April 17, 2017

A light digest for Marathon Monday. For me, the highlights today are under “Microbes in the News”, with amazing papers on viral/bacterial detection, bacterial cell size, and cluster regulation!

Human nearly-sterile sites
Evidence for polymicrobial communities in explanted vascular filters and atheroma debris – Jeremy E. Ellis – Molecular and Cellular Probes

Plant, root, and soil microbiome
Global-scale structure of the eelgrass microbiome – Ashkaan K. Fahimipour – Applied Environmental Microbiology
Note: Published as a pre-print back on November 28, 2016

Built environment
Comparing the impact of ultrafine particles from petrodiesel and biodiesel combustion to bacterial metabolism by targeted HPLC-MS/MS metabolic profiling – Fanyi Zhong – Ecotoxicology and Environmental Safety

Revealing the bacterial profile of an anoxic-aerobic moving-bed biofilm reactor system treating a chemical industry wastewater – Joao P Bassin – International Biodeterioration & Biodegradation

Probiotics / prebiotics
An extracellular cell-attached pullulanase confers branched α-glucan utilization in human gut Lactobacillus acidophilus – Marie S Moller – Applied and Environmental Microbiology

Phages and viruses (and transfers)
Class 1 integrons as invasive species – Michael R Gillings – Current Opinion in Microbiology

Bioinformatics
MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers – Cedric Chauve – bioRxiv

Techniques
Validation and application of an ultrahigh-performance liquid chromatographic-Orbitrap mass spectrometric method for the simultaneous detection and quantification of volatile and non-volatile organic acids in human faecal samples – Claudio Gardana – Journal of Pharmaceutical and Biomedical Analysis

Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw – Jiang-Hao Tian – Bioresource Technology

Nanopore detection of bacterial DNA base modifications – Alexa B.R. McIntyre – bioRxiv

Microbes in the news
Novel CRISPR Tool Rapidly Detects Viruses And Bacteria – Milla Bengtsson – ReliaWire
Original paper: Nucleic acid detection with CRISPR-Cas13a/C2c2 – Jonathan S. Gootenberg – Science

Study discovers fundamental unit of cell size in bacteria – UCSD – EurekAlert
Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli – Fangwei Si – Current Biology

Mini-Factories For Drugs? Researchers Find A Way To Switch On ‘Silent’ Gene Clusters In Bacteria – Avaneesh Pandey – International Business Times
Original paper: Discovery of scmR as a global regulator of secondary metabolism and virulence in Burkholderia thailandensis E264 – Dainan Mao – PNAS

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