June 21, 201

Today’s Microbiome Digest has quite a few articles from water environment. Both articles I would like to highlight are with cyanobacteria as stars. The first one from Anne D. Jungblut reports on Antarctic cynobacteria diversity, while the second one reveals the new freshwater cyanobacterial genome. One more thing to highlight come from news. Exxon Mobil Corps and Sintetic Genomics Inc have announced a new breakthrough with genetically modified algae which was able to convert 40% of CO2 to lipids, up from the previous 15%. Algae are still far away from being able to run the process at commercial scale and replace fossil fuels, but we love algae! Enjoy this summer reading.

Events and jobs

Microbiome Research Scientist (BS or MS or PhD) – St. John of God Foundation for Research and Teaching, Barcelona, Spain

Quality Associate Specialist – Merck, Durham, NC, US

Microbiology Manager OR Microbiology Laboratory Manager Opening, Madison, WI, US
General microbiome

A null model for microbial diversification – Timothy J. Straub – PNAS

Pregnancy and early life

Association between breast milk bacterial communities and establishment and development of the infant gut microbiome – JAMA Pediatrics
Human skin microbiome

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by competitors – Adam J. SanMiguel – Antimicrobial Agents and Chemotherapy
Human gut microbiome

Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis – Jasmohan S. Bajaj – Liver Transplatation

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans – Alan Cartmell – PNAS

Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – Kate Lawrence – PLOS
Animal microbiome 

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – The ISME Journal
Plant, root, and soil microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions – Di Wang – The ISME Journal

Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming – Calvin Ho-Fung Lau – Applied and Environmental Microbiology
Water and extremophile microbiome 

Animal-like prostaglandins in marine microalgae – Valeria Di Dato – The ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents – Dimitri V Meier – The ISME Journal

Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway – Ian Lidbury – The ISME Journal

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments – Anders Lanzén – PLOS

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters – David M Needham – The ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal

Spontaneous mutations of a model heterotrophic marine bacterium – Ying Sun – The ISME Journal

Plastid thylakoid architecture optimizes photosynthesis in diatoms – Serena Flori –  Nature Communications

Evolutionary radiation of lanthipeptides in marine cyanobacteria – Andres Cubillos-Ruiz –  PNAS

Using Captain Scott’s Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? Anne D. Jungblut – Proceedings of the Royal Society B

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs – Pedro J. Cabello-Yeves – Frontiers in Microbiology

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment – Yu Wang – Frontiers in Microbiology

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes – Tatsuhiko Hoshino – Frontiers in Microbiology
Phages and viruses

Effect of acute predation with bacteriophage on intermicrobial aggression by Pseudomonas aeruginosa – Patrick R. Secor
Bioinformatics

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data – Gerben Menschaert –

Microbes in the news 

Zombie bacteria and viruses in melting permafrost are waking up  

ExxonMobil and Synthetic Genomics Report Breakthrough in Algae Biofuel Research

Gut microbiome changes linked to numerous biomarkers of type 2 diabetes 

Funky tasting beer? Biofilms may be to blame, MSU researchers say

Bacteria in Your Coughs And Sneezes Can Stay Alive in The Air For Up to 45 Minutes

Microbes on the market

This Company Uses the Human Microbiome to Discover New Disease Mechanisms

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