Get your favorite microbial genome sequenced, for free, by DOE-JGI

Just got this email from Barny Whitman:

Genomic Sequencing of Prokaryotic Type Strains
The Community Sequencing Program (CSP) Microbial Quarterly call of the DOE Joint Genomes Institute provides a great opportunity to obtain draft genomic sequences of the type strains of bacterial and archaeal species.  The type strains may also include proposed species prior to publication. Type strains relevant to DOE mission areas, such as bioenergy, biogeochemistry, bioremediation, carbon cycling, and phylogenetic diversity are of special interest, but other type strains are also considered.  However, strains of human pathogens and human associated species are not eligible.  Proposals for genome sequencing of type strains can be submitted through the CSP Microbial Quarterly call, whose deadline is September 11, 2012, with approval usually being completed within one month.  Up to 12 strains can be included in each proposal.  Proposals for larger numbers of strains need to be submitted to the CSP annual call in the spring.

Proposals may be completed on-line at: http://proposals.jgi-psf.org/proposals.  You will need to register and sign in to this server.  Once on the server, follow the links to the “CSP Quarterly Microbial, bacterial and archaeal isolates and single cells”.  All strains will have to have been deposited in a culture collection, including proposed type strains prior to publication. If a culture collection ID is not available, you can attach a copy of the Certification of Availability. Once approved, you will need to provide 5-10 µg of high molecular weight DNA for a Minimal Draft genome.

For questions, contact Barny Whitman, University of Georgia (whitman@uga.edu).

This is an incredible opportunity. Do not pass this up.

Profile of Michael Turelli in the Sacramento Bee

Pretty good profile of Michael Turelli in the Sacramento Bee: UCD professor Michael Turelli finds biomathematics work 'ridiculously satisfying' - Living Here - The Sacramento Bee.  It discusses his career from PhD work to early research to his new work on Wolbachia.  Note of lack of objectivity on my part - Turelli was the first person to recruit me to UC Davis and, well, I love him.  He simply is great ...

Rosacea - What Causes It? News story overplays suggested connection to skin mites

Just got done reading this: Could Bacteria in Skin Mites Help Cause Rosacea? - US News and World Report.  The article leads off with a bold statement that caught my eye

"Bacteria carried by tiny mites on the skin might be responsible for the common dermatological condition known as rosacea, researchers say."

This caught my attention because I have been reading up on skin microbes recently and though many have suggested connections between microbes and rosacea as far as I know nobody has shown any causal relationship.  And causation vs. correlation has been on my mind a lot recently.

Almost like getting an email from Santa Claus

My wife just shared this with me - an email she got back from the Lego company

Thank you for getting in touch with us about your replacement LEGO® pieces.

I'm sorry to hear your LEGO pieces need replacing. We get to play with LEGO sets all day long (the best job in the world?), so I know that sometimes a piece wears out or gets lost.

That's why I've asked for a replacement piece to be sent out to you. We always try to match the color you want, but sometimes stocks run low, so we might have to send you a different one. Unfortunately part# 4498712 is licensed and was not included with this request.

Although we usually ask people to pay for replacement pieces, I'm sending this one for free - so now you can get building and have fun!

Your replacement parts will be shipped from our facility in Denmark. Please allow 7-10 business days for delivery.

Thanks again for contacting us. We are always pleased to receive feedback from LEGO fans! If you could take a moment to complete a four question survey by going to the link below, it will help us make sure we are providing the best customer service to you.

NCBI. Why? Why? Why is the default database for blasting "human G+T"

It is the little things.  The little things that can sometimes eat at you.  And here is one of my little pet peeves.  At some point - not sure how recently - NCBI changed the default database for Blastn searching to the "human G+T" database.  This Db contains human genomic and transcriptomic data.

Now - I am extremely grateful for many - if not most - of the things NCBI does.  Pubmed is great.  Pubmed Central rocks.  Sequence databases galore.  And all sorts of widgets and tools associated with sequence analysis.  Including a free blast server.  Which I use a lot.  But why? why is human G+T the default database for blastn searches?  Why?  I never only want to search this Db.  Why not have the non redundant Db of everything be the default?  Are there really that many people who only want to search human G+T?  Or is this some ploy to force people to do such searches?  This tiny little thing.  This setting.  This glitch.  Whatever it is.  It drives me batty ...

Winner of the "genome conference speakers should be male" award ...

Presenters at the World Genome Data Analysis Summit.  Women highlighted in yellow.

