Friday, June 29, 2012

Nice review on HiSeq/MiSeq rRNA sequencing from Caporaso et al #microbes

Quick post -- nice review worth checking out: The ISME Journal - Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

from Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R.

A key part of the paper, with highlighting from me:-
These observations, in agreement with studies that have addressed this question directly (Kuczynski et al., 2010), suggest that increasing the sequencing depth is not likely to provide additional insight into questions of beta diversity, and we therefore argue that (for questions of beta diversity in particular) the decreased cost of sequencing should be applied to study microbial systems using many more samples, for example, in dense temporal or spatial analyses, rather than with many more sequences per sample.  Of course, if the objective is to identify taxa that are very rare in communities, deeper sequencing will be advantageous. Additionally we note that while as few as 10 sequences per sample may be useful for differentiating very different environment types (for example, soil and feces), as environments become more similar (for example, two soil samples of different pH) more sequences will be required to differentiate them.

Thursday, June 28, 2012

Most unusual use of #microbes of the week: fermented fashion

Fermented clothing on mannequin from
Well, this is certainly unusual: The Genteel | Fermented Fashion.  I found out about this from a Tweet from Irene Kim

Anyway the article describes the "Micro'be'" project for which more details are available here.  Some interesting details at that site include a description

Imagine a fabric that grows...a garment that forms itself without a single stitch!
The fashion that starts with a bottle of wine...
Micro'be' fermented fashion investigates the practical and cultural biosynthesis of clothing - to explore the possible forms and cultural implications of futuristic dress-making and textile technologies.
Instead of lifeless weaving machines producing the textile, living microbes will ferment a garment.
A fermented garment will not only rupture the meaning of traditional interactions with body and clothing; but also raise questions around the contentious nature of the living materials themselves.
This project redefines the production of woven materials.
By combining art and science knowledge and with a little inventiveness, the ultimate goal will be to produce a bacterial fermented seamless garment that forms without a single stitch. 
So - in essence they are trying to grow clothing as a side product of wine fermentation.  Not sure what it is like to wear such clothing - or to be around someone wearing it - but it is a fun idea.

Dr. Mercola offers up some serious BS on probiotics and the human #microbiome

Aaarrrg.  Well, I was snooping around google news, search for "archaea" and this came up: - How Your Gut Flora Influences Your Health.

The archaea reference was in a quote that this article made of a Science Daily report
"The microbes in the human gut belong to three broad domains, defined by their molecular phylogeny: Eukarya, Bacteria, and Achaea."
Wow - this surprised me.  An article at some place called Food Consumer that was mentioning archaea.

But that was pretty much the only decent part.  Things went downhill fast with a link to some total BS on a way to cure every disorder on the planet by focusing on gut microbial health.

The article then pulls a classic trick - referencing some of the new human micro biome work in Nature to make the discussion here seem scientific. But alas it is not.  Consider this doozy of a line
"The ideal balance of beneficial to pathogenic bacteria in your gut is about 85 percent good bacteria and 15 percent bad.  Maintaining this ideal ratio is what it's all about when we're talking about optimizing your gut health. "
Yes that is right everyone - you want to maintain a ratio where 15% of the bacteria in your gut are pathogenic.  Aaarrggh.

Not surprisingly, when I searched around the web for detail on the person behind this article - some Dr. Mercola - who I have never heard of - I discovered that he is considered by many to be a quack.  No disagreement from me.

Wednesday, June 27, 2012

Video, slides & storify of my talk on "#Phylogeny-driven approaches to #genomics and #metagenomics" from #CSMUBC2012

Just got back from the Canadian Society for Microbiology meeting where I gave the keynote talk on the last day of the meeting (Saturday).  Was a very short, but good trip.  Got to see some key collaborators and colleagues and Vancouver was very nice for the few days I was there.

I recorded my talk on my laptop using the Keynote "Record Slideshow" function.  I then exported it to Slideshare (just the slides - no audio) and to Youtube (video of slides with audio).  They are posted below.  I also did a mini storification of my talk which is also below.


Monday, June 25, 2012

For those who missed it: "Science as an open enterprise" from Royal Society

This will be of interest to many I think: Science as an open enterprise - Report | Royal Society

It is a comprehensive report from the Royal Society with links to videos, text, previous meetings, references, EPUBs, and more relating to a report that was released a few days ago.  From the web site:
Six key areas for action are highlighted in the report:
  • Scientists need to be more open among themselves and with the public and media
  • Greater recognition needs to be given to the value of data gathering, analysis and communication
  • Common standards for sharing information are required to make it widely usable
  • Publishing data in a reusable form to support findings must be mandatory
  • More experts in managing and supporting the use of digital data are required
  • New software tools need to be developed to analyse the growing amount of data being gathered
Definitely worth a serious browsing/reading.

