February 12, 2015

Happy Darwin Day! To celebrate, I’ll start of with an older paper:

What did Darwin say about microbes, and how did microbiology respond? – Maureen A. O’Malley – Trends in Microbiology

Two San Francisco Bay Area events of interest

Sat/Sun Feb 14/15: Family Science Days. Free event. Join the LSA, NASA, Science is Elementary (where I volunteer) and more at #FamSciDays!

Tue Feb 17, VLAB forum discussion: Gut-Feeling — Ventures into the Microbiome. Will bacteria enable personalized medicine?

General human microbiome

Review: Microbial Diversity: Relevance and Relationship Between Environmental Conservation And Human Health – Jeremias Pakulski Panizzon – Brazilian Archives of Biology and Technology

Human skin microbiome

Editorial: S. epidermidis Influence on Host Immunity: More Than Skin Deep – Richard L. Gallo – Cell Host & Microbe

Human gut microbiome

What role do bacteria play in persisting fistula formation in idiopathic and Crohn’s anal fistula? – P. J. Tozer – Colorectal Disease

Review: Spondyloarthritis and the Microbiome: New Insights From an Ancient Hypothesis – Julia Manasson, Jose U. Scher – Current Rheumatology Reports

Animal models of microbiome research

Editorial: TFH-IgA Responses Keep Microbiota in Check – Kanya Honda – Cell Host & Microbe

Effects of rearing temperature and dietary short-chain fructooligosaccharides supplementation on allochthonous gut microbiota, digestive enzymes activities and intestine health of turbot (Scophthalmus maximus L.) juveniles – I. Guerreiro – Aquaculture Nutrition

Animal microbiome

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna – Saranya Peerakietkhajorn – Environmental Microbiology Reports

Catacombs microbiome

When in Rome: Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies – Lucia Krakova – Environmental Microbiology

Soil and sediment microbiome

Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems – Jun Gong – Environmental Microbiology

The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group – Travis B. Meador – Environmental Microbiology

Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica – Sean T. S. Wei – Polar Biology

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments – Anniet M. Laverman – Environmental Science and Pollution Research

Temperature Sensitivity of Microbial Respiration of Fine Root Litter in a Temperate Broad-Leaved Forest – Naoki Makita, Ayumi Kawamura – PLOS ONE

Water microbiome

Review: Marine microbial community dynamics and their ecological interpretation – Jed A. Fuhrman – Nature Reviews Microbiology

Bioreactor microbiome

Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater – Hyun Min Jang – Water Research

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus – Xiao-Mei Su – Microbial Biotechnology

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology

Opinion/review: Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities – Shaman Narayanasamy – Microbial Biotechnology

Metabolomics and Proteomics

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities – Sandi Yen – Journal of Proteome Research

Surveillance for lower airway pathogens in mechanically ventilated patients by metabolomic analysis of exhaled breath: a case-control study – Stephen J Fowler – Thorax

The Unipept metaproteomics analysis pipeline – Bart Mesuere – Proteomics

Review: A Biotechnological Approach to Microbial Based Perfumes and Flavours – Charu Gupta – Journal of Microbiology & Experimentation

Microbial Ecology

Ecological Perspectives on Synthetic Biology: Insights from Microbial Population Biology – Ana E. Escalante – Frontiers in Microbiology


A machine learning pipeline to improve De Bruijn graph metatranscriptomic assemblies – Hussein Mohsen – Bioinformatics


Identification of response classes from heavy metal-tolerant soil microbial communities by highly resolved concentration-dependent screenings in a microfluidic system – Dana Kürsten – Methods in Ecology and Evolution

Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria – Kelley A. Meinhardt – Environmental Microbiology Reports

Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples – Jan Mareš – Journal of Phycology

Other microbiology papers

Binding of the Fap2 Protein of Fusobacterium nucleatum to Human Inhibitory Receptor TIGIT Protects Tumors from Immune Cell Attack – Chamutal Gur – Immunity

Microbes in the news

Podcast on the NY Subway Microbiome paper (19 min)Listen To Our Conversation With The Microbe Map Man – Jody Avirgan – Five Thirty Eight

Another short Podcast: Subway DNA Survey Finds Microbes, Mozzarella and Mystery – Christopher Intagliata – Scientific American

What The Bacteria In Your Gut Have To Do With Your Physical And Mental Health – Carolyn Gregoire – The Huffington Post
Cecilia Westbrook Makes Yogurt With Her Own Vaginal Bacteria (NSFW) – David Moye – The Huffington Post

Bacteria, economics and our aging population – Julie Flaherty – MedicalXpress

Session Recap: Therapeutic Workshop “Trust Your Gut” with Martin Blaser et al. – BiotechNow

Is there a link between gut microbiota and Parkinson’s disease? – GutMicrobiotaWatch

Early microbiome development impacts later weight gain – Nathan Gray – NutraIngredients

Not all microbial strains are equally efficient – Kemin – All About Feed

The Nanotech View of the Microbiome (Kavli Roundtable) – Alan Brown – LiveScience

Bacteria protect intestinal tumor model from being killed by immune cells – Cell Press – Eureka Alert

A discussion of Casadevall and Pirofski’s Nature commentary: What’s The Damage? – Amesh Adalja – BifurcatedNeedle

New Non-Stick Coating Will Stop Bacteria Sticking to Medical Materials – Jamie Condliffe – GizModo

Science, publishing, and career

NIH proposal to create grant for aging scientists hits a nerve – Jocelyn Kaiser – Science

Social media: A network boost – How scientists can use Twitter to expand their social contacts and find jobs – Monya Baker – Nature

Elsevier Valentines – It all started with an innocent tweet. – Sylvain Deville – Storify

Bik’s Picks

U.S. Droughts Will Be the Worst in 1,000 Years – Mark Fischetti – Scientific American

Emaciated sea lion pup rescued from side of San Francisco highway – Reuters.com

Happy Darwin Day! Here are our favorite stories about evolution – Rachel Feltman – Washington Post


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