1. Richard LeDuc, Manager, National Center for Genome Analysis Support, Indiana University
2. Gholson Lyon, Assistant Professor, Cold Spring Harbour Laboratory
3. Christopher Mason, Assistant Professor, Cornell University
4. Liz Worthey, Assistant Professor, Medical College of Wisconsin
5. Garry Nolan, Professor of Genetics, Stanford University
6. David Dooling, Assistant Director, Genome Institute, Washington University
7. Peter Robinson, Senior Technical Marketing Manager, DataDirect Networks
8. Thomas Keane, Senior Scientific Manager, Sequencing Informatics, Wellcome Trust Sanger Institute
9. Eric Fauman, Associate Research Fellow, Pfizer
10. Geetha Vasudevan, Assistant Director and Bioinformatics Scientist, Bristol-Myers Squibb
11. Shanrong Zhao, Senior Scientist, Johnson & Johnson
12. Bill Barnett, Director, National Center for Genome Analysis Support, Indiana University
13. Zemin Zhang, Senior Scientist, Bioinformatics, Computational Biology, Genentech
14. Christopher Mason, Assistant Professor, Cornell University
15. James Cai, Head, Disease & Translational Informatics, Roche
16. Eric Zheng, Fellow of Bioinformatics Science, Regeneron
17. Monica Wang, Associate Director, Knowledge Engineering, Millennium
18. Joachim Theilhaber, Lead Bioinformatics Research Investigator, Sanofi
19. Francisco De La Vega, Visiting Scholar, Stanford University
20. Don Jennings, Manager of Data Integration, Enterprise Information Management, Eli Lilly
21. Deepak Rajpal, Senior Scientific Investigator, Computational Biology, GSK
22. Mark Schreiber, Associate Director, Knowledge Engineering, Novartis

So that is a ratio of 19:3 for a whopping 13.6% women.  Please - I beg of you - if you are organizing a conference give some thought to the diversity of speakers.  In my experience the best conferences have always ended up being ones with highly diverse speakers.  These conferences were good probably because the organizers put a lot of thought into who to invite to speak, rather than just inviting either big names or people that one knew in some way.

UPDATE: It has been pointed out that I listed one person (Chris Mason) twice -- so it is only an 18:3 ratio.  Phew.  Much better.

For other posts on this topic see

• women in science
• The Tree of Life: Diversity (of speakers, participants) at meetings: do ...
• The Tree of Life: A conference where the speakers are all women?
• A conference where the speakers are all women? (with tweets - Storify
• "Genomics: the Power and the Promise" meeting - could be called "Men Studying Genomics" instead

Bad words: Nebraska declares many words and names to be off limits when spelled/written

For immediate release
From the Nebraska State Government Headquarters

------------------------------------------
In response to criticisms of our handling of the sign language based signing of a child's name we have decided that it would only be rationale to also apply the same standard to written and spoken words.  Therefore, be it declared that any words or names that are one letter substitution away from anything bad should be banned.

For example, due to the danger associated with the word G-U-N (which we note - we are just spelling here but not actually writing the word) the following names have been banned: GUS, GUY and the following words are not allowed either GUM, GUY, BUN, RUN, SUN, FUN, GIN, PUN, GUT

For similar reasons it has been deemed that the following names and words to be banned:

• Names: Ash, Bart, Buck, Butch, Cam, Coco, Dick, Dirk, Fitch, Huck, Luck, Mitch, Nick, Santorum, Tito
• Words: abs, ads, ash, ask, asp, batch, bits, buck, bum, bunt, butch, can't, cart, cent, chit, cub, cud, cup, cut, dart, deck, dice, dink, disk, diss, ditch, dock, dock, duck, fare, farm, fits, fort, funk, hiss, hitch, hits, hum, hunt, itch, jock, kick, kiss, kits, lick, lock, luck, miss, mock, muck, mum, nits, part, pick, pitch, pits, puck, punt, rock, rum, runt, santorum, shin, ship, shot, sick, sits, skit, slit, snit, sock, spit, such, sum, tart, tats, tick, tins, tips, tots, tuck, wart, witch, wits, yuck, yum

Germs germs germs. They are everywhere. Get rid of them w/ hexochlorophene.

Now that many people consider germs to be a blessing, not a curse, it is useful to remind ourselves where we were a few years ago.  Today's episode of "bad germs" is brought to you by Tact soap.  Hat top to Liza Gross.





Or see this newspaper ad:


So what if Tact soap from that era had hexachlorophene (the active ingredient in phisohex and something that probably is not so good for you). It killed microbes. And that has to be a good thing right? Right?

Velasquez-Manoff opinion piece in the NY Times on autism, parasites & inflammation; nice ideas; not enough caveats

There is a very interesting "Opinion" piece in the New York Times today: Immune Disorders and Autism - NYTimes.com.  By Moises Velasquez-Manoff is details some recent work that the author believes relates to autism and a variety of other human ailments with an autoimmune connection.

The general logic/key points seem to be as follows:

• Some autism cases look like a form of inflammatory diseases with the immune system overactive (inflammation on high, anti-inflammation on low, or some combination thereof)
• Infection of a mother during pregnancy increases the risk of having a child with autism.
• In animal models, inducing inflammation in the mother (even without an infection) leads to an increased risk of behavioral "problems" in her offspring
• Inflammatory and/or autoimmune diseases (e.g., asthma) have increased in incidence along with autism.
• If a mother has automimmune or inflammatory diseases such as rheumatoid arthritis celiac disease she has a higher risk of having a child with autism.  Similarly if a mother has allergies or asthma during the second trimester, there is a higher risk of having children with autism.  
• Many automimmune and inflammatory disorders and autism are all more prevalent is the developed world.
• The developed world is generally cleaner that the developing world.  
• There are many fewer parasites in people in the developed world.
• Parasites are known to suppress inflammation.
• Therefore, we may be able to stop/limit autism, asthma, and other inflammatory diseases by purposefully infecting people with parasites from our evolutionary past. 

