Today’s Digest casts a wide net with focuses on antibiotic resistance , human gut microbiome and microbiome in extreme environments. Highlights include a review on fungi in the marine environment, a report on gut mucosal virome alterations in ulcerative colitis and finally, sleep well!

General microbiology

Review: Transcription in cyanobacteria: a distinctive machinery and putative mechanisms – Amber Riaz-Bradley – Biochemical Society Transactions

Preprint: How sample heterogeneity can obscure the signal of microbial interactions – David W. Armitage & Stuart E. Jones – bioRxiv

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations – Kelei Zhao et al. – BMC Biology

Antibiotic resistance

Antimicrobial photodynamic activity of toluidine blue encapsulated in mesoporous silica nanoparticles against Pseudomonas aeruginosa and Staphylococcus aureus – Paramanantham Parasuraman et al. – Biofouling

Metaphire guillelmi gut as hospitable micro-environment for the potential transmission of antibiotic resistance genes – Huizhen Chao et al. – Science of The Total Environment

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis – Haihan Zhang et al. – Journal of Environmental Sciences

Cationic Intrinsically Disordered Antimicrobial Peptides (CIDAMPs) Represent a New Paradigm of Innate Defense with a Potential for Novel Anti-Infectives – Ties Latendorf et al. – Scientific Reports

Preprint: Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz et al. – bioRxiv

Human oral microbiome

** Sleep deprivation and a non–24-h working schedule lead to extensive alterations in physiology and behavior – Huan Ma et al. – FASEB J

Human gut microbiome

Review: Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity – Xiang Meng et al. – Autoimmunity Reviews

Pearls: Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract – Matthew H. Foley et al. – PLoS Pathogens

Review: Biomarkers for Immune Therapy in Gastrointestinal Cancers – Benjamin A. Weinberg et al. – Clinical Advances in Hematology & Oncology

Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features – Yaxin Wu et al. – Nutrition and Cancer

Review: The microbiome, cancer, and cancer therapy – Beth A. Helmink et al. – Nature Medicine

Correlations of the Gastric and Duodenal Microbiota with Histological, Endoscopic, and Symptomatic Gastritis – Hye Seung Han et al. – Journal of Clinical Medicine

Gut-microbe-braint axis

Research Highlight: Depression linked to the microbiome – Hannah Stower – Nature Medicine

Animal experiments

Differential Sensitivity to Plasmodium yoelii Infection in C57BL/6 Mice Impacts Gut-Liver Axis Homeostasis – Joshua E. Denny et al. – Scientific Reports

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model – Alexandra Schutkowski et al. – Journal of Nutritional Biochemistry

Alterations of Bile Acids and Gut Microbiota in Obesity Induced by High Fat Diet in Rat Model – Hong Lin et al. – Journal of Agricultural and Food Chemistry

Effects of lifelong intake of lemon polyphenols on aging and intestinal microbiome in the senescence-accelerated mouse prone 1 (SAMP1) – Chikako Shimizu et al. – Scientific Reports

Effect of green tea and mulberry leaf powders on the gut microbiota of chicken – Yuan Chen et al. – BMC Veterinary Research

Animal microbiome

Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions – Jenny Marie Booth & Marco Fusi et al. – Scientific Reports

Plant, root and soil microbiome

Hypotheses: Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration – Radhey Shyam Sharma et al. – Ecology and Evolution

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria – Patricia Lu-Irving et al. – mSphere

Small molecule reaction networks that model the ROS dynamics of the rhizosphere – Olga Taran et al. – Chemical Communications

Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle – Dianming Wu et al. – The ISME Journal

Evidence of within-species specialization by soil microbes and the implications for plant community diversity – Jenalle L. Eck et al. – PNAS

Effects of four years of elevated ozone on microbial biomass and extracellular enzyme activities in a semi-natural grassland – Jinyang Wang et al. – Science of The Total Environment

Water and extremophile microbiome

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity – Vu Nguyen Thanh et al. – Scientific Reports

Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary) – Nóra Tünde Enyedi et al. – Journal of Environmental Radioactivity

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters – Zeynep Cetecioglu et al. – Water Research

** Review: Fungi in the Marine Environment: Open Questions and Unsolved Problems – Anthony Amend et al. – mBio

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea – Kuldeep D. More et al. – Geobiology

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents – Lucy C. Stewart et al. – The ISME Journal

Prebiotics, probiotics and synbiotics

Review: Potential prebiotics and their transmission mechanisms: Recent approaches – Ishu Khangwal & Pratyoosh Shukla – Journal of Food and Drug Analysis

A Preventive Prebiotic Supplementation Improves the Sweet Taste Perception in Diet-Induced Obese Mice – Arnaud Bernard et al. – Nutrients

Phages and viruses

Pancreas of coxsackie virus infected dams and their challenged pups: A complex issue – Sona Sarmirova et al. – Virulence

Preprint: Clades of huge phage from across Earth’s ecosystems – Basem Al-Shayeb et al. – bioRxiv

** Gut mucosal virome alterations in ulcerative colitis – Tao Zuo et al. – Gut

Bioinformatics

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches – Weizhi Song et al. – Microbiome

Scientific Communication and Education

Preprint: The life of P.I. – Transitions to Independence in Academia – Sophie E Acton et al. – bioRxiv