Today we have a very nice serving to digest, with some impactful gut microbiome studies for human health/therapeutics, a whitepaper on the challenges of clinical microbiome research. We also have clusters of related studies on the environment, drinking water, and antibiotic resistance. There are even a few studies on the microbiota found in caves! Give these all a read, there is a lot of amazing research today. Don’t forget to have yourself a few extra side servings of my own non-microbial picks, in honor of the upcoming Thanksgiving US holiday.
Human oral microbiome
Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science
Human respiratory microbiome
The microbiota protects against respiratory infection via GM-CSF signaling – Rebecca L. Brown – Nature
Human gut microbiome
Microbiota: A high-pressure situation for bacteria – David A. Relman – Nature
Quantitative microbiome profiling links gut community variation to microbial load – Doris Vandeputte – Nature
* Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature
A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li – PLOS ONE
Plant, root, and soil microbiome
[Doctoral Thesis] Plant biomass-degrading microbial consortia: Ecology, lignocellulolytic machinery and biotechnological potential – Jiménez Avella – University of Groningen
Direct evidence for the enhanced acquisition of phosphorus in the rhizosphere of aquatic plants: A case study on Vallisneria natans – Xigang Xing – Science of the Total Environment
Effect of Phosphate Solubilization Microorganisms and Plant Growth Promoting Rhizobacteria on Yield and Yield Components of Corn – Amin Fathi – Scientia Agriculturae
Water and extremophile microbiome
Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients – Alyse K. Hawley – Nature
Comparison of bacterial and archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary) – Dóra Anda – Journal of Cave and Karst Studies
Comparisons of Soil Properties, Enzyme Activities and Microbial Communities in Heavy Metal Contaminated Bulk and Rhizosphere Soils of Robinia pseudoacacia L. in the Northern Foot of Qinling Mountain – Yurong Yang – Forests
Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data – Stéphane Pfendler – Science of the Total Environment
Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system – Lingwei Meng – Journal of Environmental Sciences
Field assessment of bacterial communities and total trihalomethanes: Implications for drinking water networks – Carolina Montoya-Pachongo – Science of the Total Environment
Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water – Hao-Chang Su – Science of the Total Environment
Bioinformatics
Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene – Yifei Zhang – PLOS ONE
Microbes in the news
Probiotics: Health boost or waste of cash?
Microbes on the market
* uBiome Launches HPV, STD, Vaginal Microbiome Test for Self-Collected Samples – genomeweb
* [Whitepaper] The Microbiome in Clinical Trials: Opportunities and Challenges – Brian Murphy – MedPace
Bacteria Hysteria
Fort Mitchell woman attacked by flesh-eating bacteria back home after 45 days in hospital
Fecal Bacteria Discovered In Public Well Serving Seymour, Oxford
Ed’s non-microbiology picks
Epistemic rationality: Skepticism toward unfounded beliefs requires sufficient cognitive ability and motivation to be rational – Tomas Ståhl – Personality and Individual Differences
* Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing – Hao Yin – Nature
Increased food production and reduced water use through optimized crop distribution – Kyle Frankel Davis – Nature Geoscience
* Fructan, Rather Than Gluten, Induces Symptoms in Patients With Self-reported Non-celiac Gluten Sensitivity – Gry I. Skodje – Gastroenterology
* Does Money Matter in the Long Run? Effects of School Spending on Educational Attainment – Joshua Hyman – American Economy Journal: Economic Policy
* Hippocampal GABA enables inhibitory control over unwanted thoughts – Taylor W. Schmitz – Nature
Daytime variation of perioperative myocardial injury in cardiac surgery and its prevention by Rev-Erbα antagonism: a single-centre propensity-matched cohort study and a randomised study – David Montaigne – The Lancet Cardiac Surgery
The reminiscence bump: why America’s greatest year was probably when you were young
Study: Americans are retiring later, dying sooner and sicker in-between
Microbiome Digest - Bik's Picks 