Now, personally, I like the general hypothesis here.  It makes complete sense.  But alas, it is suffers from this issue that is spreading almost as fast as these diseases - a lack of a discussion of the distinction between correlation and causation.  I have been obsessing about this a bit recently with studies of the microbiome.   Overall, I do like this current article.  It mixes human epidemiological studies with controlled animal studies with discussion of conceptual models.  But alas there is really no discussion of the challenges if disentangling correlations vs. causation. And I think it is a bit dangerous in the latter parts with the jump to potentially curing these various ailments by purposeful infection with parasites.  Again, I like the idea.  But a few caveats would have been nice.  I am glad it was marked as an opinion piece but even when one states an opinion about a medical issue, one can still say "there are reasons why this might not be true .. such as ...".  Too bad that wasn't done here.

UPDATE - Emily Willingham has written a VERY detailed critique of the article that I think everyone interested in anything related to this topic should read: Emily Willingham: Autism, immunity, inflammation, and the New York Timeswww.emilywillinghamphd.com.

Spammy journal of the day: Journal of Proteomics and Genomics ...

Just got this email posted below.  Certain aspects of it make me a little skeptical of the editorial quality of the journals from this publisher ... (highlighting a few parts done by me).

--------------------------------
Dear Dr.jonathan a. eisen,

Call for papers – to be published in the month of September and there on

Journal of Proteomics and Genomics

The scientific research is on its wheels now a day more than it has ever been. All the research and results are being accumulated enormously and in this race, you can come into lime light, only if you are noticeable enough. Are you sure the resource you have chosen provides you with such a benefit?
If you are not sure go through this list and make sure if you are at the right place, learn few facts to choose wisely when publishing your valuable research work:

1. Is it an open access online journal: Being online enhances the reachability of the journal worldwide and being open access means removing barriers for all the researchers, without any discrimination of dissipating the knowledge. (Subscription based is available only for who can afford.)
2. Does it provide xml files: Xml files are important for deposition into the repositories. Generally high prices are obtained for providing these files by publishing companies. (We provide free of cost.)
3. Proper communication and support during publication: The most important and the actual tyranny lies in publishing the research paper which is the sweat and time of your hardship. But it would be more hardship if you have to publish with a poorly communicating and non-supportive journal. (Our advanced online system enhances communication effectively.)
4. Through peer review of original and revised manuscripts: Value of your research paper is enhanced only if it is peer reviewed. (Peer review is one of the main quality element provided by us.)
5. Revision made easy: And the revision part out there is so terrific. (But with us it is easy due to the detailed comments of our reviewers.)
6. High profile experts with lot of experience: Editors with specialized expertize are an asset when dealing with scientific manuscripts. They can provide very accurate suggestions with experience and help improving the quality of the paper in-depth. (We are rich with them.)
7. Support for enhanced citations even after publishing : Paper has been published, everything is done, now what? Have you ever wondered what is happening with your paper? Is it reaching the required?  Not only social media but there are hundred other ways to get you to the right place. (The secret is only with us.)
8. Appropriate Fee : Open Access journals now a days cost nothing less than $1000. (We charge only $ 540)

Now if you wish to submit your manuscript and publish with us, please follow the below link, the call for papers is open and up 

-----------------------------

Note - I have not included the link so as to not in any way contribute to their Google Ranking.  But wow - journal spam is pooping up so often it is hard to keep up with it.

Notes from some recent meetings about microbiology of the built environment

Quick post here.  At the microBEnet site that I run we have posted some notes, slides, videos and other information from a few recent meetings on the topic of "microbiology of the built environment" that may be of interest so I am posting links here

• Put a microbe on it: “The Great Indoors” session at the Ecological Society of America’s annual meeting
• Videos and slides from GSC13 meeting session on “microbiology of the Built Environment” | microBEnet: The microbiology of the Built Environment network.
• GSC13: From Genomes to Interactions to Communities to Models blog post by Holly Bik
• Guest Post: Metadata for the Built Environment – MIxS-BE package blog post by Lynn Schriml
• Report of 13th Genomic Standards Consortium Meeting including microbiology of the built environment session
• “Challenges in Microbial Sampling in Indoor Environments” – Workshop Report Summary
• Summary: Healthy Buildings 2012
• An outdoor microbiologist indoors: Thoughts and ramblings from ASM2012 post by Lizzy
• Guest Post by David Thaler: Thoughts on the Inaugural Conference on the Microbiology of the Built Environment guest post by David Thaler
• ASM Live video on bacteria in hotel rooms

"Genomics: the Power and the Promise" meeting - could be called "Men Studying Genomics" instead

Just got another email advertising this meeting: Genomics: the Power and the Promise.  Organized by Genome Canada and the Gairdner Foundation.  And, well, though I love some of the things Genome Canada has done, this conference really stick in my craw in the wrong way. Why?  It has a serious male speaker overabundance.  Here is the list of speakers:

Day 1 

1. Pierre Muelien
2. John Dirks
3. Gary Goodyear
4. Eric Lander
5. Craig Venter
6. Philip Sharp
7. Svante Paabo
8. Tom Hudson
9. Peter Jones
10. Stephen Scherer
11. Michael Hayden
12. Bertha Maria Knoppers

Day 2

1. Stephen Mayfield
2. Elizabeth Edwards
3. Curtis Suttle
4. Peter Langridge
5. Michel Georges
6. William Davidson
7. Klaus Ammann

That is 17:2 male: female ratio. That is one female speaker per day.  Not impressive.

