A busy Monday digest to start your week well. Quite a few pieces from the Journal of Biological Chemistry today, as it released a special issue on host-microbiome metabolic interplay. A lot of review pieces on microbes and human health, specially in the Microbial Diseases section.

General microbiome

Introduction to the Thematic Minireview Series: Host-Microbiome Metabolic Interplay.
Banerjee R – Journal of Biological Chemistry

Human epitelial microbiome

Review: Microbiota in Exhaled Breath Condensate and the Lung
Glendinning L – Applied Environmental Microbiology

Review: The microbiota of the respiratory tract: gatekeeper to respiratory health
Wing Ho Man – Nature Reviews Microbiology

Human gut microbiome

Review: Influence of diet on the gut microbiome and implications for human health
Singh RK – Journal of Trans. Medicine

Review: Glucuronides in the Gut: Sugar-Driven Symbioses Between Microbe and Host
Pellock SJ – Journal of Biological Chemistry

Review: Chemical signaling between gut microbiota and host chromatin: What is your gut really saying?
Krautkramer KA – Jorunal of Biological Chemistry

Exposure to household furry pets influences the gut microbiota of infant at 3–4 months following various birth scenarios
Hein M. Tun – Microbiome

Review: Microbial Metabolites in Health and Disease: Navigating the Unknown in Search of Function
Martinez KB – Journal of Biological Chemistry

Review: Understanding the role of the gut ecosystem in Diabetes Mellitus
Aw W & Fukuda S – Journal of Diabetes Investigation

Microbial diseases

Review: Colonization Resistance: The Deconvolution of a Complex Trait
Olsan EE – Journal of Biological Chemistry

Helicobacter pullorum: An Emerging Zoonotic Pathogen
Sundus Javed – Frontiers in Microbiology

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections
Henry L. Schreiber IV – Science Trans. Medicine

Distribution of Integrons and Phylogenetic Groups among Enteropathogenic Escherichia coli Isolates from Children
Taru Singh – Frontiers in Microbiology

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin
Javier Querol-García – Frontiers in Microbiology

Gene Expression Profiling of Transcription Factors of Helicobacter pylori under Different Environmental Conditions
Miguel A. De la Cruz – Frontiers in Microbiology

The gut-kidney axis in IgA nephropathy: role of microbiota and diet on genetic predisposition
Coppo R. – Pediatrical Nephrology

Animal experiments

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves
Gomez DE – Journal of Veterinary Internal Medicine

High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice
Liang Xiao – Microbiome

Plant, root, and soil microbiome

Leaf Litter Chemistry Drives the Structure and Composition of Soil Testate Amoeba Communities in a Tropical Montane Rainforest of the Ecuadorian Andes
Krashevska V – Microbial Ecology

Water, estuarine and sediment microbiome

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment
Wurzbacher C – Microbiome

Built environment

Deciphering conjugative plasmid permissiveness dynamics in wastewater microbiomes
Jacquiod S – Molecular Ecology

Microbial biotechnology

Targeting of Microbe-Derived Metabolites to Improve Human Health: The Next Frontier for Drug Discovery
Brown JM & Hazen SL – Journal of Biological Chemistry

Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1
Boliang Gao – Frontiers in Microbiology

Phytochemical Characterization of Terminalia catappa Linn. Extracts and Their antifungal Activities against Candida spp.
Analucia G. Terças – Frontiers in Microbiology

Natural Product Discovery from the Human Microbiome
Wilson MR – Journal of Biological Chemistry

Enhanced methane production by semi-continuous mesophilic co-digestion of potato waste and cabbage waste: Performance and microbial characteristics analysis
Mu H – Bioresource Technology

General microbiology and evolution

Evidence for early life in Earth’s oldest hydrothermal vent precipitates
Matthew S. Dodd – Nature

Determining the bacterial cell biology of Planctomycetes
Christian Boedeker – Nature Communications

Phages and viruses

Letter: CRISPR–Cas systems exploit viral DNA injection to establish and maintain adaptive immunity
Joshua W. Modell – Nature

Multiple origins of viral capsid proteins from cellular ancestors
Mart Krupovic & Eugene V. Koonin – PNAS

Molecular Dynamics Simulation of the Influenza A(H3N2) Hemagglutinin Trimer Reveals the Structural Basis for Adaptive Evolution of the Recent Epidemic Clade 3C.2a
Masaru Yokoyama – Frontiers in Microbiology

Techniques and methods

The Use of Degenerate Primers in qPCR Analysis of Functional Genes Can Cause Dramatic Quantification Bias as Revealed by Investigation of nifH Primer Performance
Gaby JC & Buckley DH – Microbial Ecology

Review: The impact of culturomics on taxonomy in clinical microbiology
Rita Abou Abdallah – Antonie van Leeuwenhoek

Review: Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review
Wang H – Water Research

Microbes in the news

One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly
Sara Kamouni – The Sun UK

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge
Eleni Roussos – ABC News

Vini’s non-microbiology picks

Novel soil-inhabiting clades fill gaps in the fungal tree of life.
Tedersoo L – Microbiome

Pre-print: Looking into Pandora’s Box: The Content of Sci-Hub and its Usage
Bastian Greshake – F1000 Research