Hi all, it’s Elisabeth Bik, doing a rare blog post here, after having run this blog for 3 years in a row. I am having a blast working at uBiome, but as I wrote in January, with my long commute and continuing science integrity work I can not spend much time here at Bik’s Picks. Fortunately, the Microbiome Digest has been able to continue to run through the fantastic work of a group of 20 people from all over the world. In the last couple of months, some new people joined, and some other people left, so it was time for a update on the team members and their background and interest. I am so grateful that this team could take over from me, and that they are running the blog so I can currently focus on other things.

So here is the new Microbiome Digest Team page where you can read more about the fantastic group of scientists who are currently writing the Microbiome Digest posts.

Thank you all, team, for providing this continuous stream of new microbiome papers and articles.

Interaction of gut microbiota metabolites with host chromatin, modulation of T cell responses by Propionibacterium acnes in healthy and diseased skin, metatranscriptomics of the termite gut microbiota.

Multi-site human microbiome

Review: The potential of the microbiota to influence vaccine responses – David J Lynn – Journal of Leukocyte Biology

Human skin microbiome

Phenotype and antimicrobial activity of Th17 cells induced by Propionibacterium acnes strains associated with healthy and acne skin – George W Agak – Journal of Investigative Dermatology

Human gut microbiome

Review: The intricate connection between diet, microbiota, and cancer: A jigsaw puzzle – Melek Canan Arkan – Seminars in Immunology

Animal experiments

Characterization of vaginal microbiota of endometritis and healthy sows using high-throughput pyrosequencing of 16S rRNA gene – Jun Wang – Microbial Pathogenesis

Paneth Cell Defects Induce Microbiota Dysbiosis In Mice And Promote Visceral Hypersensitivity – Ambre Riba – Gastroenterology

Novel Interactions between Gut Microbiome and Host Drug-processing Genes Modify the Hepatic Metabolism of the Environmental Chemicals PBDEs – Cindy Yanfei Li – Drug Metabolism and Disposition

Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa) – Qianqian Huang – Archives of Microbiology

Effect of dietary copper level on the gut microbiota and its correlation with serum inflammatory cytokines in Sprague-Dawley rats – Feng Zhang – Journal of Microbiology

Animal microbiome

Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome – Martyna Marynowska – BMC Genomics

Plant, root, and soil microbiome

Review: Wetland management using microbial indicators – Hidetoshi Urakawa – Ecological Engineering

Impacts of Repeated Glyphosate Use on Wheat-Associated Bacteria are Small and Depend on Glyphosate-Use History – Daniel C Schlatter – Applied and Environmental Microbiology

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest – Can Du – Journal of Microbiology

Water and extremophile microbiome

Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters – Zhen-Chao Zhou – Environmental Science and Pollution Research

Probiotics/prebiotics

Intestinal Microbiota in Infants at High-risk for Allergy: Effects of Prebiotics and Role in Eczema Development – Harm Wopereis – Journal of Allergy and Clinical Immunology

Metabolomics

Review: Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin – Kimberly A Krautkramer – Translational Research

Microbes in the news

Baby bottle dish soap recalled due to harmful bacteria in the soap – ABC Action News

Microbes on the market

This Biotech Clothing Automatically Ventilates When You Start to Sweat – Kyree Leary – Futurism

A short list to digest today toward the end of the month.

Multi-site human microbiome

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples – Clarke EL – American Journal of Respiratory and Critical Care Medicine

Human oral microbiome

Smoking May Lead to Marginal Bone Loss around Non-submerged Implant during Bone Healing by Altering Salivary Microbiome: A Prospective Study – Xiaobo Duan – Journal of Periodontology

Human skin microbiome

The mammalian skin microbiome – Ross, Ashley Anne – UWSpace

Human vaginal microbiome

Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity – Abdelmaksoud AA – PLoS One

The cervico-vaginale microbiota in chlamydia trachomtais notified women: a case–control study at the sexually transmitted infection outpatient clinic in Amsterdam – Charlotte van der Veer – Virus Evolution

