May 31, 2016

Feces for forensic investigations, respiratory tract microbiome in premature infants, soil microbes in cereal rotation, sourdough microbiota, kombucha bacteria making cellulose, GutCyc metabolic models, and 157 new microbial genomes from biogas reactors.

Pregnancy and birth

The Microbiome of the Lower Respiratory Tract in Premature Infants with and without Severe Bronchopulmonary Dysplasia – Takashi Imamura – American Journal of Perinatology

High fecal IgA is associated with reduced Clostridium difficile colonization in infants – Sarah L. Bridgman – Microbes and Infection

Human gut microbiome

Microbial population analysis improves the evidential value of faecal traces in forensic investigations – Frederike C. A. Quaak – International Journal of Legal Medicine

Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis – Rajesh Shah – Gut Microbes

Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection – Mária Džunková – mSphere

Review: Tolerance to the Intestinal Microbiota Mediated by ROR(γt)+ Cells – Caspar Ohnmacht – Trends in Immunology

Review: Vegetarian diets and gut microbiota: important shifts in markers of metabolism and cardiovascular disease – Vinicius A. do Rosario – Nutrition Reviews

Review: Microbiome and its Impact on Gastrointestinal Atopy – Amanda B. Muir – Allergy

Review: Gut microbiota and inflammatory joint diseases – Maxime Breban – Joint Bone Spine

Review: Faecal microbiota transplantation: applications and limitations in treating gastrointestinal disorders – Hani Sbahi – BMJ Open Gastroenterology

Book chapter with not a lot of data: Gut Microbiota: A Possible Role in the Pathogenesis of Multiple Sclerosis – Takashi Yamamura – Neuro-Immuno-Gastroenterology

Review: Recent Advances and Understanding of Using Probiotic-Based Interventions to Restore Homeostasis of the Microbiome for the Prevention/Therapy of Bacterial Diseases – Jan S. Suchodolski – Microbiology Spectrum

ReviewThe human gut microbiome impacts health and disease – Stanislav Dusko Ehrlich – Comptes Rendus Biologies

Animal microbiology

Analysis of cultivable microbiota and diet intake pattern of the long-lived naked mole-rat – Tewodros Debebe – Gut Pathogens

EditorialMicrobial ecology: Algae feed a shift on coral reefs – Melissa Garren – Nature Microbiology

Grandeur Alliances: Symbiont Metabolic Integration and Obligate Arthropod Hematophagy – Rita V.M. Rio – Trends in Parasitology

Plant, root, and soil microbiome

Pastures to woodlands: changes in soil microbial communities and carbon following reforestation – T.R. Cavagnaro – Applied Soil Ecology

The legacy effect of cover crops on soil fungal populations in a cereal rotation – Andrew P. Detheridge – Agriculture, Ecosystems & Environment

Microbial utilization of double-labeled aspen litter in boreal aspen and spruce soils – Charlotte E. Norris – Soil Biology and Biochemistry

Isolating a functionally relevant guild of fungi from the root microbiome of Populus – Gregory Bonito – Fungal Ecology

Review Lichen-Associated Bacteria as a Hot Spot of Chemodiversity: Focus on Uncialamycin, a Promising Compound for Future Medicinal Applications – Delphine Parrot – Planta Med

Book Chapter: Plant-Rhizobacteria Interaction and Drought Stress Tolerance in Plants – Cohen Ana Carmen – Drought Stress Tolerance in Plants, Vol 1

Water microbiology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Food microbiology

New insight into microbial diversity and functions in traditional Vietnamese alcoholic fermentation – Vu Nguyen Thanh – International Journal of Food Microbiology

Evolution of sourdough microbiota in spontaneous sourdoughs started with different plant materials – Valery Ripari – International Journal of Food Technology

Review: Drivers for the establishment and composition of the sourdough lactic acid bacteria biota – Marco Gobbetti – International Journal of Food Microbiology

Pollution and waste microbiology

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes – Laura Treu – Bioresource Technology

Differential impacts of willow and mineral fertilizer on bacterial communities and biodegradation in diesel fuel oil-contaminated soil – Mary-Cathrine C. Leewis – Frontiers in Microbiology

Spatial variation of microbial community structure in the Zijinshan commercial copper heap bioleaching plant – Xingyu Liu – Minerals Engineering


Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples – Angela Glassing – Gut Pathogens


A metagenomic comparison of endemic viruses from broiler chickens with runting stunting syndrome and from normal birds – Ryan Devaney – Avian Pathology


GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models – Aria S. Hahn – bioRxiv

metaBIT, an integrative and automated metagenomic pipeline for analyzing microbial profiles from high-throughput sequencing shotgun data – Guillaume Louvel – Molecular Ecology Resources

A resource-frugal probabilistic dictionary and applications in (meta)genomics – Camille Marchet – arXiv

Book Chapter: An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings – Sharma V. Thankachan – Bioinformatics Research and Applications

More microbiology

Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain – Michael Florea – PNAS

Bacteria In Kombucha Tea Could Be Key To Materials Useful For Mars Mission – Ted Ranosa – Tech Times
Engineering ‘tea bacteria’ could lead to advanced materials – Colin Smith – Imperial College London

Microbes in the news

This genetically engineered bacteria can inhale CO2 and produce energy – Futurism
Harvard Scientist Engineers Bacterium That Inhales CO2, Produces Energy – Jeff McMahon – Forbes

Daily Beast Fails in Its Reporting on Probiotics – David Wild – Gastroenterology & Endoscopy News

Why Ice Cream And Peanut Butter May Promote Gut Inflammation – Both contain emulsifiers, which are added to improve texture and extend shelf life – Rachael Rettner – Huffington Post

Scientists find novel enzymes encoded by giant virus – TASS Russian News Agency

Science, publishing and career

We need to do more for women in science – H. Ahmed – Science


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