For more on this see ...

Sunday, June 24, 2012

Saturday, June 23, 2012

Best. Microbiology. Video. Ever.

Well, I could say so so much about this.  But it speaks for itself.  Funny.  Gross.  Cute.  And more.  Just watched it - like - seven times in a row.  Best. Microbiology. Video. Ever.

From Jennifer Gardy.

Friday, June 22, 2012

Major lesson from #ASM2012 meeting: microblogs & microbiology go together well

Well without a doubt the biggest surprise to me of the American Society for Microbiology General Meeting was the massive increase in the use of Twitter compared to previous years.  Microbiologist are clearly just way way ahead of the curve compared to other scientists on this.  The tweets and retweets and discussion of tweets was so extensive that #ASM2012 was a trending topic on twitter for much of the time during the meeting:

For those not familiar with Twitter - this abbreviation w/ the # is known as a hashtag - and if everyone at a meeting uses this hashtag in their posts about the meeting then it is easy to keep track of all the meeting posts by searching for posts with that hashtag.  Such searches can be done in real time with various Twitter clients or via the Twitter website.

Thursday, June 21, 2012

Ooh - cool - got to get this "Illustrated Children’s Book Introduces Invisible World Of #Microbes"

Just saw this news story: Illustrated Children’s Book Introduces Invisible World Of Microbes.  This looks like a potentially good addition to the list of books that could be called "Microbiology for Kids."  I have made a collection at Amazon of examples in this area.  Any other suggestions for microbiology books for kids?

Tuesday, June 19, 2012

Quick summary of session at #ASM2012 on “The Great Indoors” #microBEnet

 The session at the ASM 2012 meeting on “The Great Indoors” seems to have gone well. I will be writing up a more detailed report but here is a quick summary done via “Storify”.

Sunday, June 17, 2012

Some notes from GSC13 session on microbiology of the built environment #microBEnet

At the GSC13 meeting a few months ago there was a session on microbiology of the built environment which was sponsored by my microBEnet project.

Posting some details from the meeting here.

Meeting notes and reports
Talk videos:

Paula Olsiewski


Saturday, June 16, 2012

Collecting links to blogs that focus entirely or partly on microbiology topics #ASM2012

