June 3, 2017

There were over 100 alerts today! Here are plenty of papers after the few light digests.

Events and jobs
Bioinformatics Scientist, Microbiome – Human Longevity, Inc, Greater San Diego Area

MSc position in Microbiology – Teagasc, London/Europe

General microbiome
Review: The multi-omics promise in context: from sequence to microbial isolate – Johanna Gutleben – Critical Reviews in Microbiology

Review: Symbiosis-inspired approaches to antibiotic discovery – Navid Adnani – Natural Product Reports

Pregnancy and early life
The Microbiome of Infants Recruited to a Randomised Placebo-controlled Probiotic Trial (PiPS Trial) – Michael Millar – EBioMedicine

Safety and tolerability of Bifidobacterium longum subspecies infantis EVC001 supplementation in healthy term breastfed infants: a phase I clinical trial – Jennifer T. Smilowitz – BMC Pediatrics

Human vaginal microbiome
Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women – Nichole R. Klatt – Science

Changes in vaginal community state types reflect major shifts in the microbiome – J. Paul Brooks – Microbial Ecology in Health and Disease

Human gut microbiome
Chemoproteomic Profiling of Bile Acid Interacting Proteins – Shentian Zhuang – ACS Central Science

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota – Tingting Chen – Scientific Reports

Vancomycin Taper and Risk of Failure of Fecal Microbiota Transplant in Patients With Recurrent Clostridium difficile Infection – Roberto L. Patron – Clinical Infectious Diseases

Surgically induced changes in gut microbiome and hedonic eating as related to weight loss: Preliminary findings in obese women undergoing bariatric surgery – Claudia P. Sanmiguel – Psychosomatic Medicine

Intestinal microbiota in patients with chronic hepatitis C with and without liver cirrhosis compared to healthy controls – Benjamin Heidrich – Liver International

Dimethyl fumarate reduces the risk of mycotoxins via improving intestinal barrier and microbiota – Ning Ma – Oncotarget

Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity – Eliot T. McKinley – JCI Insight

Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombus formation via Toll-like receptor-2 – Sven Jäckel – Blood

Review: Trust your gut – metformin and diabetes – Conor A. Bradley – Nature Reviews Endocrinology

Review: Gut microbiota: Inulin regulates endothelial function: a prebiotic smoking gun? – Francesca Fava – Nature Reviews Gastroenterology and Hepatology

Review: Gut Microbiota, Endocrine-Disrupting Chemicals, and the Diabetes Epidemic – Ganesan Velmurugan – Trends in Endocrinology and Metabolism

Review: Gut Microbiota and the Gut-Brain Axis: New Insights in the Pathophysiology of Metabolic Syndrome – de Clercq – Psychosomatic Medicine

Animal experiments
Genetic mouse models with intestinal-specific tight junction deletion resemble an ulcerative colitis phenotype – Wolfgang Stremmel – Journal of Crohn’s and Colitis

Deciphering the landscape of host barriers to Listeria monocytogenes infection – Ting Zhang – PNAS

Rifaximin exerts beneficial effects in PI-IBS mouse model beyond gut microbiota – Yu Jin – Journal of Gastroenterology and Hepatology

Farnesoid X Receptor Agonist Treatment Alters Bile Acid Metabolism but Exacerbates Liver Damage in a Piglet Model of Short-Bowel Syndrome – Prue M. Pereira-Fantini – Cellular and Molecular Gastroenterology and Hepatology

Faecal transplantation for the treatment of Clostridium difficile infection in a marmoset – Yumiko Yamazaki – BMC Veterinary Research

Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs – Htun Myint – Animal Science Journal

A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs – Kristin M. V. Herstad – BMC Veterinary Research

Animal microbiome
Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks – Georg Steinert – Scientific Reports

The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats – Caitlin E. Older – PLoS One

Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life – A. Schoster – BMC Veterinary Research

