July 11, 2017

Welcome to your Tuesday Digest. Today, some interesting pieces from Science mag about scientific career. A few pre-prints in the Plant & Soil section, including a paper by Hubbard et al. that presents an interesting concept on plant’s diel cycle and rhizosphere community. Enjoy!

Events and jobs
Director, Sterile and Microbiology Quality Assurance Job
Merck – West Point – PA, US

Multi-site human microbiome
The influence of the commensal microbiota on distal tumor-promoting inflammation.
Buchta Rosean CM, Rutkowski MR – Seminars in Immunology

Human gut microbiome
Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life
Weili Xiong et al. – Microbiome

Genome-scale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle
Ottman N et al. – Applied Environmental Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy
Sivaranjani Namasivayam et al. – Microbiome

Animal experiments
Host specificity of Segmented Filamentous Bacteria (SFB) flagellins affects their interaction patterns with mouse ileal mucosal proteins.
Chen H et al. – Applied Environmental Microbiology

Plant, root, and soil microbiome
Pre-print: The plant circadian clock influences rhizosphere community structure and function
Charley Hubbard et al. – bioRxiv

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau
Zhu LX et al. – Ecotoxicology and Environmental Safety

Review: Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites
Thavamani P. et al – Environmental Pollution

Review: Microbial activity and the dynamics of ecosystem processes in forest soils
Baldrian P. – Current Opinion in Microbiology

Pre-print: Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth
Heather C. Manching et al. – bioRxiv

Water, estuarine and sediment microbiome
Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France)
Gautier Chaix et al. – Frontiers in Microbiology

Vertical and horizontal assemblage patterns of bacterial communities in a eutrophic river receiving domestic wastewater in southeast China.
Gao Y et al. – Environmental Pollution

Extremophile and space microbiome
Human presence impacts fungal diversity of inflated lunar/Mars analog habitat
A. Blachowicz et al. – Microbiome

Built environment
Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements
Guo J et al. – Water Research

Review: The potential implications of reclaimed wastewater reuse for irrigation on the agricultural environment: The knowns and unknowns of the fate of antibiotics and antibiotic resistant bacteria and resistance genes – A review.
Christou A et al – Water Research

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures.
Cai W. et al – Water Reseach

Pre-print: Cyanobacterial Growth on Municipal Wastewater Requires Low Temperatures
Travis C. Korosh et al. – bioRxiv

Microbial biotechnology
Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs
Qingjing Wang & Jian Sun et al. – Microbiome

General microbiology and evolution
Effect of a Pseudomonas fluorescens tailocin against phytopathogenic Xanthomonas observed by atomic force microscopy
M. Fernandez et al. – Journal of Biotechnology

Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation
Townsley L. & Shank EA – Trends in Microbiology

Bioinformatics and statistics
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Jie Ren & Nathan A. Algren et al. – Microbiome

Pre-print: A supervised statistical learning approach for accurate Legionella pneumophila source attribution during outbreaks
Andrew H. Buultjens et al. – bioRxiv

Review: Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
Key FM et al – Trends in Genetics

Techniques and methods
Formulation, stabilisation and encapsulation of bacteriophage for phage therapy
Malik DJ et al. – Advances in Colloid and Interface Science

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Eric J. de Muinck et al. – Microbiome

Microbes in the news
I gave my cat a poop transplant—here’s what happened next
Jonathan Gitlin – arstechnica

Gonorrhea is getting even harder to treat
Ashley Welch – CBS News

Science, publishing, and career
Reprogramming my career
Charmaine Tam – Science

The cyberscientist
John Bohannon – Science

The scientists’ apprentice
Tim Appenzeller – Science

Food and microbiota in the FDA regulatory framework
Jonathan M. Green et al. – Science


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