Human gut microbiome

Targeting the gut microbiota by dietary nutrients: a new avenue for human health – Li D – Critical Reviews in Food Science and Nutrition

Animal experiments

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome – Lamoureux EV – mSystems

Plant, root, and soil microbiome

The Effects of Low Concentrations of Silver Nanoparticles on Wheat Growth, Seed Quality, and Soil Microbial Communities – Guangfu Liu – Water, Air, & Soil Pollution

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease – Wei-Yu Chen – Nature Scientific Reports 7

Microbes in the news

Science Is Showing How Gut Bacteria Affect The Brain, But Don’t Bother Taking Probiotics Yet – David DiSalvo – Forbes

Over 80% of airborne bacteria identical in Seoul, Beijing: report – Kim Da-sol – The Korea Herald

Ed’s non-microbiology picks 

Spontaneous fine-tuning to environment in many-species chemical reaction networks – Jordan M. Horowitz – PNAS

Bee-derived antibacterial peptide, defensin-1, promotes wound re-epithelialisation in vitro and in vivo – Marcela Bucekova – Nature Scientific Reports 7

Family Planning Funding Cuts and Teen Childbearing – Analisa Packham – Miami University

General microbiome
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins – Andreas Zanzoni – Microbiome

Pregnancy and early life
Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates – Alicja Nogacka – Microbiome

Multi-site human microbiome
Probiotics protect mice from CoCrMo particles-induced osteolysis – Zhenheng Wang – International Journal of Nanomedicine

Human respiratory microbiome
The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections – Marcos Pérez-Losada – PLoS One

Human skin microbiome
Review: Impact of nasopharyngeal microbiota on the development of respiratory tract diseases – S. Esposito – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome
Community characteristics of the gut microbiomes of competitive cyclists – Lauren M. Petersen – Microbiome

Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia – Pedro Pereira – PLoS One

Assessment of therapeutic response in Crohn’s disease using quantitative dynamic contrast enhanced MRI (DCE-MRI) parameters: A preliminary study – Jianguo Zhu – Medicine

Review: Bridging the Gap between Gut Microbial Dysbiosis and Cardiovascular Diseases – Kimberley Lau – Nutrients

Animal experiments
Statin therapy causes gut dysbiosis in mice through a PXR-dependent mechanism – Jose A. Caparrós-Martín – Microbiome

The Microbiome Activates CD4 T-cell-mediated Immunity to Compensate for Increased Intestinal Permeability – Karen L.Edelblum – Cellular and Molecular Gastroenterology and Hepatology

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas J. Sharpton – bioRxiv

Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice – Phillip T. Brooks – Microbiome

Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet – Spenser Reed – PLoS One

Gut dysbiosis in mice genetically selected for low antibody production – Ana Carolina da Silva Santos – Gut Pathogens

Plant, root, and soil microbiome
Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome – Yunzeng Zhang – Microbiome

Water and extremophile microbiome
Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Phages and viruses
Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples – Dagmara W. Lewandowska – Microbiome

HIV DNA-Adenovirus Multiclade Envelope Vaccine Induces Gp41 Antibody Immunodominance in Rhesus Macaques – Qifeng Han – Journal of Virology

Techniques
A method for measuring sulfide toxicity in the nematode Caenorhabditis elegans – Leonid Livshits – MethodsX

A novel plant-based-sea water culture media for in vitro cultivation and in situ recovery of the halophyte microbiome – Mohamed Y.Saleh – Journal of Advanced Research

Genomes
Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements – Rupa Iyer – Genomics Data

Description of ‘Arabia massiliensis’ gen. nov., sp. nov., ‘Gordonibacter massiliensis’ sp. nov., and ‘Bacilliculturomica massiliensis’ gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman – S.I. Traore – New Microbes and New Infections

Science, publishing, and career
By now, you may have all heard of the Google Engineer fired over his criticism of diversity efforts. The full memo is here. My particular thoughts resonate with the Atlantic article below, because it reminds me of how important science communication is, and how quickly it devolves into black and white:
The Most Common Error in Media Coverage of the Google Memo – Conor Friedersdorf – The Atlantic