Human Microbiome: Gut
Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)
News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology
Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)
Human Microbiome: Respiratory tract
Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology
State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)
Human Microbiome: Mouth
The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports
Built microbiome
Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports
Animal Microbiome
Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology
Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports
Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports
Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens
Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)
Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang – Frontiers in Microbiology
Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology
Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports
Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition
Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv
Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia – Scientific Reports
Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)
Probiotics, Prebiotics and Synbiotics
Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology
The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal – Frontiers in Microbiology
Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports
Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology
A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature
Pathogen Research
High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology
In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science
Bioactive compounds
Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology
Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports
Bacteriophages
Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology
Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE
Soil and Environmental Microbiology
Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology
The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology
Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science
Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv
Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints
Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)
Bioinformatics and Genomics
Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv
Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari – BMC Bioinformatics
Non-microbiology picks
A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science
Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology
Lessons from between the white lines for isolated data scientists – Benjamin S Baumer - PeerJ preprints
Microbiome Digest - Bik's Picks 