July 22, 2015

Disappearance of intestinal diversity with Westernization, microbial responses in the Namib Desert after “wetting events”, how fast do ocean bacteria grow, irradiation of oral microbiota, and paying $8 to read 2 sentences.

Human gut microbiome

Antibiotic Exposure and Juvenile Idiopathic Arthritis: A Case–Control Study – Daniel B. Horton – Pediatrics

Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery – Charles Robb Flynn – Nature Communications

Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory bowel disease – S. K. Hourigan – Alimentary Pharmacology & Therapeutics

Review: Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity – Nicola Segata – Current Biology

Models of microbiome research

Dual zinc transporter systems in Vibrio cholerae promote competitive advantages over gut microbiome – Ying Sheng – Infection and Immunity

Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

You have to pay $8 to read the remaining 2 sentences of this In Brief: Engineered microbes treat experimental hyperammonemia – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Review: The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution – Andreas Brune and Carsten Dietrich – Annual Review of Microbiology

Plant, root, and soil microbiome

Effects of silver sulfide nanomaterials on mycorrhizal colonization of tomato plants and soil microbial communities in biosolid-amended soil – Jonathan D. Judy – Environmental Pollution

Phylogenic diversity and tissue specificity of fungal endophytes associated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach – Hui Jin – Antonie van Leeuwenhoek

Water regime history drives responses of soil Namib Desert microbial communities to wetting events – Aline Frossard – Scientific Reports

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility – Acacio Aparecido Navarrete – Antonie van Leeuwenhoek

Water microbiome

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms – Marine Landa – The ISME Journal

Review: Growth Rates of Microbes in the Oceans – David L. Kirchman – Annual Review of Marine Science

Metagenomics, bioinformatics

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data – Will Rowe – PLOS ONE

Protective tunicate endosymbiont with extreme genome reduction – Jan-Christoph Kehr – Environmental Microbiology


Microbial Urease in Health and Disease – Diego Mora – PLOS Pathogens


Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae) – Anush Kosakyan – European Journal of Protistology

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets – Guoqin Yu – PLOS ONE

Bacteria in the news

Fungi—key to tree survival in warming forest – Phys.org

Story behind the paper: Backbones of evolutionary history test biodiversity theory for microbes – James O. Dwyer – The Tree of Life

New open source uBiome github repository for data analysis tools – Alexandra Carmichael – uBiome

Bik’s Picks

The picture almost made me cry. Early signs that drug ‘may delay Alzheimer’s decline’ – James Gallagher – BBC News

Earth’s Most Famous Climate Scientist Issues Bombshell Sea Level Warning – Eric Holthaus – Slate

Space travel thins your skin: Spending a significant amount of time in space has several negative effects on the body. The latest discovery: thinner skin – Michelle Starr – CNET



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