On Day 2 there are two panels (which generally I do not count as "speakers" but at least there are a few more women on these):

• Panel 1: Sally Aitken, Vincent Martin, Elizabeth Edwards, Curtis Suttle, Gerrit Voordouw, Steve Yearley
• Panel 2: William Davidson, Martine Dubuc, Isobel Parkin, Graham Plastow, Curtis Pozniak, Peter Phillips 

So if you count these that then comes to a ratio of presenters of 25: 6.  Do I want quotes for meetings?  No, but given that the ratio of men: women in biology is close to 1:1 this suggests to me some sort of bias.  Where does this bias come from?  I don't know.  Could be at the level of who gets invited.  Could be at the level of who accepts.  Could be some non obvious criterion for selecting speakers that leads to a bias towards men.  I don't know.  But I personally think they could do better.  And I note - they could probably do better in terms of other aspects of diversity of speakers, but I am focusing here just on the male vs. female ratio.  Again, I am not suggesting one should have quotas for all meetings but at the same time, a 17:2 male to female speaker ratio suggests something could use some working on.

As a side story I decided to look at some past conferences sponsored by Genome Canada.  I worked my way down the list ... see below:

• 2008 Joint IUFRO-CTIA International conference. Speakers: 8:2 male: female
• 6th Canadian Plant Genomics Workshop Plenary Speakers 8:2
• 8th Annual International Conference of the Canadian Proteomics Initiative.  See below.  32:2 male to female.  I have no idea what the ratio is in the field of proteomics but this is a very big skew in the ratio.  94% male.  
1. Leigh Anderson (Plasma Proteome Institute)
2. Ron Beavis (UBC)
3. John Bergeron (McGill)
4. Christoph Borchers (UVic)
5. Jens Coorssen (U Calgary)
6. Al Edwards (U Toronto)
7. Andrew Emili (U Toronto)
8. Leonard Foster (UBC)
9. Jack Greenblatt (U Toronto)
10. Juergen Kast (UBC)
11. Gilles Lajoie (U Western Ontario)
12. Liang Li (U Alberta)
13. John Marshall (Ryerson)
14. Susan Murch (UBC Okanagan)
15. Richard Oleschuk (Queens)
16. Dev Pinto (NRC)
17. Guy Poirier (Laval)
18. Don Riddle (UBC)
19. David Schreimer (University of Calgary)
20. Christoph Sensen (University of Calgary)
21. Michael Siu (York)
22. John Wilkins (University of Manitoba)
23. David Wishart (University of Alberta)
24. Rober McMaster (Universiyt of British Columbia)
25. Peter Liu (University of Toronto)
26. Christopher Overall (Universiyt of British Columbia)
27. John Kelly (NRC, Ottawa)
28. Joshua N. Adkins (Pacific Northwest National Laboratory, USA)
29. Dustin N.D. Lippert (University of British Columbia)
30. David Juncker (McGill University)
31. Jenya Petrotchenko (University of Victoria)
32. Detlev Suckau (Bruker Daltonik GmbH)
33. Peipei Ping (University of California)
34. Robert McMaster (University of British Columbia)

I couldn't bear to go on any further.

Now - note - I am not accusing anyone of bias here.  But I do think it might be a good idea for Genome Canada to put some more effort into figuring out why the conferences they sponsor have such skewed ratios.  And perhaps they can try to do something about this.  For more on this issue from my blog see

• The Tree of Life: Diversity (of speakers, participants) at meetings: do ...
• The Tree of Life: A conference where the speakers are all women?
• A conference where the speakers are all women? (with tweets - Storify

Got poo?: Clinical trial on fecal transplants (aka fecal bacteriotherapy) to treat C. difficile infections

Normally I avoid covering press releases here on my blog but this one is actually worth noting: Groundbreaking Clinical Trial Looks at Fecal Transplant as Treatment for C. Difficile | Women's Medicine Collaborative.  It details the funding of a clinical trial to study the effectiveness of fecal transplants in treating Clostridium difficile infections.

Fecal transplants have gotten a growing amount of publicity over the last few years.  And they certainly seem to have potential.  But though they have been shown to be safe, they have not yet been shown in a clinical trial to be effective in treating anything.  So it is good to see a funded clinical trial on such transplants (though I note, transplant is probably the wrong word to use - maybe fecal bacteriotherapy is more appropriate.

For some background on fecal transplants see

• The Tree of Life: Transfaunation and Fecal Transplants: What Goes Around Comes Around. Literally and Figuratively  ...
• Mendeley Reference Collection on Fecal Transplants and related topics. 
• Jonathan Eisen: Meet your microbes | Video on TED.com

Referring to 16S surveys as "metagenomics" is misleading and annoying #badomics #OmicMimicry

Aargh.  I am a big fan if of ribosomal RNA based surveys of microbial diversity.  Been doing them for 20+ years and still continue to - even though I have moved on to more genomic/metagenomic based studies.  But it drives me crazy to see rRNA surveys now being called "metagenomics".

