January 29, 2016

Prescription drugs and microbiome analyses, antimicrobial targets in sarcoidosis granulomas, host-microbiota interactions in antibiotic-associated diseases, and iridescence in self-organizing biofilms.

General microbiome

Perspective: Prescription drugs obscure microbiome analyses – Suzanne Devkota – Science

Review: The role of microbiota in cancer therapy – Ernesto Perez-Chanona – Current Opinion in Immunology

Human respiratory microbiome

COPD and the microbiome – Manoj J. Mammen – Respirology

Molecular Analysis of Sarcoidosis Granulomas Reveals Antimicrobial Targets – Joseph E Rotsinger – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Review: The microbiome and atopic eczema: More than skin deep – Charlotte L Thomas – Australasian Journal of Dermatology

Human gut microbiome

Gut microbiota and allergic disease in children – Sarah L. Bridgman – Annals of Allergy, Asthma & Immunology

Effects of enteral polymeric diet on gut microbiota in children with Crohn’s disease – Chloé Guinet-Charpentier – Gut

Review: Effect of antibiotics on gut microbiota, glucose metabolism and bodyweight regulation – a review of the literature – Kristian Hallundbæk Mikkelsen – Diabetes, Obesity and Metabolism

Animal models

Effects of dispersal limitation in the face of intense selection via dietary intervention on the faecal microbiota of rats – Heli J. Barron Pastor – Environmental Microbiology Reports

Fecal dysbiosis in miniature dachshunds with inflammatory colorectal polyps
Hirotaka Igarashi – Research in Veterinary Science

Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine – Kwang Soon Kim – Science

Translocation of microbes and changes of immunocytes in the gut of rapid- and slow-progressor Chinese rhesus macaques infected with SIVmac239 – Lin-Tao Zhang – Immunology

From the Sonnenburg lab: Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases – Joshua S. Lichtman – Cell Reports

Effect of Antimicrobial Consumption and Production Type on Antibacterial Resistance in the Bovine Respiratory and Digestive Tract – Boudewijn Catry – PLOS ONE

Animal microbiome

Symbiotic Bacteria in Gills and Guts of Chinese Mitten Crab (Eriocheir sinensis) Differ from the Free-Living Bacteria in Water – Meiling Zhang – PLOS ONE

Earthworm: Isolation, identification, and characterization of gut microflora of Perionyx excavatus collected from Midnapore, West Bengal – Tanushree Tulsian Samanta – Journal of Basic Microbiology

Plant, root, and soil microbiome

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction – Kiley W Seitz – The ISME Journal

Not a good paper (poor figures and language problems – see my comments on PubPeer), about carnivorous plantMicrobiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid – Xin-Yue Chan – Scientific Reports

Microbial diversity drives multifunctionality in terrestrial ecosystems – Manuel Delgado-Baquerizo – Nature Communications

Various fungal communities colonise the functional wood tissues of old grapevines externally free from grapevine trunk disease symptoms – E. Bruez – Australian Journal of Grape and Wine Research

Arbuscular mycorrhizal fungi regulate soil respiration and its response to precipitation change in a semiarid steppe – Bingwei Zhang – Scientific Reports

Sewage sludge addition modifies soil microbial communities and plant performance depending on the sludge stabilization process – Eva Lloret – Applied Soil Ecology

Review: Engineering the Rhizosphere – Yves Dessaux – Trends in Plant Science

Water and extremophile microbiome

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea – Qi Ye – Microbiology Open

Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities – Francisco Dini-Andreote – The ISME Journal

Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China – Weimin Sun – Science of The Total Environment

More microbiology

A unique self-organization of bacterial sub-communities creates iridescence in Cellulophaga lytica colony biofilms – Betty Kientz – Scientific Reports

Bioinformatics and metagenomics

Ten Simple Rules for a Bioinformatics Journal Club – Andrew Lonsdale – PLOS Computational Biology

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes – Gabriel A. Al-Ghalith – PLOS Computational Biology

Microbes in the news

Stop pooping! You’re killing sentient beings! – PZ Myers – Pharyngula

ASM’s Commitment to Interdisciplinary Microbiome Research – American Society for Microbiology

Fermentation Farm wants you to eat better bacteria – Kathleen Luppi – LA Times

This bacteria can live for years in distilled water, and causes abscess, seizures and death: Melioidosis / Burkholderia pseudomallei – Jacinta Bowler – Science Alert

Science, publishing, and career

How to read a scientific paper – Adam Ruben – Science

High rejection rates by journals ‘pointless’– Analysis suggests higher selectivity fails to increase journals’ impact factors – David Matthews – Times Higher Education

How to stop the sexual harassment of women in science: reboot the system – Zuleyka Zevallow – The Conversation

Bik’s Picks

Arthropods of the great indoors: characterizing diversity inside urban and suburban homes – Matthew A Bertone



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