Making a list of blogs that focus entirely or partly on microbiology topics.  Here are some.  Would love suggestions for others. Obviously not all are of equal quality in terms of the writing or the science but the diversity is impressive.
  1. Aetiology from Tara Smith
  2. A Flu Diary
  4. Antibiotics: the perfect storm from David Shlaes
  5. Antimicrobial Resistance from Miriam Barlow
  6. Aspergillus Website Blog
  7. Avian Flu Diary
  8. BacterioFiles from Jesse Noar
  9. Bacpathogenomics
  10. Bacteriophage, microbiology and the battle for funding from Philip Skipper
  11. BioBE center Blog:
  12. Blastocystis Blog:
  13. Barf Blog 
  14. Chimeras
  15. CoastalPathogens
  16. Contagions from Michelle Ziegler
  17. Controversies in Hospital Infection Prevention
  18. Creepy Deadly Wonderful Parasites
  19. Curiosidades de la Microbiología
  20. Cyanobacterial Adventures
  21. Daily Parasite
  22. Daniel Wilson's Blog
  23. Dawn in Antarctica
  24. El buit del temps
  25. End the Neglect
  26. Epidemonomics
  27. ERV from Abbie Smith
  28. Food Poison Journal
  29. Food Safety and Environmental Health blog
  30. Foraminifera Blog
  31. Fun with Microbiology (What's Buggin' You?)
  32. History of Vaccines
  33. HIV This Week
  34. Hospital Infection Control and Prevention
  35. Human Microbiome Journal Club
  36. Indian Initiative for Management of Antibiotic Resistance
  37. Infection Landscapes
  38. Infectious Diseases Today
  39. International AIDS Vaccine Initiative 
  40. It's a small world
  41. Jason Tetro at the Huffington Post *
  42. JHU Phage Hunters
  43. Lab Rat
  44. mBIO
  45. Malaria World
  46. Matryoshka from Jeff Smith
  47. Memory Reactivation
  48. Memoirs of a Defective Brain
  49. microbelog
  50. MicroBichitos
  51. Microbial Diversity from Irene Newton
  52. microBEnet blog from Jonathan Eisen, David Coil, Holly Bik 
  53. Microbe Matters from KD Shives
  54. Microbiology Bytes from AJ Cann
  55. Microblogology from Lorraine Cramer
  56. Microbiology Stories
  57. Mike the Mad Biologist
  58. Miss Parasitos  AND
  59. Monotreme's Blog *
  60. MyChrobial Romance from David Baltrus
  61. Mycorant
  62. MycorWeb Fungal Genomics
  63. Mystery Rays from Outer Space
  64. Not Exactly Rocket Science from Ed Yong
  65. Of Bacteria and Men from Robin Tecon
  66. One in Seven People
  67. Outbreak News
  68. Parasite of the Day
  69. Parasites
  70. Pathogens, Genes and Genomes
  71. Pharmaceutical Microbiology by Tim Sandle
  72. Public Health Matters from the CDC
  73. Rapid Microbiology Methods 
  74. RRResearch from Rosie Redfield
  75. Rule of 6ix from Connor Bamford
  76. Russell's Blog from Russell Neches
  77. Safe Food from John Brooks
  78. Skeptic Wonder
  79. Skewed Distribution
  80. Small Things Considered
  81. Smaller Questions
  82. Sociobiology
  83. Spirochetes Unwound
  84. Superbug
  85. Superbugs and Drugs
  86. Stringent Response
  87. Symbionticism from Seth Bordenstein
  88. The Artful Amoeba
  89. The Febrile Muse
  90. The Genome Factory
  91. The "Germ Guy" Blog:
  92. The Hyphal Tip by Jason Stajich
  93. The Intestinal Gardner
  94. The Loom from Carl Zimmer
  95. The Oceloid from PSI Wavefunction
  96. The Parasite Diary
  97. The Tree of Life from Jonathan Eisen
  98. Ultraphyte from Joan Slonczewski
  99. We Beasties from Kevin Bonham
  100. The View from a Microbiologist from Samantha Price
  101. Viroblogy from Ed Rybicki
  102. Virology Blog from Vincent Racaniello
  103. Viral Bioinformatics from Chris Upton
  104. Worms and Germs
  105. Zoonotica

Friday, June 15, 2012

Coming up at the #ASM2012 mtg. "The Great Indoors: Recent Advances in the Ecology of Built Environments"

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there.  These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM - 5:30 PM

Session Room: Esplanade Ballroom 300

Description: Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors - microorganisms - and their interactions with humans.

Thursday, June 14, 2012

The human #microbiome project (HMP): new papers and news stories

Just collecting here the new papers from the Human Microbiome Project and some news stories discussing them.

Main papers in Nature
PLoS Collection (all free)
Other paper out in Nature on the topic though not from the HMP
Some news stories:

Tuesday, June 12, 2012

At IOM Forum on Microbial Threats "Science And Applications of Microbial Genomics" #SAMG12

At IOM Forum on Microbial Threats "Science And Applications of Microbial Genomics" meeting in DC. To find out current details on the meeting check out Twitter hashtag #SAMG12. See feed below (though it is easier to go to Twitter to follow #SAMG12).

Monday, June 11, 2012

Updates on the #UCDavis Academic Freedom situation

A few days ago I wrote a post: Report on "Egregious Academic Freedom Violation" at #UCDavis.  The post provides some detail on an investigation carried out by the UC Davis Academic Senate into a case of apparent retribution at the UC Davis medical school.  In the case the Dean of the Medical School (Claire Pomeroy), the Executive Associate Dean Fred Meyers and the Health System Counsel appear to have carried out a retribution of sorts against a member of the faculty at the medical school (NOTE - I have a half appointment at the medical school).  The faculty member - Michael Wilkes had the gall to write an editorial (with Jerome Hoffman) for the SF Chronicle expressing opinions about a medical issue and actions of some people at the UC Davis Medical School.  Apparently, some people at the medical school did not like being criticized.  The result?  A threat to take away his space, to remove him as instructor of a medical school course, and other incites including a threatening email/letter from the medical school counsel.  Lovely.

Fortunately, the UC Davis Academic Senate was brought into the case by Wilkes and a committee of the academic senate responded VERY strongly with a report (see my previous post with more detail).  Meanwhile - news of the report spread and was covered in Inside Higher Ed.  It was then that I heard about it and felt the need to blog about it.  And news has spread a bit more (thank you PZ Myers and others).  On Friday, the UC Davis Academic Senate met (and though I am not a member of the Senate, I went to the meeting).  And the Senate passed three resolutions coming out strongly in support of Prof. Wilkes and critiquing the behavior of the Dean, Asst. Dean and Counsel from the Med. School.  Just after the resolution was passed the faculty received an email from the Provost Ralph Hexter that was very strongly saying he supported academic freedom on campus.

