May 16, 2017

Our Tuesday Digest came a bit late but still it is packed with content! Lots going on, specially in the Plant & Soil Microbiome section. Good reading!

Events and jobs

Scientist for Food Microbiology and Modelling – nationale vacaturebank (Link in Dutch)

General human microbiome

The Threat of Antimicrobial Resistance on the Human Microbiome
Lauren Brinkac et al – Microbial Ecology

Human epitelial microbiome

Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences
Emily K. Cope et al – Microbiome

Review: Is the role of human female reproductive tract microbiota underestimated?
D. Kaminska & M. Gajecka – Beneficial Microbes

Human gut microbiome

Uncovering the trimethylamine-producing bacteria of the human gut microbiota
Silke Rath et al – Microbiome

Pre-print: The effect of treatment on the microbiota of patients diagnosed with colonic lesions
Marc A Sze et al – bioRxiv

Microbial diseases

Targeted Metagenome Based Analyses Show Gut Microbial Diversity of Inflammatory Bowel Disease patients
Zhibing Qiu et al – Indian Journal of Microbiology

Report: Zinc metalloproteinase ZmpC suppresses experimental pneumococcal meningitis by inhibiting bacterial invasion of central nervous systems
Masaya Yamaguchi et al – Virulence

Review: Fungal Biofilms and Polymicrobial Diseases
Caroline B. Costa-Orlandi et al – Journal of Fungi

Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma
Nezar Noor Al-hebshi et al – Scientific Reports

Identification of Atypical El Tor V. cholerae O1 Ogawa Hosting SXT Element in Senegal, Africa
Bissoume Sambe-Ba et al – Frontiers in Microbiology

General environmental microbiome

Following Rapoport’s Rule: The geographic range and genome size of bacterial taxa decline at warmer latitudes
Gavin Lear et al – Environmental Microbiology

Animal experiments

Examining the efficacy of intravenous administration of predatory bacteria in rats
Kenneth Shatzkes et al – Scientific Reports

Animal microbiome

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats
James T. Price et al – PLoS One

Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors
Dagne Duguma et al – Microbial Ecology

Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health
Nilusha Malmuthuge & Le Luo Guan – Journal of Dairy Science

Pre-print: Uncovering the drivers of animal-host microbiotas with joint distribution modeling
Johannes R. Björk – bioRxiv

Plant, root, and soil microbiome

Ecology and Genomic Insights on Plant-Pathogenic and -Nonpathogenic Endophytes
Günter Brader et al – Annual Review of Phytopathology

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis
Z Song et al – Weed Research

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region
Dominika Chmolowska et al – Science of the Total Environment

Microbial Community Dynamics in Soil Depth Profiles over 120,000 Years of Ecosystem Development
Stephanie Turner et al – Frontiers in Microbiology

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions
Stilianos Louca et al – Environmental Microbiology

Thesis: Culture-Independent Analysis of Microbial Communities Associated with Hydroponically Grown “Living Lettuce”
Abby Matthews – The University of Mississippi

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling
Jun Li et al – Environmental Pollution

Review: The influence of bacteria on multi-trophic interactions among plants, psyllids, and pathogen
Cecilia Tamborindeguy et al – Insect Science

Pre-print: Yeasts dominate soil fungal communities in three lowland Neotropical rainforests
Micah Dunthorn et al – bioRxiv

Bacterial inoculants for enhanced seed germination of Spartina densiflora: Implications for restoration of metal polluted areas
Paredes-Páliz K et al – Marine Pollution Bulletin

A Phloem-Feeding Insect Transfers Bacterial Endophytic Communities between Grapevine Plants
Sebastiàn Lòpez-Fernàndez et al – Frontiers in Microbiology

Water, estuarine and sediment microbiome

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)
Jessica M. Morrison et al – PLoS One

Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting
Megan J. Huggett et al – FEMS Microbiology Ecology

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond
Aurélien Saghaï et al – Environmental Microbiology

Extremophile and space microbiome

Thesis: Microbial Biogeography of the Arctic Cryosphere
Aviaja Zenia Edna Lyberth Hauptmann & Thomas Sicheritz-Pontén – Technical University of Denmark

Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis
F. Mandelli et al – Extremophiles

Aspergillus atacamensis and A. salisburgensis: two new halophilic species from hypersaline/arid habitats with a phialosimplex-like morphology
Livia Martinelli et al – Extremophiles

Built environment

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants
Wei Chen et al – Environmental Science and Pollution Research

Microbiota and Particulate Matter Assessment in Portuguese Optical Shops Providing Contact Lens Services
Carla Viegas et al – Healthcare

QAC modified PVDF membranes: Antibiofouling performance, mechanisms, and effects on microbial communities in an MBR treating municipal wastewater
Mei Chen et al – Water Research

Microbial biotechnology

Green energy generation from plant microbial fuel cells (PMFC) using compost and a novel clay separator
A. Carmalin Sophia & S. Sreeja – Sustainable Energy Technologies and Assessments

Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water
Bohanis J. Oko et al – Biotechnology for Biofuels

Optimization of the extraction and purification of the compatible solute ectoine from Halomonas elongate in the laboratory experiment of a commercial production project
Ruifeng Chen et al – World Journal of Microbiology and Biotechnology

Review: Large scale cultivation of genetically modified microalgae: A new era for environmental risk assessment
Tracey A. Beacham et al – Algal Research

Subcellular localization based comparative study on radioresistant bacteria: A novel approach to mine proteins involve in radioresistance
Divya Vishambra et al – Computational Biology and Chemistry

Food microbiology

Meta-omics insights in the microbial community profiling and functional characterization of fermented foods
Gu Chen et al – Trends in Food Science & Technology

Sulfites and the Wine Metabolome
Chloé Roullier-Gall et al – Food Chemistry

Meta-omics insights in the microbial community profiling and functional characterization of fermented foods
Gu Chen et al – Trends in Food Science & Technology

Biofilms

Pre-print: Bifunctionality of a biofilm matrix protein controlled by redox state
Sofia Arnaouteli et al – bioRxiv

General microbiology and evolution

The biology and the importance of Photobacterium species
Ibrahim Musa Moi et al – Applied Microbiology and Biotechnology

Review: A Metagenomic Approach to Cyanobacterial Genomics
Danillo O. Alvarenga et al – Frontiers in Microbiology

In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
Michael Banasik et al – Journal of Biotechnology

Report: Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1
Yue Guan et al – Environmental Microbiology Reports

Phages and viruses

Characterization of prophages of Lactococcus garvieae
Giovanni Eraclio et al – Scientific Reports

Review: Viruses and miRNAs: More Friends than Foes
Patrice Bruscella et al – Frontiers in Microbiology

Bioinformatics and statistics

SteadyCom: Predicting microbial abundances while ensuring community stability
Siu Hung Joshua Chan et al – PLoS Computational Biology

Techniques and methods

Preview: An Elegan(t) Screen for Drug-Microbe Interactions
Alison Vrbanac et al – Cell Host & Microbe

Microbes in the news

Gut microbiome may predict response to biologic therapy for inflammatory bowel disease
ScienceDaily – Original Paper

Diseased Microbiome Varies From Condition to Condition
Ciara Curtin – GenomeWeb

Vini’s non-microbiology picks

Sociomics: Using Omic Approaches to Understand Social Evolution
Melanie Ghoul et al – Trends in Genetics

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