Here are some examples of cases where rRNA surveys are referred to as metagenomics:

• Deep 16S rRNA metagenomics and quantitative PCR analyses of the premature infant fecal microbiota ... - Wow -- rRNA as metagenomics even made it into the title here
• Paper: 16S rRNA metagenomics-based survey of oral biofilms in obese children... Poster Abstract
• Gastroenterology & Endoscopy News - Studies Link Composition of ... News Story
• Metagenomic study of the oral microbiota by Illumina high-throughput sequencing - paper is only about rRNA sequencing, not metagenomics
• Dr. Dag Harmsen publishes first 16S metagenomic study on the Ion PGM Sequencing ... a Youtube video highlighting a PLoS One paper
• Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing - PLOS One paper from the video above
• EUREKA GENOMICS | 16S metagenomic analysis service - a company pushing their services
• A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy ... PLoS One paper

I found these examples in about five minutes of googling.  I am sure there are many many more.  

Why does this drive me crazy?  Because rRNA surveys focus on a single gene.  They are not gnomicy in any way.  Thus it is misleading to refer to rRNA surveys as "metagenomics".  Why do people do this?  I think it is pretty simple.  Genomics and metagenomics are "hot" topics.  To call what one is doing "metagenomics" makes it sound special.  Well, just like adding an "omic" suffix does not make ones work genomics - falsely labeling work as some kind of "omics" also does not make it genomics.

Enough of this.  If you are doing rRNA surveys of microbial communities - great - I love them.  But do not refer to this work as metagenomics.  If you do, you are being misleading, either accidentally or on purpose.    So I think I need a new category of #badomics - "Omic Mimicry" or something like that ...

------------------------------

Note - this post was spurred on by a Twitter conversation - which is captured below (note - I am certain I have complained about this before but cannot find a record of it ...)

How to find an Open Access journal for submitting your paper(s) #Jane #DOAJ

Got asked a question on Twitter that seems worthwhile to post here

@phylogenomics any suggestions for appropriate open access journal for a geomicrobio/clay mineral - Cr reduction/ kinetics paper?
— Paul Glasser (@glasserp) August 21, 2012

Well, @glasserp a good place to start is "Directory of Open Access Journals" doaj.org
— Jonathan Eisen (@phylogenomics) August 21, 2012

Also @glasserp a great tool is Journal/Author Name Estimator "JANE" biosemantics.org/jane/ - w/ "extra options" you can choose access policies
— Jonathan Eisen (@phylogenomics) August 21, 2012

And @glasserp for JANE just paste in your abstract or key words and search journals and it will ID good candidates
— Jonathan Eisen (@phylogenomics) August 21, 2012

Basically what I was suggesting was two possible steps. The first is to search the Database of Open Access Journals which is a great place to browse to see what the possibilities are. Another great resource/tool is JANE - the Journal/Author Name Estimator. I love Jane and use it all the time (if interested also see the paper on Jane here). The default screen for Jane looks like this:

And you can certainly use the default options. Just type in some keywords, or copy and paste a document or abstract of a paper and select "Find Journals" and voila you get some suggested journals which match your text. So for example if I paste in "evolution genomes novelty phylogeny microbes" and search for journals I get some useful suggested journal matches

And you can also select the "show articles" option which will, well, show you some of the article matches

Also you can even export the citations, which is a nice option for adding references to various collections you might have or for looking later.

You can also look for authors or articles that match your text/keywords instead of journals.  The "find authors" option is great for searching for possible reviewers if you are handling the review of a paper (or a grant). 

But my favorite part of Jane is what you can do with the "Show extra options" option. This is the menu you get

This allows one search for kinds of articles as well as for kinds of access.  For example, if I select "only journals with immediate access" I get a list of places I would submit papers

I am sure there are other resources out there but I particularly like these two ... Any other suggestions from the world out there?

Wow - who would have thought? Microbes are central to election in Wyoming

Fascinating story from a microbiology point of view: Republican candidates disagree on water rights in Yellowstone.  Seems that one of the three main candidates in this Republican primary election is focusing partly on microbes.  Here are some microbial quotes from the story:

"Jennings fervently believes that the microbes found in Yellowstone National Park’s boiling waters should be working for Wyoming, generating royalties to help fund state programs. The notion has received criticism from Anderson and Radosevich."

"Radosevich simply refuted the notion that the state should seek monetary gain from Yellowstone microbes in the first place" 

"Jennings maintains that Wyoming is sitting on an “enormous bank of microbes” that have yet to be discovered. "

See more on this issue:

• 2012 Primary Election: Senate District 28 
• Kit Jennings (R) Wyoming Senate District 28
• Wyo Senate District 28 primary candidates vary on experience, issues

The microbiome in the news: risk of overselling but not always bad coverage

Well, in the space of about five or so years we have gone from everyone ignoring the "cloud" of microbes that live in and on various plants and animals (the so called microbiomes of these species) to everyone now basically implying that the microbiomes do EVERYTHING.  Over the last few years I started to get stressed about this and started giving out "Overselling the microbiome" awards here.  Some previous posts on this topic include:

• Overselling the microbiome award: Scientists look to mummies for obesity cure
• Probiotics are the new viagra & the risks of overselling of probiotics
• Probiotic use spreading, lots of money being made, known benefits still murky
• Overselling the microbiome award #2: The Marshall Protocol
• Overselling the microbiome award: Stephen Barrie on pre and probiotics at the Huffington Post

