-free method that targets plasmid DNA, a total of 42,440 and 32,232 (including 67 and 548 complete circular units) scaffolds > 2 kb were obtained from the two wells. The taxonomic distribution of bacteria in the two wells showed greater similarity based on their plasmidome sequence, relative to 16S rRNA sequence comparison. This similarity is also evident in the plasmid encoded functional genes. Among functionally annotated genes, candidates providing resistance to copper, zinc, cadmium, arsenic, and mercury were particularly abundant and common to the plasmidome of both wells. The primary function encoded by the most abundant circularized plasmid, common to both wells, was mercury resistance, even though the current ground water does not contain detectable levels of mercury. This study reveals that the plasmidome can have a unique ecological role in maintaining the latent capacity of a microbiome enabling rapid adaptation to environmental stresses.

microbiology↗

bioRxiv2017

Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.

bioinformatics↗