In today’s digest, check among many interesting articles: the evolution within human microbiome by T.D. Lieberman, unique microbial biodiversity residing in hadal trenches by L.M. Peoples, changes in community composition in coastal water following exposure to oil and oil dispersant by S.H. Doyle. While in news — a story about “microbial hitchhikers” in restroom hand dryers.
General microbiome
Seven Billion Microcosms: Evolution within Human Microbiomes – Tami D. Lieberman – mSystems
Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead – Benjamin E. Wolfe – mSystems
Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems
Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation – Hyaekang Kim – PLOS One
New insight into the early stages of biofilm formation – Catherine R. Armbruster – PNAS
Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation – Jeronimo Rodriguez-Beltran – Nature Ecology & Evolution
Considering the Lives of Microbes in Microbial Communities – Elizabeth A. Shank – mSystems
Oral microbiome
Inflammatory Bacteriome and Oral Squamous Cell Carcinoma – M. Perera – Journal of Dental Research
Human gut microbiome
The cardiovascular macrophage: a missing link between gut microbiota and cardiovascular diseases? – X. Chen – European Review for Medical and Pharmacological Sciences
Can Diet Influence Our Health by Altering Intestinal Microbiota – Derived Fecal Metabolites? – Qiang Lyu – mSystems
Toward Personalized Control of Human Gut Bacterial Communities – Lawrence A. David – mSystems
Role of the Gut Microbiome in Vertebrate Evolution – Thomas J. Sharpton – mSystems
Dietary nutrition and gut microflora: A promising target for treating diseases – Ying Nie – Trends in Food Science & Technology
Reduction in hepatic secondary bile acids caused by short-term antibiotic-induced dysbiosis decreases mouse serum glucose and triglyceride levels – Takuya Kuno – Scientific Reports
A snapshot of gut microbiota of an adult urban population from Western region of India – Disha Tandon – PLOS One
Animal experiments
Mice harboring pathobiont-free microbiota do not develop intestinal inflammation that normally results from an innate immune deficiency – Benoit Chassaing – PLOS One
Animal microbiome
The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita) – Joachim Spergser – PLOS One
Plant, root, and soil microbiome
Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching – F1000 Research
Exploring the Potentiality of Novel Rhizospheric Bacterial Strains against the Rice Blast Fungus Magnaporthe oryzae – Narayanappa Amruta – The Plant Pathology Journal
The sensitivity of soil enzymes, microorganisms and spring wheat to soil contamination with carfentrazone-ethyl – Monika Tomkiel – Journal of Environmental Science and Health, Part B
Water and extremophile microbiome
Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology
Vertically distinct microbial communities in the Mariana and Kermadec trenches – Logan M. Peoples – PLOS One
The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum – Tianyong Zheng – PLOS One
Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy – Shawn E. McGlynn – Applied and Environmental Microbiology
Addressing Confounding Factors in Algal Phosphorus Limitation Experiments – Whitney S. Beck -bioRxiv
Effect of Siderophore on Iron Availability in a Diatom and a Dinoflagellate Species: Contrasting Response in Associated Bacteria – Nicolas Sanchez – Frontiers in Marine Science
Robust Mercury Methylation across Diverse Methanogenic Archaea – Cynthia C. Gilmour – mBio
Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris – Anthony R. Miller – mBio
Trichodesmium physiological ecology and phosphate reduction in the western Tropical South Pacific – Kyle R. Frischkorn – Biogeosciences
Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea – Michael F. Graw- Frontiers in Microbiology
Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit – Shawn M. Doyle – Frontiers in Microbiology
Understanding Diatom Cell Wall Silicification—Moving Forward – Mark Hildebrand – Frontiers in Marine Science
The hunt for the most-wanted chemolithoautotrophic spookmicrobes – Michiel H in ‘t Zandt – FEMS Microbiology Ecology
Biotechnology
Electron transport chains in organohalide-respiring bacteria and bioremediation implications – Shanquan Wang – Biotechnology Advances
Food microbiology
Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments – Even Heir – International Journal of Food Microbiology
Review: Titanium dioxide (TiO2) photocatalysis technology for nonthermal inactivation of microorganisms in foods – Zhiwei Zhu – Trends in Food Science & Technology
The complexity of wine: clarifying the role of microorganisms – Sophie Tempère – Applied Microbiology and Biotechnology
Probiotics / prebiotics
The effect of Lactobacillus acidophilus and Lactobacillus casei on the in vitro bioaccessibility of flaxseed lignans (Linum usitatissimum L.) – O. Muñoz – Food & Function
The “Golden Age” of Probiotics: A Systematic Review and Meta-Analysis of Randomized and Observational Studies in Preterm Infants – Dermyshi E. – Neonatology
Phages and viruses
Screening of FDA-approved Drugs and Identification of Novel Lassa Virus Entry Inhibitors – Peilin Wang – bioRxiv
Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater – Nichole E. Brinkman – PLOS One
Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus – Piotr M. Skowron – PLOS One
Bioinformatics
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data – Li Chen – PeerJ
Techniques
Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae – Matthew A. Croxen – Microbial Genomics
Paraffin Embedding and Thin Sectioning of Microbial Colony Biofilms for Microscopic Analysis – William C. Cornell – Journal of Visualized Experiments (Jove)
Microbes in the news
Bugs, microbes and death can inform the living
Gut bacteria keeps bears healthily obese
Restroom Hand Dryers Are Blowing Bacteria Everywhere
Survival strategy: How one enzyme helps bacteria recover from exposure to antibiotics
Oil-eating bacteria could clean up the next spill
Microbiome Digest - Bik's Picks 