So that is where we stand now.  I am very pleased with the Provost's statement.  At the same time I am still dismayed at the reported behavior of the Medical School administration.  And I think this issue needs to still get some air until there are repercussions for the Medical School actions ...

Here are some related links and updates that I collected as the story has unfolded.

Sunday, June 10, 2012

Crowdsourcing help needed: how many microbes are brought into human GI tract via food? #microbiome

Quick but somewhat complex question here that came up at a recent meeting I went to - someone wanted to know:

How many microbes come into the human GI tract from outside sources (e.g., food)?

Other related questions:

  • How many cells /day?
  • How many are alive?
  • How many kinds come in?
  • How much flow through is there vs. digestion vs. colonization?

Note - I know there have been many studies of pathogens on food and how they get into the GI tract, but what about non pathogens?

Any references or #s would be very helpful.


Friday, June 08, 2012

#UCDavis Provost Ralph Hexter very strong statement in support of Academic Freedom #Awesome

Just got this email in regard to the recent Academic Freedom Issue at UC Davis.
The following statement was issued today by UC Davis Provost and Executive Vice Chancellor Ralph Hexter:

In March, 1953 the Association of American Universities (AAU) adopted a statement articulating "The Rights and Responsibilities of Universities and Their Faculties." It includes these words:

"A university must…be hospitable to an infinite variety of skills and viewpoints, relying upon open competition among them as the surest safeguard of truth. Its whole spirit requires investigation, criticism, and presentation of ideas in an atmosphere of freedom and mutual confidence. This is the real meaning of 'academic' freedom."

A committee of our campus's Academic Senate has devoted considerable time and effort to examining an assertion by a faculty member of the UC Davis School of Medicine that his academic freedoms were compromised by school administrators. Our Senate's Representative Assembly earlier today heard and ratified the committee's findings.

Academic freedom is sacrosanct at UC Davis, and the underlying assertions in this matter are deeply troubling. My office will review this case and take appropriate actions.
Some related links:

Wednesday, June 06, 2012

Report on "Egregious Academic Freedom Violation" at #UCDavis

Crossposting this here --- posted originally on my lab blog.  NOTE - many updates down below at the bottom of page.

Wow -- just got this email regarding Academic Senate issues at UC Davis and found out about this report on “Egregious Academic Freedom Violation” in relation to an issue at the Medical School. See email below as well as the report (see link) - starting on p62. It is a pretty sordid tale ... (with some highlighting now added by me)

The email I received: 
*Sent on behalf of the Academic Senate Chair* 
Dear Academic Senate Members, 
On Friday, the Academic Senate Committee on Academic Freedom and Responsibility (CAFR) will be presenting their report, “Egregious Academic Freedom Violation” which begins on page 62 of the June 8 Representative Assembly meeting call ( The Committee on Elections, Rules and Jurisdiction (CERJ) has put the recommendations of the CAFR report into the form of resolutions, which are attached. In order to be voted on by the Representative Assembly, the resolutions would have to be moved and seconded. We hope that the attachment will assist the Representative Assembly as its members review and consider CAFR’s recommendations.

Thank you.
From: Edwin M Arevalo
Sent: Friday, June 01, 2012 11:30 AM
To: ''
Cc: Edwin M Arevalo

Subject: 2011-2012 Representative Assembly (RA): June 8 Meeting Call Notice

Tuesday, June 05, 2012

Does phylogeny matter? (In Eco-Evo meta-analyses) ... Apparently, yes, but it depends.

As many may know - I am pretty obsessed with the uses of phylogeny in biological studies.  In fact, one could say this has driven almost all of my work.  Thus when an email went around a little bit ago about an article for a journal club at UC Davis where the title begins with "Does phylogeny matter?", well, I had to take a look.  Alas, I was a bit worried when I saw the article was in Ecology Letters because I am at home and was not sure about access policies for this journal.

But I was pleasantly surprised to get full access without any library - VPN login to the following article: Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis - Chamberlain - 2012 - Ecology Letters - Wiley Online Library.  I cannot figure out WHY it is freely available right now, nor how long it will be, but I took the chance to look the article over.

