Microbial biomarkers for diabetes, gut sialidases, pathogens in stranded sea turtles, microbial biodeterioration of an ancient staircase, and how bacterial stay in shape.
Events
‘Microbiome-based Foods for Health and Sustainability’ workshop, 23 February, Brussels – APC Microbiome Institute
Call for Entries! ASM’s 2016 Agar Art Contest. Deadline: May 6.
Human oral microbiome
Intracerebral hemorrhage and deep microbleeds associated with cnm-positive Streptococcus mutans; a hospital cohort study – Shuichi Tonomura – Scientific Reports
Review: Oral Microbiome: Contributions to Local and Systemic Infections – Kerri T. Simpson – Current Oral Health Reports
Human gut microbiome
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes – Moran Yassour – Genome Medicine
Postoperative changes in fecal bacterial communities and fermentation products in obese patients undergoing bilio-intestinal bypass – Vania Patrone – Frontiers in Microbiology
The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments – Rima M Shobar – Clinical and Translational Gastroenterology
Registered report: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma – John Repass – eLIFE
Review: Sialidases from gut bacteria: a mini-review – Nathalie Juge – Biochemical Society Transactions
Review: Akkermansia muciniphila and its role in regulating host functions – Muriel Derrien – Microbial Pathogenesis
Models of microbiome research
Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice – Jun Li – PNAS
The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility – Cory A Gall – ISME Journal
Have clay will lay: Chicken: Dietary supplementation with the clay mineral palygorskite affects performance and beneficially modulates caecal microbiota in laying pullets – S. Chalvatzi – Journal of Applied Microbiology
Animal microbiome
Bacterial agents in 248 ticks removed from people from 2002 to 2013 – Camille Aubry – Ticks and Tick-borne Diseases
Bacterial and viral pathogens detected in sea turtles stranded along the coast of Tuscany, Italy – G. Fichi – Veterinary Microbiology
Poor English (but US lab): Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria – Zhenyu Shen – Omics’ Journal of Data Mining in Genomics & Proteomics
Editorial: Developmental biology: Females have a lot of guts – Justin Fear – Nature
The sexual identity of adult intestinal stem cells controls organ size and plasticity – Bruno Hudry – Nature
Plant, root, and soil microbiome
Bacterial predator–prey dynamics in microscale patchy landscapes – Felix J. H. Hol – Proceedings of the Royal Society B
Variation in soil microbial communities associated with critically endangered Wollemi pine affects fungal, but not bacterial, assembly within seedling roots – J.L. Rigg – Pedobiologia
The Effects of Nitrogen Fertilizer on Soil Microbial Communities Under Conventional and Conservation Agricultural Managements in a Tropical Clay-Rich Ultisol – Miura, Toshiko – Soil Science
Cover Crop and Irrigation Effects on Soil Microbial Communities and Enzymes in Semiarid Agroecosystems of the Central Great Plains of North America – Francisco J. Calderón – Pedosphere
Effect of soil disinfection with chemical and biological methods on bacterial communities – Md Rokunuzzaman – Egyptian Journal of Basic and Applied Sciences
Water and extremophile microbiome
Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines – Charlotte D. Vavourakis – Frontiers in Microbiology
Characterization of bacterial communities in wetland mesocosms receiving pharmaceutical-enriched wastewater – Dongqing Zhang – Ecological Engineering
Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome – Fabyano Alvares Cardoso Lopes – PLOS ONE
Thesis: Tightly-coupled sulfur-cycling microbial mats of the White Point hydrothermal vent field, CA: An analog for deep-sea vents – Priscilla J Miranda – California State University Long Beach
Thesis: The microbial diversity and function of Arctic supraglacial biomes – Stefanie Lutz – University of Leeds
Built environment microbiome
Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms – Guadalupe Piñar – PLOS ONE
The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens – Jerneja Zupančič – PLOS ONE
Bioinformatics and metagenomics
IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – BioRxiv
Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads – Yvan Le Bras – GigaScience
Shannon: An Information-Optimal de NovoRNA-Seq Assembler – Sreeram Kannan – BioRxiv
RECKONER: Read Error Corrector Based on KMC – Maciej Długosz – ArXiv
A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing – Tian-Hao Zhang – BMC Genomics
More microbiology
HT: Liz Costello: Universal resilience patterns in complex networks – Jianxi Gao – Nature
Microbially assisted recording of the Earth’s magnetic field in sediment – Xiangyu Zhao – Nature Communications
High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection – Jeroen De Smet – The ISME Journal
Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway – Sung Ryeol Park – Nature Communications
Review: Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments – Desirée C. Yang – Microbiology and Molecular Biology Reviews
Microbes in the news
Oral bacteria linked to risk of stroke – Betty Coffman – University of Louisville
Opportunistic Fungal Pathogens in Dishwashers and Kitchens – Alex Alexiev – MicroBEnet
UVA: Bacteria Overgrowth Could Be Major Cause of Stunting in Children – University of Virginia Health System – NBC29
A new method to dramatically improve the sequencing of metagenomes – EurekAlert
What your gut bacteria can tell you about type 2 diabetes – MedicalXpress
New anti-biofilm compounds show promise against drug-resistant bacteria linked to hospital infections – Ian Demsky – University of Michigan
Crowdfunding project: How Insects and Bacteria Can Solve Murder Mysteries: estimate the time since death (TSD) at a crime scene – Experiment
Crowdfunding project: E pluribus unum: how honey bee bacteria coordinate behaviors – Irene Newton – Experiment
uBiome Named One of World’s Top 10 Most Innovative Companies in Healthcare by Fast Company – PR Web
MIT Spinout Synlogic Grabs $40M To Program Microbes Into Living Drugs – Luke Timmerman – Forbes
Science, publishing, and career
Biologists urged to hug a preprint: ASAPbio meeting discusses the ins and outs of posting work online before peer review – Ewen Callaway – Nature
Accelerating Science with Preprints – Peter Binfield – PeerJ Blog
XY Bias: How Male Biology Students See Their Female Peers. In three large classes, men overrated the abilities of male students above equally talented and outspoken women – Ed Yong – The Atlantic
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