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Persistent memory as an effective alternative to random access memory in metagenome assembly

BackgroundThe assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method… [Read More]

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates… [Read More]

Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils

Acid sulfate soils release metal laden, acidic waters that affect the environment, buildings, and human health. In this study, 16S rRNA gene amplicons, metagenomes, and metatranscriptomes all demonstrated distinct microbial communities and activities in the unoxidized potential acid sulfate soil, the overlying transition zone, and uppermost oxidized actual acid sulfate soil. Assembled genomes and mRNA… [Read More]

Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the dominant fermentative producer of ethanol in industry and a preferred host for production of other biofuels. That said, rewiring the metabolism of S. cerevisiae to produce other fermentation products, such as isobutanol, remains an academic challenge. Many studies report aerobic production of isobutanol, but ethanol remains a substantial by-product under these… [Read More]

Environmental predictors of electroactive bacterioplankton in small boreal lakes

Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET’s function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake’s bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich… [Read More]

Poisson hurdle model-based method for clustering microbiome features

MOTIVATION: High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may… [Read More]