Of note today: non-exclusive breastfeeding increases the risk of HIV transmission via the alteration of gut microbiome/T-cell activation; Fasting altered the gut microbiome in beneficial ways but only in mice previously fed a high fat diet; An investigation into new species of the honey and bumblebee gut commensal genus Gilliamella; Catfish development shapes gut microbial community structure independent of diet; A metagenomic analysis of the skin microbiome of the frog, Craugastor fitzingeri; The microbiome is altered during the bioremediation of herbicide contaminated soil; The impact of urban density on the soil microbiome; A randomized placebo controlled clinical trial of a microbiota based drug for the prevention of Clostridium difficile Infection; and the virome of the Cuatro Ciénegas Basin of Mexico

 
Pregnancy and early life

*Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants – Lianna F Wood – Clinical Infectious Diseases

Comparative Analysis of Gut Microbial Communities in Children under 5 Years Old with Diarrhea – Hongyu Wen – Journal of Microbiology and Biotechnology

Review: Microbiome in Embryonic Implantation and Implantation Failure – Jason M. Franasiak – Recurrent Transplant Failure

Human oral microbiome

The cultivable bacterial flora of the esophagus in subjects with esophagitis – Elisabeth Norder Grusell – Scandinavian Journal of Gastroenterology

Human urogenital microbiome

The upper and lower tract urinary microbiomes of stone formers are similar: a pilot study – Heiko Yang – The Journal of Urology

Human gut microbiome

Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy – Evgenii I – bioRxiv

The microbial metabolite TMAO in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages – Catharina Missailidis – AIDS

Review: Microbiome-Mediated Upregulation of MicroRNA-146a in Sporadic Alzheimer’s Disease – Yuhai Zhao – Frontiers in Neurology

Review: Interplay Between the Gut-Brain Axis, Obesity and Cognitive Function – Ana Agustí – Frontiers in Neuroscience

Review: The Brain–Intestinal Mucosa–Appendix– Microbiome–Brain Loop – Luis Vitetta – Diseases

Review: New Therapeutic Drugs from Bioactive Natural Molecules: the Role of Gut Microbiota Metabolism in Neurodegenerative Diseases – Francesco Di Meo – Current Drug Metabolism

Review: Microbial Effects on Immunity in HIV: Virus, Gender or Sexual Preference Induced? – Nichole R. Klatt – EBioMedicine

Review: Microbiome and Gut Dysbiosis – José E. Belizário – Metabolic Interaction in Infection

Review: Clostridium Bacteria and Autism Spectrum Conditions: A Systematic Review and Hypothetical Contribution of Environmental Glyphosate Levels – Isadora Argou-Cardozo  – Medical Science

Review: Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions – Edmund B. Chen – Journal of Gastrointestinal Surgery

Review: Maintenance of intestinal homeostasis by mucosal barriers – Ryu Okumura – Inflammation and Regeneration

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Animal experiments

*Food withdrawal alters the gut microbiota and metabolome in mice – Xiaojiao Zheng – The FASEB Journal

Animal microbiome

*Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera) – Jane Ludvigsen – International Journal of Systematic and Evolutionary Microbiology

*Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water – Zhimin Zhang – Frontiers in Microbiology

*The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data – Eria A. Rebollar – Frontiers in Microbiology

Gut Microbiota-Regulated Pharmacokinetics of Berberine and Active Metabolites in Beagle Dogs After Oral Administration – Ru Feng – Frontiers in Pharmacology

Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season – Allison Clark – Frontiers in Physiology

Review: Opinion: Pesticides Could Alter Amphibian Skin Microbiomes and the Effects of Batrachochytrium dendrobatidis – Krista A. Mccoy – Frontiers in Microbiology

Preprint: Earthworms and Cadmium – heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils? – Maja Šrut – bioRxiv

Effect of Dietary Non-phytate Phosphorus Levels on the Diversity and Structure of Cecal Microbiota in Meat Duck from 1 to 21 d of age – S J Dai – Poultry Science

Rumen bacterial community structure impacts feed efficiency in beef cattle – Henry A Paz – Journal of Animal Science

Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein  – E A Latham – Journal of Animal Science

Plant, root, and soil microbiome

*Dynamic changes in microbial communities during the bioremediation of herbicide (chlorimuron-ethyl and atrazine) contaminated soils by combined degrading bacteria – Jian Wang – PLOSone

Comparison of Microbial Community Structure in Kiwifruit Pollens – Min-Jung Kim – The Plant Pathology Journal

*Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces – Haitao Wang – Environmental Science and Technology

Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China – Baihui Ren – Scientific Reports

Preprint: Social Motility: Interaction between two sessile soil bacteria leads to emergence of surface motility – Lucy M McCully – bioRxiv

Water and extremophile microbiome

Sulphate-reducing bacteria (SRB) in the Yangtze Estuary sediments: Abundance, distribution and implications for the bioavailibility of metals – Zuo-shun Niu – Science of The Total Environment

Bacterial community succession and degradation patterns of hydrocarbons in seawater at low temperature – Leendert Vergeynst – Journal of Hazardous Materials

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition – Emily B. Graham – PeerJ

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries – Kai Wang – Science of The Total Environment

Nitrate amendment reduces biofilm biomass and shifts microbial communities in remote, oligotrophic ponds – Carmella Vizza – Freshwater Science

Microbial Ecology

Bacterial interspecies quorum sensing in the mammalian gut microbiota – Karina Bivar Xavier – Comptes Rendus Biologies

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass – Aoife Joyce – Frontiers in Microbiology

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Probiotics / prebiotics

*Results from a Randomized Placebo-Controlled Clinical Trial of a RBX2660—a Microbiota-based Drug for the Prevention of Recurrent Clostridium difficile Infection – Erik R Dubberke – Clinical Infectious Dieases

Outer Membrane Vesicles From Probiotic and Commensal Escherichia coli Activate NOD1-Mediated Immune Responses in Intestinal Epithelial Cells – María-Alexandra Cañas – Frontiers in Microbiology

Fecal Transplants

Recruitment of feces donors among blood donors: Results from an observational cohort study – Simon Mark Dahl Jørgensen – Gut Microbes

Fecal microbiota transplantation associated with 10 years of stability in a patient with SPMS – Seraj Makkawi – Neurology, Neuroimmunology & Neuroinflammation

Phages and viruses

Metagenomic analysis of ssDNA viruses in surface seawater of Yangshan Deep-Water Harbor, Shanghai, China – Hongming Wang – Marine Genomics

*The viral structure of the Cuatro Ciénegas Basin, a unique oasis in Northern Mexico, reveals a highly diverse population at a small geographic scale – B. Taboada – Applied and Environmental Microbiology

Waste and Pollution

Metataxonomy and functionality of wood-tar degrading microbial consortia – Lorenzo Brusetti – Journal of Hazardous Materials

Variations in the denitrifying microbial community and functional genes during mesophilic and thermophilic anaerobic digestion of cattle manure – Kaiyu Zhang – Science of The Total Environment

Techniques

Electrochemical detection of viable bacteria in urine and antibiotic selection – Noriyuki Nakamura – Biosensors and Bioelectronics

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Microbes in the news

Nova-like explosion of spinning live bacteria explained – A’ndrea Elyse Messer – Phys.org

New ‘NanoZymes’ use light to kill bacteria – Science Daily

The Germs That Love Diet Soda – Moises Velasquez-Manoff

Bacteria can pass on memory to descendants, researchers discover – Melody Pupols – Phys.org

Charting an underexplored landscape: The genitourinary microbiome – Medical Press