Pharmacobiomics, liver-microbiome axis, starvation effect on gut microbiota of shrimp,  influence of gut microbiome on the larvae of a lepidopteran pest, microbiota of berries, building a local scientific community in data science and lots of articles for today’s digest.

General microbiome

Pharmacology in the age of the Holobiont – P Norvaisas – Current Opinion in Systems Biology

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production – D Gallagher – Bioresource Technology

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium – N Vardanyan – Environmental Technology

Variation in Electrode Redox Potential Selects for Different Microorganisms Under Cathodic Current Flow From Electrodes in Marine Sediments – BR Lam – Environmental Microbiology

Diurnal patterns of airborne algae in the Hawaiian Islands: a preliminary study – HW Singh – Aerobiologia

Novel human microbe-disease associations inference based on network consistency projection – S Zou – Scientific Reports

Multi-site human microbiome

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans – A Vanhatalo – Free Radical Biology and Medicine

Review: Biodiversity of the Human Oral Mycobiome in Health and Disease – HMHN Bandara – Oral Diseases

 

Human nearly-sterile sites 

Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation – D-L Vu – Clinical Microbiology and Infection

Human gut microbiome

Review: Liver–Microbiome Axis in Health and Disease – TE Adolph – Trends in Immunology

Preprint: Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis. – MM David – bioRxiv

Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome – N Maharshak – Digestive Diseases and Sciences

Prevention and treatment of Clostridium difficile associated diarrhea by reconstitution of the microbiota – N Eliakim-Raz – Human Vaccines & Immunotherapeutics

Animal experiments 

Bifidobacterium spp. reshaping in the gut microbiota by low dose of juçara supplementation and hypothalamic insulin resistance in Wistar rats – G Jamar – Journal of Functional Foods

Salvianolic acid B alters the gut microbiota and mitigates colitis severity and associated inflammation – X Wu – Journal of Functional Foods

Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model – X Zhang – Journal of Functional Foods

Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities – W-F Dai – Fish & Shellfish Immunology

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Z Ge – Scientific Reports

Animal microbiome 

Preprint: The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – MT Schwarz – bioRxiv

Plant, root, and soil microbiome

Review: High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota – A pilot study – J Lukša – Food Research International

Microbial functional responses to long-term anthropogenic impact in mangrove soils – L Cabral – Ecotoxicology and Environmental Safety

Foliage application of nitrogen has less influence on soil microbial biomass and community composition than soil application of nitrogen – X Huang – Journal of Soils and Sediments

Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments – Y Chen – Science of The Total Environment

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5 – J Gao – Ecotoxicology and Environmental Safety

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+‐pumping pyrophosphatase in pepper plants – G Vigani – Environmental Microbiology

Defining plant growth promoting rhizobacteria molecular and biochemical networks in beneficial plant-microbe interactions – A Rosier – Plant and Soil

Roles of Plant-Associated Microbiota in Traditional Herbal Medicine – W Huang – Trends in Plant Science

Spatial structuring of soil microbial communities in commercial apple orchards – G Deakin – Applied Soil Ecology

Effects of root colonization by zinc-solubilizing bacteria on rice plant (Oryza sativa MR219) growth – NMI Othman – Agriculture and Natural Resources

Promising filamentous native fungi isolated from paddy soils for arsenic mitigation in rice grains cultivated under flooded conditions – FR Segura – Journal of Environmental Chemical Engineering

Soil respiration in Chinese tea gardens: autotrophic and heterotrophic respiration – LC Fan – European Journal of Soil Science

Water and extremophile microbiome 

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and ‘Candidatus Methanohalarchaeum thermophilum’, extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. – DY Sorokin – International Journal of Systematic and Evolutionary Microbiology

 

Food microbiology

The Genus Wallemia—From Contamination of Food to Health Threat – J Zajc- Microorganisms

Phages and viruses

Biological species in the viral world – L-M Bobay – PNAS

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium – K Moon – Scientific Reports

 

Non-microbiology picks

Preprint: Building a local community of practice in scientific programming for Life Scientists – SLR Stevens – bioRxiv