November 25, 2015

My apologies for 2 missed posts (due to overseas family circumstances). Gut microbiota of infants with botulism, gut microbial diversity in US Midwest population, decomposing pig carcasses, oil-degrading microbes and sunlight.


5th Annual Microbiology of the Built Environment Conference – June 1-3 2016, Boulder, CO


Our lab at Stanford University is hiring a Clinical Study Coordinator to be based out of UCSF School of Dentistry. Great position for someone who eventually wants to go to medical or dental school.

Pregnancy and birth

The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Epigenomics

Human oral microbiome

The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis – Ming Chen – Journal of Dental Sciences

Human gut microbiome

Characterizing the fecal microbiota of infants with botulism – T. Brian Shirey – Microbiome

Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults – Sushmita G. Yallapragada – Pediatric Annals

Impact of demographics on human gut microbial diversity in a US Midwest population – Jun Chen – PeerJ Preprint

Review: Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development – Manu S. Goyal – PNAS

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Review: The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Future Medicine

Microbiome models

Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth – Jonathan Breton – Cell Metabolism

Plant, root, and soil microbiome

From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation – Sebastián Fuentes – Applied and Environmental Microbiology

Metabarcoding analysis of Phytophthora diversity using genus specific primers and 454 pyrosequencing – Maria I Prigigallo – Phytopathology

Structures of microbial communities in alpine soils: seasonal and elevational effects – Anna Lazzaro – Frontiers in Microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

The community structures of prokaryotes and fungi in mountain pasture soils are highly correlated and primarily influenced by pH – Anders Lanzen – Frontiers in Microbiology

Water microbiome

Application of Microfluidic QPCR (MFQPCR) Technique to Monitor Bacterial Pathogens in Beach Water and Complex Environmental Matrices – Muruleedhara Byappanahalli – Environmental Science & Technology Letters

Natural sunlight shapes crude oil-degrading bacterial communities in northern Gulf of Mexico surface waters – Hernando P. Bacosa – Frontiers in MIcrobiology

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis – Yu Wang – ICES Journal of Marine Sciences

Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India – C. M. Mehta – Compost Science & Utilization

Extremophile microbiome

Microbial metagenomics of oil sands tailings ponds: small bugs, big data – Julia M. Foght – Genome

Built environment microbiome

Changes in Microbes of the Built Environment in Early Stages of Urbanization – Maria Gloria Dominguez-Bello

Microbiome of death

The impact of carrion decomposition on the fatty acid methyl ester (FAME) profiles of soil microbial communities in southern Canada – Heloise Breton – Canadian Society of Forensic Science Journal

Metagenomics and bioinformatics

Assembly: a resource for assembled genomes at NCBI – Nucleic Acid Research

Web Resources for Metagenomics Studies – Pravin Dudhagara – Genomics, Proteomics & Bioinformatics

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data – Martial Marbouty – Trends in Genetics

EBI metagenomics in 2016 – an expanding and evolving resource for the analysis and archiving of metagenomic data – Alex Mitchell – Nucleic Acids Research

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 – Daniel Greuter – Nucleic Acids Research

Microbial ecology / more microbiology

Review: Microbial Invasions: The Process, Patterns, and Mechanisms – Cyrus Alexander Mallon – Trends in Microbiology

Review: Microbial diversity — exploration of natural ecosystems and microbiomes
Sean M Gibbons – Current Opinion in Genetics & Development

Microbes As Friends, Not Foes: Shifting the Focus from Pathogenesis to Symbiosis – Sheila A. Homburger – The American Biology Teacher

Microbes in the news

Leading Antibiotic Doomsayer Mellows on Infection Armageddon – Michael Byrne – Motherboard
I believed we would face an antibiotics apocalypse – until now – Richard James – The Guardian

TardigradesInside the Bizarre Genome of the World’s Toughest Animal – Ed Yong – The Atlantic

C&EN Talks With Microbiome Surveyor Stefanie Kandels-Lewis: The laboratory technician turned fixer kept the Tara Oceans project, an expedition to map the oceans’ microbial populations, afloat for four years – Sarah Everts – C&EN

Kiwi scientists invent stomach ulcer cure – Olivia Wannan – Stuff NZ

A Doctor Wrestles With Whether To Keep Wearing His White Coat – John Henning Schumann – NPR

When will the world wake up to the potential of poo power? – John Vidal – The Guardian

At TEDMED 2015: How microbiome studies could improve the future of humanity – ScopeBlog

Two Types of Diet May Protect Against Type 2 Through Regulation of Gut Microbiota – Diabetes in Control

Symberix lands two SBIRs for GI drug that targets the microbiome – Meghana Keshavan – MedCity News

Diet study overturns all we know about healthy eating – Israel21c

Liberia monitors over 150 Ebola contacts as virus re-emerges – James Harding Giahyue – Reuters

Now We Can Use Microbes to Make Designer Chocolate Flavors – Esther Inglis-Arkell – Gizmodo

Fossils show sign of ancient vampire microbes – Punctures in fossils suggest predation drove the evolution of self-defense systems – Thomas Sumner – Student Science

Science, publishing and career

Stepping Away from the Lab:Emilie, Can I Ask You? Why I made the decision to leave academic research and become an editor.- Cell



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