That was five or so posts over a few years.  But i certainly have seen more cases of overhyping and it does seem to be getting worse. One of the key aspects of overhyping is the continuous danger of correlation vs. causation.  Microbial communities can be very very complex ecosystems.  What many people/researchers do is the following:

1. identify a few groups of hosts (e.g., healthy vs. disease) 
2. collect samples and characterize the microbial communities in the samples
3. carry out some clustering/correlation analysis to look for features of the microbial community that are correlated with the host classes (e.g., healthy vs disease)

#Badomics word of the day & Worst New Omics Word Award: CircadiOmics

Really?  We need this new omics word in this paper?: CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics : Nature Methods : Nature Publishing Group

The good news?  I can't actually get the full text of the paper right now so I can't read what they say about this word.  The bad news?  A lot.  First, the definition is in the title.  And it is pretty clearly a badomics word.  Also, they seem to be serious that other people should use this word without laughing.  There is a website: http://circadiomics.igb.uci.edu.  Uggh.  This is an unnecessary addition to the biology lexicon.  Why not just saw "genomics of circadian rhythms"?  Does this really need a new word?  I don't think so.  So I am giving these authors my "Worst new omics word award" though I am not 100% sure how new the word is ..

For more on #badomics words see also::

• bad omics word of the day
• GigaScience | Full text | Badomics words and the power and peril of ...
• My new paper in #Gigascience: #Badomics words and the power and peril of the ome-meme
• Heres an Omical Tale: Scientists Discover Spreading Suffix – WSJ.com

The Ballad of #UCDavis from Aaron Heuckroth

The Ballad of UC Davis from the brilliant and talented Aaron Heuckroth.
Hat tip to the Davis Patch.

More playing around with Total Impact

I am continuing to play around with Total Impact (see for example total-impact: Jonathan Eisen). This is a new (beta) system for tracking individual impact of scientific productivity including papers, presentations, data, etc.

So far I like the general things I am seeing there.  They ask for feedback on their site and in the interest of openness I am posting some things I would love to see here

1. Sorting by publication date or any of the metadata categories (e.g., citations, downloads)
2. Better way of saving DOI lists such that if you get a new publication you can just add to the list

...

Lots of other things obviously but it is an early beta version so I am willing to be patient.  Definitely worth playing around with.

Some articles on the uses and misuses of the "impact factor"

Collecting some articles and blog posts on impact factor uses and misuses.  Inspired by this blog post: Sick of Impact Factors | Reciprocal Space

• U Toledo JOURNAL IMPACT FACTORS: USE AND MISUSE
• The Journal Impact Factor: Too Much of an Impact? Ha et al. in Ann Acad Med Singapore 2006;35:911-6
• PPT from U. Illinois Journal Impact Factors A tool to help identify key research in your field
• More reason to outlaw Impact Factors from personnel discussions ... from The Occasional Pamphlet blog June 14, 2012
• EASE statement on inappropriate use of impact factors The journal ...
• NHMRC: Use of Journal Impact factor in peer review of individual applications.  Contains lots of very useful references.
• Dempsey 2009 IMPACT FACTOR AND ITS ROLE IN ACADEMIC PROMOTION: A  statement adopted by the International Respiratory Journal Editors 12 Roundtable. J. Appl. Physiology
• Trends in the Usage of ISI Bibliometric Data: Uses, Abuses, and ...History of the journal impact factor: Contingencies and consequences Cameron, Brian D., "Trends in the Usage of ISI Bibliometric Data: Uses, Abuses, and Implications" (2005). Librarian and Staff Publications. Paper 3.
• Does the Journal Impact Factor Help make a Good Indicator of Academic Performance? PDF from SK Mishra.
• 2006 PLoS Medicine Editorial: The Impact Factor Game
• Citrome 2007. Impact Factor? Shmimpact Factor!
• A Biologist's Guide to Impact Factors - Michael Rosenberg from ASU
• Impact factors: uses and abuses. Neuberger and Counsell. 2002. 
• The use, misuse, and misconception of impact factor. Asari & Aziz. 2005. International Medical Journal. 
• The Misuse of the Impact Factor - Mushtaq 2007.
• The impact factor and other measures of journal prestige

Suggestions welcome for other articles ...

UPDATE 1: 130 PM 8/18

Some additional articles

• Impacting our Young Editorial by Marder et al. in PNAS 2012
• Seglen in BMJ 1997 Why the impact factor of journals should not be used for evaluating research (not open access)
• Garfield E. The Agony and the Ecstasy - The History and Meaning of the Journal Impact Factor...
• Holden et al. Should Decisions About Your Hiring, Reappointment, Tenure,  or Promotion Use the Impact Factor Score as a Proxy Indicator of the Impact of Your Scholarship? ....  Includes video ..
• Richard Smith: The power of the unrelenting impact factor Is it a force for good or harm?- International Journal of Epidemiology...
• Ogden and Bartley 2008 The Ups and Downs of Journal Impact Factors

UPDATE 2: 8/19 8 PM 

• Created a Mendeley Group on this topic

Impact Factor is a group in Biological Sciences on Mendeley.

