March 14, 2017

A short Digest today, many news pieces, a new bioinformatics tool from the Rob Knight lab, and papers on genome-scale metabolic models.

General microbiology

Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance – Jonathan M. Stokes – Nature Microbiology

Press: Antiprotozoal drug, Pentamidine, used with antibiotics effective against ‘superbugs’: McMaster research – Outbreak News Today

Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis – Gang Luo – Environmental Science & Technology

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families – Ana Popovic – Scientific Reports

Animal experiments

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis – Huijuan Jia – Scientific Reports

Animal microbiome

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants – Jon G. Sanders – bioRxiv

Plant, root, and soil microbiome

Book chapter – Chapter 16: Growth Promotion Features of the Maize Microbiome: From an Agriculture Perspective – Ubiana de Cássia Silva – Plant-Microbe Interaction: An Approach to Sustainable Agriculture

Metabolomics

Evaluating the Capabilities of Microbial Chemical Production Using Genome-Scale Metabolic Models – Hugh M. Purdy and Jennifer L. Reed – Current Opinion in Systems Biology

Model-based quantification of metabolic interactions from dynamic microbial-community data – Mark Hanemaaijer – PLoS One

Review: Current state and applications of microbial genome-scale metabolic models – Won Jun Kim – Current Opinion in Systems Biology

Bioinformatics

Deblur: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping – Amnon Amir – mSystems

Deblur: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns – Amnon Amir – mSystems

Microbes in the news

Common Bacteria May Control Disease-Carrying Insects – Jessica Berman – VOA

Study finds new evidence that viruses and bacteria may be found in some public water supply wells – Home Town Source

Your mobile phone has more germs than a toilet seat, but should you worry? – The News Minute

Mining nature for the next groundbreaking antibiotic – Julia Franz – PRI

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