Report and Storify from Lake Arrowhead: Day 2

Another great day at the Lake Arrowhead Microbial Genomics meeting.   The session titles today were “Metagenomics/Pathogens/Antibiotics/Evolution” and “Antibiotic Resistance”.  As always, the best summary of the talks can be found in the Storify below.   My random notes are here… these are just the things that struck me. Thanks to Surya Saha for the Storify! ————– Antibiotic resistance is ancient and very widespread. Antibiotic usage in livestock is responsible for a whole mess of resistance-related problems.  Has impacts well beyond the practitioners. People are better at identifying faces than they are at comparing stacked bar charts and we might … Continue reading

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Rob Knight Reddit AMA Tomorrow (9/17)!

Join Dr. Rob Knight for a Reddit AMA tomorrow, September 17, 10-11:30am MT.  This will be a great opportunity to ask one of the foremost microbiome researchers in the world about anything and everything related to the human microbiome, the American Gut Project, the Earth Microbiome Project, and, well, anything you can think of related to the wonderful world of microbes!

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Report and Storify from Lake Arrowhead Microbial Genomics: Day 1

Day 1 at the Lake Arrowhead Microbial Genomics Meeting was as always full of great talks relating to a variety of topics.  Officially the session topics were “Microbial Communities I: Microbiomes; Biodiversity” and “Microbial Communities II: Metagenomics/Biodiversity/Natural Products”. Rather than summarize all the talks, I thought I’d embed the Storify of tweets here (thanks to Surya Saha for that) and summarize the things that I personally thought were exciting. In no particular order: The human gut microbiome is surprisingly resilient to perturbations (i.e. can return to the initial state) Two of the talks showed really interesting data wherein commensal bacteria … Continue reading

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Estimating average genome size from metagenomes

We recently submitted a paper to biorxiv on the estimation of average genome size from shotgun metagenomics data and it’s application to the human microbiome ( It is currently undergoing peer review. This study was motivated by the troubling observation that many universal single-copy genes appear to vary significantly across metagenomes. How can this be? It turns out that differences in genome size between microbial communities can lead to this strange pattern. Specifically, these single-copy genes will appear to be less abundant in the communities with the larger genomes despite that these genes are actually present at the same copy-number … Continue reading

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A germaphobe’s dilemma: stop washing raw chicken

Over dinner the other night, a friend brought up ongoing public health efforts to get people to stop washing raw chicken because it spreads Campylobacter onto kitchen surfaces. I have to confess that I have been washing, drying and salting a raw chicken nearly once a week for years, following Judy Roger’s (Zuni Cafe) fabulous recipe for roast chicken. We have reported on chicken washing before (see but washing raw chicken is a surprisingly hard habit to break. There was some more recent press on this topic back in June in honor of Food Safety week (in the Mirror and BBC News), including … Continue reading

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Bacterial communities on plants grown indoors

We recently published a paper ( reporting that plants grown indoors have different leaf-surface (phyllosphere) bacterial communities than those grown outdoors. We found that Romaine lettuce grown in environmental chambers contains 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown lettuce plants was also significantly lower and contained higher proportions of Betaproteobacteria as opposed to the Gammaproteobacteria-enriched communities on field lettuce. Relocation of field-grown plants to the growth chamber resulted in less diverse bacterial populations over time. Field microbiota transplantation experiments showed that field-like bacterial communities can be established on lettuce plants grown … Continue reading

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Fish Want Probiotics Too

Researchers in Egypt did a fascinating study recently on probiotics for fish. They tested the effect of three different types of Psuedomonas fluorescens on two pathogens that affect tilapia in the Nile (P. angulliseptica and S. faecium). Their aim was to find a more eco-friendly way of controlling the pathogens in aquaculture compared to chemical antimicrobials. The probiotic was indeed able to control the pathogens, decreasing fish mortality from about 80% to 10-20% over a week. A few reasons for its antimicrobial effect are that P. fluorescens produces its own antibiotics, and it competes more effectively for iron than the pathogens can. This has interesting ramifications on antibiotic … Continue reading

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Job Posting (Grad Student) at Virginia Tech studying aerosol microbiology

Just received the following job posting from Linsey Marr at Virgina Tech: The Department of Civil and Environmental Engineering at Virginia Tech invites applications for a Ph.D. student to study the influence of environmental conditions and aerosol chemistry on the infectivity of airborne bacteria and viruses. Contact Dr. Linsey C. Marr at to find out more about this opportunity. Additional information about the research group can be found at Virginia Tech’s Department of Civil and Environmental Engineering is ranked 7th at the graduate level. The university is located in Blacksburg, a small mountain town in southwestern Virginia (four … Continue reading

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10 (well, 9) ways to ensure your next grant application fails

Got this in an email from the Bioinformatics Core at the Genome Center. I saw a lot of these mistakes in an NSF Biodiversity panel that I served on earlier this year. One thing I disagree with is the notion that you cannot do bioinformatics on a personal computer. I do this all the time. Nevertheless, this is a great resource for the UC Davis crowd. 10 ways to ensure your next grant application fails: 1. Budget for data creation (e.g. sequencing) but not bioinformatics (analysis, storage, backup, dissemination) 2. Propose bioinformatics experiments that cannot answer your question 3. Design … Continue reading

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“Tiny Creatures: The World of Microbes”

I just stumbled across a NY Times article about a children’s book by Nicola Davies by the title Tiny Creatures: The World of Microbes. The article and the quotes from the book make me both excited and optimistic for how microbes are portrayed. A huge problem I have found in talking to non-microbiologists about microbiology is that there is a stark focus on pathogens; despite the fact that most microbes are beneficial and necessary for human life. If the general perception of these “tiny creatures” is changed, subjects like antibiotic resistance and microbes in the built environment will become way easier … Continue reading

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