Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.

Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within bacterial communities, both abundant and rare. We collected composite soil samples over 2 years from an experimentally maintained pH gradient ranging from 4.5 to 7.

AXIOME: automated exploration of microbial diversity.

Background: Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.

Findings: AXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur.

Targeted recovery of novel phylogenetic diversity from next-generation sequence data.

Next-generation sequencing technologies have led to recognition of a so-called 'rare biosphere'. These microbial operational taxonomic units (OTUs) are defined by low relative abundance and may be specifically adapted to maintaining low population sizes. We hypothesized that mining of low-abundance next-generation 16S ribosomal RNA (rRNA) gene data would lead to the discovery of novel phylogenetic diversity, reflecting microorganisms not yet discovered by previous sampling efforts.

PANDAseq: paired-end assembler for illumina sequences.

Background: Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.

Results: PANDAseq assembles paired-end reads rapidly and with the correction of most errors.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Microbial communities host unparalleled taxonomic diversity. Adequate characterization of environmental and host-associated samples remains a challenge for microbiologists, despite the advent of 16S rRNA gene sequencing. In order to increase the depth of sampling for diverse bacterial communities, we developed a method for sequencing and assembling millions of paired-end reads from the 16S rRNA gene (spanning the V3 region; ∼200 nucleotides) by using an Illumina genome analyzer.

Nucleic acid contamination of glycogen used in nucleic acid precipitation and assessment of linear polyacrylamide as an alternative co-precipitant.

Molecular-grade glycogen is widely used to recover nanogram or picogram quantities of DNA and RNA across molecular biology applications in the life sciences. As a result, its purity is critical to obtain reliable results. Using agarose gel electrophoresis, we detected pg/microL (DNA) to ng/microL (RNA) concentrations of nucleic acid in two of the nine glycogen samples obtained from commercial suppliers.

What is worse for your sex life: starving, being depressed, or a new baby?

Objective: To compare the current sexual functioning of women in an intimate relationship with anorexia nervosa, with major depression, and in the postpartum period.

Method: Complete data were available for 76 women who reported being in an intimate relationship (anorexia = 10; depression = 24; postpartum = 42). Sexual functioning was assessed using the Social Adjustment Scale (Weissman and Bothwell, Arch Gen Psychiatry, 33, 1111-1115, 1976).