Just in time to end 2015 with a bang, mSystems has published its first batch of articles online. The publication includes three articles: an introductory essay by Editor-In-Chief Jack Gilbert and three research articles. Today’s launch makes mSystems the most recent open-access, online-only journal in ASM’s family of research journals.
mSystems will publish important biological and biochemical findings found through large-scale analyses, as well as computational and methodological discoveries to accelerate these breakthroughs. The first publications encompass both ends of this goal, with two “Methods and Protocols” papers and a “Research Article” rounding out this week’s publishings.
mSystems opens with an editorial in which Gilbert explains what systems biology is, how it applies to microbial sciences, and why he likes this approach of asking questions. The Senior Editorial Board, representing the leaders in microbial systems biology, has high hopes for mSystems’ technical and collaborative opportunities.
Novel System Biology Techniques
The first of the methods articles proposes a system for better-identified samples in high-throughput studies. The cual-id software program proposed by first author John H. Chase and lead author J. Gregory Casporaso generates 4- to 12-character identifiers that are short, centralized, legible, and unique within a project and the software is easy to install, easy to use, and free. The proposed nomenclature system eliminates many sources of human error and minimizes labeling time, since printing epindorf-friendly labels is part of the program (hooray! shout grad students everywhere).
The identification system also plays nice with other programs, such as Qiita and Integrated Microbial Genomes Data Warehouse. This means the cual-id system supports integrative data sharing across different software platforms. Each sample is tied to a universally unique identifier (UUID), from which each CualID of necessary length can be pulled. Any lab wishing to implement a more systematic method for sample nomenclature is welcome to check out and use the software.
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The manuscript from co-first authors William Walters and Embriette R. Hyde represents a large collaboration, with researchers from eleven institutions represented. The problem being addressed: How do primer modifications affect results? 16S rRNA gene primers can carry biases in their amplification preferences. The primers used by the Earth Microbiome Project, for example, have recently been shown to carry biases against several environmental archaeal and bacterial species. Newly generated (and previously published) primers reduce these biases, but do these new primers replicate previously-observed data?
The scientific team compared several primer sets for 16S rRNA and ITS amplification. They compared results from several previously recorded studies, including studies such as the skin microbiome, agricultural soil, and decomposition samples. The modified ITS primers, used for fungal sequencing, increased the number of reads by nearly double, although they did affect the taxonomies amplified for some studies. However, the bacterial 16S rRNA primers showed highly similar results with similar relative abundances. These results demonstrate no detrimental biases introduced by the primer modifications, and set the stage for the use of these primer pairs for future sequencing-based surveys.
Ecological and Evolutionary Science
The purple nonsulfur photosynthetic bacterium Rhodopseudomonas palustris uses different light-harvesting protein complexes to harvest light energy from different intensities. Several pucBA operons encode the α and β peptides composing these light-harvesting complexes, but it was unclear how much variation exists in sequence, structure, and transcriptional activity of these genes and their products. Kathryn R. Fixen, Yasuhiro Oda, and lead author Caroline S. Harwood used an integrative genomics approach to understanding gene diversity in this group.
The scientists compared the light-harvesting genes in the genomes of 20 strains of Rhodopseudomonas grown under different light intensities. Their data suggest that complexes adapted to high-light intensity can partially compensate for those adapted to low-light intensity, but only to certain extremes, necessitating multiple complexes per strain. The unique combinations of differently-adapted complexes in each Rhodopseudomonas strain likely represents its specific water- or soil-based niche, which includes a specific light exposure level, conclude the authors.
Check out mSystems for abstracts, PDFs, and supplementary data for all the above articles – and check back soon for newly published papers, released here at mSystems!
-- Julie Wolf