November 23, 2017

Today we have pretty much diverse Microbiome Digest particularly in the section of General microbiome. Interesting papers on E coli as a model organism for metabolic engineering, influence of exercise on our gut microbiota and influence of antibiotics on genetic diversity of honeybee gut microbiota. Enjoy reading these and many many more articles and news about microbes.

Events and jobs

PhD in Soil Microbiology, Teagasc Johnstown Castle, UK

PhD Fellowship in Molecular Microbiology, Copenhagen, Denmark

Postdoctoral Research Associate – Bacterial Evolutionary Genomics, Missoula, MT, US

Postdoctoral researchers – (Lemon Lab), Cambridge MA, US

Associate Professor/Professor in Microbiology, Nottingham, UK

General microbiome

The Immunomodulatory Drug Glatiramer Acetate is Also an Effective Antimicrobial Agent that Kills Gram-negative Bacteria – Stig Hill Christiansen – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China – Sudhakar G. Bhandare – Genome Announcements

Survival of microbes in Earth’s stratosphere – Priya Das Sarma – Current Opinion in Microbiology

Review: Cable Bacteria Take a New Breath Using Long-Distance Electricity – Filip J.R. Meysman – Trends in Microbiology

Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation – Edgardo Sepulveda – Frontiers in Microbiology

The effect of the 2015 Earthquake on the bacterial community compositions in water in Nepal – Sital R. Uprety – Frontiers in Microbiology

Rokubacteria: genomic giants among the uncultured bacterial phyla – Eric D. Becraft – Frontiers in Microbiology

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Pregnancy and early life

Microbial Mechanistic Insight into the Role of Inulin in Improving Maternal Health in a Pregnant Sow Model – Pan Zhou – Frontiers in Microbiology

Human respiratory microbiome

A practical molecular identification of nonfermenting Gram-negative bacteria from cystic fibrosis – Carolina Paulino da CostaCapizzani – Brazilian Journal of Microbiology

Oral microbiome

Over-the-counter mouthwash use and risk of pre-diabetes/diabetes – Kaumudi J.Joshipura – Nitric Oxide

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing – Yuan Wang – Frontiers in Microbiology

Exploring the association between Alzheimer’s disease, oral health, microbial endocrinology and nutrition – Alice Harding – Frontiers in Aging Neuroscience

Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet – Florent Lassalle – Molecular Ecology

Human skin microbiome

Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo – K Johani – Journal of Antimicrobial Chemotherapy

Human gut microbiome

Review: Influence of microbiota on intestinal immune system in ulcerative colitis and its intervention – Sailong Zhang – Frontiers in Immunology

Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans – Allen, Jacob M – Medicine & Science in Sports & Exercise

The Kynurenine Pathway As a Novel Link between Allergy and the Gut Microbiome – Aaron P. Van der Leek – Frontiers in Immunology

The gut microbiota: A new potential driving force in liver cirrhosis and hepatocellular carcinoma – Marco Sanduzzi Zamparelli – United European Gastroenterology Journal

Animal experiments 

Aged Gut Microbiota Contributes to Systemical Inflammaging after Transfer to Germ-Free Mice – Floris Fransen – Frontiers in Immunology

Animal microbiome

Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages – Manuela Oliveira Ramalho – PLOS One

Spontaneous body contractions are modulated by the microbiome of Hydra – Andrea P. Murillo-Rincon – Sceintific Reports

Age-related differences in the respiratory microbiota of chickens – Laura Glendinning – PLOS One

A potential new species of porcine Actinobacillus defined by multi-locus sequence analysis – C. Turni – Animal Production Science

Prevalence survey of Toxoplasma gondii in hearts from Western Australian sows – K. Hodgson – Animal Production Science

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome – Kasie Raymann –  Molecular Ecology

Plant, root, and soil microbiome

Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato – Anastasis Antoniou – Frontiers in Plant Science

Exogenous nitrogen addition reduces the temperature sensitivity of microbial respiration without altering the microbial community composition – Hui Wei – Frontiers in Microbiology

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities – Theodore M. Flynn – Frontiers in Microbiology

The effect of Lobelia dortmanna L. on the structure and bacterial activity of the rhizosphere – KatarzynaLewicka-Rataj – Aquatic Botany

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xue-Ying Tian – Frontiers in Microbiology

Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession – Miao Wang – Frontiers in Microbiology

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Water and extremophile microbiome

Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation – Marta Sebastián – Environmental Microbiology

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods – Alexis L. Pasulka – Environmental Microbiology

Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity – Abigail Tomasek – Frontiers in Microbiology

Chapter 4.1 – The Biota of Intermittent Rivers and Ephemeral Streams: Prokaryotes, Fungi, and Protozoans – Anna M. Romaní – Intermittent Rivers and Ephemeral Streams

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge – Wei Xu – Deep Sea Research Part I

Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems – Dongwei Hou – Frontiers in Microbiology

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams – Ze Ren – Frontiers in Microbiology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology
Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Zhichao Zhou – Frontiers in Microbiology


Food microbiology

Novel insights into microbial community dynamics during the fermentation of Central European ice wine – Mária Bučková – International Journal of Food Microbiology

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

Probiotics / prebiotics

Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals – Mia C. Theilmann – mBio

Phages and viruses

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers – Sophie Nguyen – mBio

MVP: a microbe–phage interaction database  – Na L. Gao – Nucleic Acids Research


Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments – Emine Gozde Ozbayram – Applied Microbiology and Biotechnology

Escherichia coli as a model organism for systems metabolic engineering – Paul A.Adamczyk – Current Opinion in System Biology


Review: Computational Approaches for Integrative Analysis of the Metabolome and Microbiome – Jasmine Chong – Metabolites


Nucleic acid purification from plants, animals and microbes in under 30 seconds – Yiping Zou – PLOS Biology

Lighting Van Leeuwenhoek’s samples – Lesley A. Robertson – FEMS Microbiology Letters

Analysis of Microbiome Data in the Presence of Excess Zeros – Abhishek Kaul – Frontiers in Microbiology

Stripping flow cytometry: How many detectors do we need for bacterial identification? – Peter Rubbens – Cytometry

Microbes in the news 

Plague Bacteria Entered Europe During Neolithic Age, Genetic Analysis Finds 

How the Immune System Identifies Invading Bacteria

Scientists Program Remote-Controlled Nanobots to Kill Cancer

Microbes on the market 

Qualitative Report on Human Microbiome Market 

Microbes and art

Superbugs And Rockets Side By Side At Science Museum




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