Cost-effective screening and isolation of xylano-cellulolytic positive microbes from termite gut and termitarium – Libin Mathew Varghese – 3 Biotech

Plant, root, and soil microbiome
Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities – Hoang Nam Pham – Environmental Science and Pollution Research

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism – Yun-Juan Bao – Journal of Environmental Sciences

Impact of microbial communities from tropical soils on the mobilization of trace metals during dissolution of cinnabar ore – Clarisse Balland-Bolou-Bi – Journal of Environmental Sciences

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition – Xingyu Ma – Molecular Ecology

Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island – Juanli Yun – Applied Microbiology and Biotechnology

Water and extremophile microbiome
Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships – Justin R. Seymour – Nature Microbiology

Genetic characterization of periphyton communities associated with selenium bioconcentration and trophic transfer in a simple food chain – Vanessa Friesen – Environmental Science and Technology

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora – Rachel M. Wright – Scientific Reports

Metabolic network analysis reveals microbial community interactions in anammox granules – Christopher E. Lawson – Nature Communications

Hot springs of Indian Himalayas: potential sources of microbial diversity and thermostable hydrolytic enzymes – Harmesh Sahay – 3 Biotech

High throughput sequencing of microbial eukaryotes in Lake Baikal reveals ecologically differentiated communities and novel evolutionary radiations – Zhenzhen Yi – FEMS Microbiology Ecology

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure – Xiao Ma – Environmental Science and Technology

Built environment
Evolution of microbial communities growing with carbon monoxide, hydrogen and carbon dioxide – Sofia Esquivel-Elizondo – FEMS Microbiology Ecology

Adaptation of microbial community of the anode biofilm in microbial fuel cells to temperature – Xiaoxue Mei – Bioelectrochemistry

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer – Jesus D. Fernandez-Bayo – Journal of Environmental Sciences

Bacterial community structure transformed after thermophilically composting human waste in Haiti – Yvette M. Piceno – PLoS One

Food microbiology
Characterization of the peptide fraction from digested Parmigiano Reggiano cheese and its effect on growth of lactobacilli and bifidobacteria – Benedetta Bottari – International Journal of Food Microbiology

Impact of food grade and nano-TiO2 particles on a human intestinal community – William Dudefoi – Food and Chemical Toxicology

Probiotics / prebiotics
Probiotic yogurt and acidified milk similarly reduce postprandial inflammation and both alter the gut microbiota of healthy, young men – Kathryn J. Burton – British Journal of Nutrition

Phages and viruses
Phylogenetic Diversity of T4-Type Phages in Sediments from the Subtropical Pearl River Estuary – Maoqiu He – Frontiers in Microbiology

Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space – Junyu Zhang – Microbiome

Bioinformatics
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities – Jonathan L. Golob – BMC Bioinformatics

Techniques
Review: Capturing the genetic makeup of the active microbiome in situ – Esther Singer – ISME

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions – Thomas J. Moutinho Jr. – bioRxiv

Optimization of high-yielding protocol for DNA extraction from the forest rhizosphere microbes – Sadam D. V. Satyanarayana – 3 Biotech

DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing – Steffi Rocchi – Journal of Microbiological Methods

Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets – Blair Lawley – PeerJ

Microbes in the news
Unhealthy vagina microbiome can make HIV drugs less effective – Bob Roehr – New Scientist
Article featured above!

Gut microbiota and melanoma treatment responses – Caroline Robert and Franck Carbonnel – OUPblog

Biologists examine biofilm as part of port field studies – Sandor Gyarmati – Delta Optimist

Bacteria used as factories to produce cancer drugs – Phys.Org

Boffins find evidence of strange uranium-producing bacteria lurking underground – Katyanna Quach – The Reigster

Man dies from flesh-eating bacteria after swimming with new tattoo – MSN

Microbes on the market
Why Should we be Excited about the Emerging Microbiome Field? – Antonio – LabBioTech

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