August 10, 2018

This Friday enjoy reading about the global topsoil microbiome, human pharyngeal microbiota profiles and microbial biomarkers associated with chronic kidney disease. There’s an interesting podcast [Mapping microbes on the metro]! Happy weekend!

Human gut microbiome

Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition – Marcus Fulde – Nature

*Altered gut microbiota and microbial biomarkers associated with chronic kidney disease – Hengzhong Lun – Microbiologyopen.

Review: Rebuilding the Gut Microbiota Ecosystem – Antonella Gagliardi – Int. J. Environ. Res. Public Health

Human respiratory microbiome

*Human pharyngeal microbiota in age-related macular degeneration – Eliza Xin Pei Ho – PLoS One

Plant, root and soil microbiome

*Structure and function of the global topsoil microbiome – Mohammad Bahra – Nature

Mini review: Root colonization: imperative mechanism for efficient plant protection and growth – Swati Sachdev and Rana Pratap Singh – MOJ Ecology & Environmental Sciences

Review: From Microscopy to Genomic Approach in Soil Biodiversity Assessment – Lucia Popescu and Zhi-Ping Cao – Curr. Issues Mol. Biol.

Review: You Are What You Can Find to Eat: Bacterial Metabolism in the Rhizosphere – Nicola Holden – Curr. Issues Mol. Biol.


*Gut bacteria vs the immune system; Mapping microbes on the metro – Adam Levy and Benjamin Thompson – Nature Podcast

Microbes in the news

Checkpoint for gut microbes after birth – Andrew J. Macpherson and Stephanie C. Ganal-Vonarburg – Nature News and Views


July 30, 2018

Today’s digest features the microbiomes of a XVIII century mummy (Krásna Hôrka, Slovakia), an interesting initiative out of Belgium (Disbiome, a database of microbiota-disease associations), exciting news from Kamagata lab about improved culturing of environmental samples, promising findings on gut bacteria byproduct that protects against Salmonella, and much more. Happy reading!

Human microbiome

*Disbiome database: linking the microbiome to disease – Yorick Janssens – BMC Microbiol.

*The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment – Lucia Kraková – Environ Microbiol.

Gut microbiome

*A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection – Amanda Jacobson – Cell Host & Microbe

Simulation and modeling of dietary changes in the infant gut microbiome – Daniel Medina – FEMS Microbiol Ecol.

Human gut bacteria as potent class I histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid – Samantha Yuille – PLoS One

Review: An update on the role of gut microbiota in chronic inflammatory diseases, and potential therapeutic targets – Bobbi Laing – Expert Rev Gastroenterol Hepatol.

A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode – Annamaria Painold – Bipolar Disord.

Review: The Gut-Brain Axis, the Human Gut Microbiota and Their Integration in the Development of Obesity – Edward Bliss – Front Physiol.

Fungal dysbiosis in cirrhosis – Jasmohan S Bajaj – Hepatology

Urinary tract microbiome

The bacterial microbiota in first-void urine from men with and without idiopathic urethritis – Maria Frølund – PLoS One

Lung microbiome

Lower respiratory tract microbial composition was diversified in Pseudomonas aeruginosa ventilator-associated pneumonia patients – Xiaoling Qi – Respir Res.

Plant microbiome

Bacterial community assemblages in the rhizosphere soil, root endosphere and cyst of soybean cyst nematode-suppressive soil challenged with nematodes – Muzammil Hussain – FEMS Microbiology Ecology

Exploring plant-microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR-Cas9 system – Yanglei Yi – Environ Microbiol.

Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling – Garcia Joshua – Front Microbiol.

Water microbiome

Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater – Roland Wilhelm – Environ Microbiol.


*Isolation of Previously Uncultured Slow-growing Bacteria by Using a Simple Modification in Preparation of Agar Media – Souichiro Kato – Applied and Environmental Microbiology

Review: The role of the gut microbiota on animal model reproducibility – Patricia Turner – Animal Model Exp.

Review: Environmental enrichment and mouse models: Current perspectives – Kathryn Bayn – Animal Model Exp.

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – J Vis Exp.