And I was even more pleasantly surprised to look over the article.  Many meta-analyses can seem forced - if not almost unbearable to look through.  But this one is very well done.  Basically they did a massive comparison of conclusions that one could reach when one either does or does not take into account the phylogenetic non-independence of taxa when conducting meta-analyses in evo-eco studies.  They searched published literature for meta-analyses and then .. well I will use their words here (from the end of their introduction):

Monday, June 04, 2012

Jonathan Eisen's #Genomics #Microbiology #Evolution Online Office Hours

OK.  I love that people ask me lots of questions about evolution, genomics, microbes, a mix of the two, etc.  But I just cannot keep answering single one-off emails about these topics.  So I am starting online office hours.  If you have any general questions about phylogenetics, evolution, genomics, microbes, or any of the work done in my lab, please post your questions here.  And I will try to answer them.


Overselling genomics award #7: Ron Davis & Forbes for PR presented as "essay"

Wow.  Just saw this tweet by Dan Vorhaus:

So I decided to check it out. The piece is titled It's Time to Bet on Genomics and it is, well, just completely in appropriate.  Sure - it does take on an article that itself was over the top in downplaying the power of genomics (see Erika Check Hayden's article about that issue here).  But then Davis goes on to write about a company founded by an ex post doc of his for which Davis is one of the advisors (he does kindly let us know this, but still ...).  And what he writes he is a big big pile of fluff with no evidence presented.  Among the lines in the "essay" I find disturbing:

  • One of the most interesting of these is being developed by Genophen
  • Genophen’s application is rather breathtaking in its ambition.
  • Genophen’s “risk engine”—a simple term for some very complex data mining and computer modeling—will map your risk factors against the world’s vast library of medical research and then offer up a personalized set of behavior and treatment recommendations that can help you reduce those risks . . .  and even prevent disease itself.
  • We are now at the point where genomics-enabled medical technology can run various what-if scenarios and show you whether diet, exercise, medication, or some other factor or combination of factors has the greatest statistical likelihood of reducing that risk. The information can then be visually displayed through charts and graphs and made available to patients and their doctors via secure web-based portals.
  • But instinctively I believe it to be true, and anecdotally Genophen’s first trial provided some confirmation.
  • “The trial changed my life,” one female participant who wishes to remain anonymous told me.

All of this without any link to a paper, without any data, without any real details.  Shameful.  Not saying genomic medicine does not have a lot of promise.  But this "essay" is so excessively focused on PR for one company that there is no reason to have any faith in anything said in it.  I am therefore giving Ron Davis and Forbes my coveted Overselling Genomics Award (#7).  Plus I think Forbes deserves some sort of award for "Publishing PR" but I will have to think one of those up.  This piece almost certainly never should have been published at Forbes.Com without many many more caveats.  Yuck.

UPDATE - here is a screenshot from the Forbes Web site.  It is marked as "Forbes Leadership Forum" ... hard to tell whether it is meant as an essay, editorial, op-ed, or what.

Saturday, June 02, 2012

Preparation Y: Michelle Ellsworth - Performance art mixing dance, genomics, evolution, humor, sex #brilliant

Just got back from a Sloan Foundation funded meeting in Boulder, Colorado that focused on microbiology of the built environment.  More on that another time.  What I want to tell you about - no - what I need to tell you about - is the entertainment that the meeting organizers arranged at dinner Thursday night.

We had dinner at Red Lion Restaurant - a phenomenally gorgeous spot in the canyon just West of Boulder.  And while we were milling around before dinner I saw out of the corner of my eye a woman walking in to the tent where we were to have dinner.  She was dressed in almost all white and was carrying a giant silver spoon.  So I asked the meeting organizer - Mark Hernandez - if she was the entertainment.  And surprisingly he said - yes - she was a dancer and Professor at Boulder and also did a kind of science performance art.

Her name was Michelle Ellsworth and he said she was amazing.  So I was very intrigued as I am a big fan of mixing science and art.  So I went over to where she had set up and asked her a few questions and took her picture ...

I grabbed a seat near the front of the area they set up for her.  And Mark Hernandez introduced her

And then I witnessed what I consider to be - seriously - the most entertaining presentation I have ever seen at a conference.  She presented her "Preparation Y" project focused on what should be done to prepare for "the obsolescence of the Y chromosome."  She then proceeded to discuss some relatively recent work on Y chromosome evolution in humans as well as an article about this by Maureen Dowd.   And she posed the questions (tongue planted firmly in cheek ... though done in a style that was remarkably earnest ...)

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