Bill and Melinda Gates want to give you $250,000 #Vaccines

All you have to do is apply and, well, win ... just got this email from the Gates Foundation - definitely worth nominating someone if you think they are doing good work.  Once again, the Gates Foundation is helping change the world ... Jenny McCarthy need not apply.  Here is the email:

Dear Colleagues: Do you know someone who is improving vaccine delivery in the developing world? Now is the time to nominate that person or group of people for the second annual Gates Vaccine Innovation Award. Time is running out -- the deadline for nominations is August 31, 2012. The Gates Vaccine Innovation Award is open to individuals from any discipline who work on the delivery of vaccines. Candidates from academic institutions, governments, health care facilities, research institutions, non-profit organizations and for-profit companies may be nominated. We are looking for ideas, big or small, that have resulted in tangible improvements in immunization coverage in developing countries. We invite you to nominate individuals or groups of individuals who have achieved significant improvements in the prevention, control, or elimination of vaccine preventable diseases through immunization. The winning nomination will be recognized with a $250,000 award. Read about the 2012 Gates Vaccine Innovation Award winner Dr. Asm Amjad Hossain here. Thank you for your continued support of this important award.

MMMMM: Microbes, Metagenomics, Minnesota, Mississippi, & Morrison

A really cool project is discussed in an issue of the University of Minnesota News: Microbes in the Mississippi : UMNews : University of Minnesota.  I found out about it through an automated web search I have running in the background via Google.  The news story discusses a project in which scientists from U. Minnesota are sampling the microbes in the Mississippi River using metagenomics.  Their data is (apparently) deposited into the IMG database and shared with the world (though I note - no link is provided).  This is exactly the kind of new project that cheap sequencing enables ...  I hope to see many many more like this ...

Amazing video from Louie Schwartzberg / Moving Art "The Beauty of Pollination" #scifoo

I met Louie Schwartzberg at the SciFoo meeting last week. He makes absolutely amazing Nature videos ... here is one.

The recursive tree of life - how a Twitter -> Blogger loop was created and broken

Earlier today I wrote a post that went something like this

Still searching for a good way to post a roundup of my twitter conversations to my blog. There don't seem to be any good systems for doing this on Blogger. So I have, at least this week, created a Storification of my tweets and some of the associated conversations ... not ideal probably but still ...

I am not sure how it finished because, well, I deleted the post by accident a bit later in the day as you will see.

I do recall I posted an embedded version of this storification.

And this led to some useful responses such as

@phylogenomics emckiernan.wordpress.com seems to have figured out good way using wordpress. Not sure about blogger
— John Hewitt (@jhewitt123) August 12, 2012

@phylogenomics what about ifttt? ifttt.com/recipes/36261
— Giovanni Coppola (@giovanniucla) August 12, 2012

@phylogenomics Look into IFTTT.
— Michael Batz (@mbbatz) August 12, 2012

SO this seemed potentially interesting .. and I decided to look into IFTTT. It took a bit to figure out anything about it but at first glance it seemed not right. So I posted a response

@giovanniucla @mbbatz IFTTT does not seem right - I want a weekly archive of my tweets/twitter conversations posted to my blog ..
— Jonathan Eisen (@phylogenomics) August 12, 2012

@phylogenomics @giovanniucla 1. IFTTT all tweets w links to dropboxed archive, 2. IFTTT weekly post of dropboxed archive…
— Michael Batz (@mbbatz) August 12, 2012

@mbbatz @giovanniucla nice - am experimenting w/ IFTTT - looks great - will see what I can come up with
— Jonathan Eisen (@phylogenomics) August 12, 2012

@phylogenomics @giovanniucla not 100% sure it will work, but a great tool
— Michael Batz (@mbbatz) August 12, 2012

Interested in MiSeq Illumina sequencing of low diversity libs - read this

Everyone -if you are interested in using the Illumina MiSeq to sequencing low diversity libraries - read this ... Sequencing low diversity libraries on Illumina MiSeq from THE Nick Loman.

History of the Lake Arrowhead Microbial Genomes meetings

Recommended meeting for those interested in microbial diversity and/or microbial genomics: Microbial Genomics - ARROWHEAD 2012

Among the reasons to go:

• Session on microbiology of the built environment
• Lots of other good sessions
• Lake Arrowhead is a very nice place to have a meeting
• Past meetings have been both good scientifically and fun

And if you want to know more about past meetings see below:

• Blog posts of mine
• The Story behind the Meeting: Lake Arrowhead Microbial Genomes 2010 #LAMG10
• It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin
• Lake arrowhead notes - UPDATED
• Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics
• Programs and notes from past meetings
• 1998_LakeArrowhead1998Notes
• 1998_ArrowheadAdobeOCR
• 2000_ArrowheadAdobeOCR
• 2002 Lake_Arrowhead
• LakeArrowhead2004  notes and booklet
• 2006_ArrowheadAdobeOCR
• 2008_ArrowheadAdobeOCR
• 2010_ArrowheadAdobeOCR
• I have uploaded slides from my previous presentations at the meeting

Jonathan Eisen talk on "Phylogenomics of DNA repair" at Lake Arrowhead Small Genomes Meeting 2000 from Jonathan Eisen

Wow - Google Scholar "Updates" a big step forward in sifting through the scientific literature

I logged on to Google Scholar a few minutes ago and discovered something very new

This "updates" thing was not there earlier in the day.  So I clicked on the link and got to this page: Scholar Updates: Making New Connections - Google Scholar Blog where James Connor from Google reports

Since Google Scholar launched nearly eight years ago, we’ve been helping people find the research they’re looking for.  But often the spark for discovery comes from making a new connection or looking in a direction that you hadn’t yet considered and that -- before your aha! moment -- you wouldn’t have known to look for.  Today we hope to start fostering these new connections with Scholar Updates. 