Bioprinting microbial communities to examine interspecies interactions in
time and space – William Frederick Hynes – Biomed. Phys. Eng. Express

July 16, 2018

Today’s Digest is all about cows! Microbiome of healthy cows and cows developing postpartum endometritis, and metabolic pathways of rumen microbiota. Ok, almost. Find out whether anthropogenic radionuclides at Chernobyl (Ukraine) impact the gut microbiome of the bank vole. Also, there’s an interesting read on human microbiome and microbial metabolites that contribute to the accumulation of lipids in the liver. Happy week!

Animal microbiome

*Preprint: Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis – Raúl Miranda-CasoLuengo – bioRxiv

Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria – E.H. Hart – Scientific Report

*Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus – Anton Lavrinienko – The ISME Journal

The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus – Eldin Jašarević – Nature Neuroscience

Human microbiome

*Microbiome metabolomics reveals new drivers of human liver steatosis – Nathalie M. Delzenne – Nature Medicine

The gut–liver axis and the intersection with the microbiome – Anupriya Tripathi – Nature Reviews Gastroenterology & Hepatology

Longevity extension in Drosophila through gut-brain communication – Susan Westfall — Scientific Reports

Gut microbiota composition is related to cardiorespiratory fitness in healthy young adults – Ryan P. Durk – International Journal of Sport Nutrition and Exercise Metabolism

Microbes in the news

Data on transfer of gut microbiota from hen to chick can inform probiotic R&D [A Czech team’s research findings provide insights for the development of next generation probiotics for poultry production in the absence of antibiotics.] – Jane Byrne

*The future of the microbiome: A conversation with Michael Fischbach [Discussion on the growing knowledge of the bacteria in our bodies, their role in our health, and how researchers like Fischbach are shaping the future of microbiome-mediated disease therapy.] – Russ Altman

June 30, 2018

This Saturday enjoy reading and learning about effects of herbal chemicals on the modulation of cell metabolism, powerful Lactobacilli in vaginal environment or how halophylic bacteria can mitigate salt stress of halophytes. Happy weekend!

Human gut microbiome

Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells – Camille Martin-Gallausiaux – Scientific reports

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization – Matthew L. Jenior – mSphere

* Review: Novel therapeutic strategy for cancer and autoimmune conditions: Modulating cell metabolism and redox capacity – Xing-Xing Fan – Pharmacology & Therapeutics

Review: Gut microbiome and aging: Physiological and mechanistic insights – Ravinder Nagpal – Nutrition Healthy Aging

Editorial: Brain, antibiotics, and microbiota – how do they interplay? An Editorial for ‘Antibiotics‐induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets’ – Elena Rybnikov – Journal of neurochemistry

Human vaginal microbiome

Randomized, placebo controlled phase I trial of safety, pharmacokinetics, pharmacodynamics and acceptability of tenofovir and tenofovir plus levonorgestrel vaginal rings in women – Andrea Ries Thurman – PLoS One

* Review: The Vaginal Microenvironment: The Physiologic Role of Lactobacilli – Emmanuel Amabebe – Frontiers in Medicine

Human lung microbiome

Profiling of lung microbiota in the patients with obstructive sleep apnea – Lu Dongmei – Medicine

Review: The consequence of matrix dysfunction on lung immunity and the microbiome in COPD – Tracy Hussell – European Respiratory Review

Water and extremophile microbiome

Tile Drainage and Anthropogenic Land Use Contribute to Harmful Algal Blooms and Microbiota Shifts in Inland Water Bodies – Igor Mrdjen – Environmental Science and Technology

Viral Communities of Shark Bay Modern Stromatolites – Richard Allen White III –
Frontiers in Microbiology

Plant, root, and soil microbiome

Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid – Wang Z – PLoS One

* Bacterial microbiome of root-associated endophytes of Salicornia europaea in correspondence to different levels of salinity – Sonia Szymańska – Environmental Science and Pollution Research


The Prebiotic Inulin Improves Substrate Metabolism and Promotes Short-Chain Fatty Acid Production in Overweight to Obese Men – Christina M. van der Beek – Metabolism