We analyze your articles (as identified in your Scholar profile), scan the entire web looking for new articles relevant to your research, and then show you the most relevant articles when you visit Scholar.  We determine relevance using a statistical model that incorporates what your work is about, the citation graph between articles, the fact that interests can change over time, and the authors you work with and cite.  You don’t need to configure updates or enter any queries.  We’ll notify you about new updates by displaying a preview on the homepage and highlighting a bell icon on search results pages: ...

To get article updates relevant to your work, all you need to do is create a public Scholar profile. Article updates will automatically start to appear within a few days. 

Wow.  Completely awesome if it works well.  So, well, let's see if it works well.  For me the system recommends the following

Evolutionary Diversity of the Mitochondrial Calcium UniporterAG Bick, SE Calvo… - Science, 2012 

REGEN: Ancestral Genome Reconstruction for BacteriaK Yang, LS Heath… - Genes, 2012

Both have some relevance to me.  The first one is about evolution of a gene family and has a line in the abstract that clearly might have driven the automated suggestion: "Here, we characterize the phylogenomic distribution of the uniporter’s membrane-spanning pore subunit (MCU) and regulatory partner (MICU1)." But, well, I am not too interested in this paper.  Not really my thing.

Silly microbiologist, genomes are for mutualists

New paper in PLoS Genetics of possible interest: PLoS Genetics: Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medica.

The abstract does an OK job with the technical details:

Abstract:
The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5–2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome – with mean diversity (θπ) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization.

I think the author summary is a bit more, well, friendly:

Facultative mutualisms are relationships between two species that can live independently, but derive benefits when living together with their mutualistic partners. The facultative mutualism between rhizobial bacteria and legume plants contributes approximately half of all biologically fixed nitrogen, an essential plant nutrient, and is an important source of nitrogen to both natural and agricultural ecosystems. We resequenced the genomes of 44 strains of two closely related species of the genus Sinorhizobium that form facultative mutualisms with the model legme Medicago truncatula. These data provide one of the most complete examinations of genomic diversity segregating within microbial species that are not causative agents of human illness. Our analyses reveal that horizontal gene transfer, a common source of new genes in microbial species, disproportionately affects genes with direct roles in the rhizobia-plant symbiosis. Analyses of nucleotide diversity segregating within each species suggests that strong selection, along with genetic hitchhiking has sharply reduced diversity along an entire chromosome half in S. meliloti. Despite the two species' ecological similarity, we did not find evidence for selection acting on the same genetic targets. In addition to providing insight into the evolutionary history of rhizobial, this study shows the feasibility and potential power of applying population genomic analyses to microbial species.

I have highlighted the section dissing pathogen studies ...

As with every good paper, it starts with a tree

Curiosity on Mars

Trying to track down source of cartoon about coining "ome" words #badomics

I have this cartoon of direct relevance to my crusade to end the use of badomics words.  I have been trying to track where it came from for - like - ever.  And though I did not want to post it without getting permission I have decided to do so to try and track it's source.  Here it is

I note - I tried using Google Image search (see a discussion of how to do this here) and it finds some other versions of this cartoon online but none of them have a source for it either.  

So - does anyone out there know where this came from?

Scifoo Notes via Storify

#PLoSOne paper on the "horse #microbiome" and colitis; wonder if they will study 'poo tea'

There is a new paper on the horse microbiome: PLoS ONE: Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

They discuss the microbial community in the feces of healthy horses and those with colitis.  In the conclusions, they also discuss the possibility of "fecal transplants" to treat problems in the gut microbiome.

"Bacterial species richness and diversity are thought to be important components of a ‘healthy’ intestinal microbiome. Decreases in richness and diversity have been associated with conditions such as chronic diarrhea and recurrent C. difficile infection (CDI) in humans [24], [40]. Restoration of bacterial diversity and richness is the principle behind fecal microbiota transplantation, an approach that has received much attention recently for successful treatment of recurrent CDI [41], [42]. Surprisingly, equine colitis was not associated with loss of diversity and richness, but further studies using more uniform groups of horses with specific etiologies are required. Microbiota transplantation might potentially be an effective treatment to restore this complex environment towards is considered more ‘normal’."

I find it very surprising that they do not discussion "transfaunation" which is basically fecal transplantation in animals.  For more on transfaunation see:

• The Tree of Life: Transfaunation and Fecal Transplants: What Goes Around Comes Around
• Transfaunation and Fecal Transplants | Mendeley Group

And I think they should have / could have mentioned "poo tea" which some old school horse caretakers make for horses with colitis.  For more on that I suppose you can watch my Tedmed/Ted talk where I talk about this issue briefly