Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively

In 2006 when I had just moved to UC Davis from TIGR, I was on a Southwest flight from Sacramento to (I think) Arizona. The person sitting next to me and I did the normal chit chat – what do you do? where are you going? etc. And the conversation became fascinating. The person sitting next to me was Mike Lagrone – a farrier (I forget people’s names frequently ten minutes after meeting them – but his name I remember even today, so he clearly made an impression). He travelled around the West helping take care of people’s horses. (I note – I think more information about him is here Mike Lagrone | EquiMed – Horse Health Matters).
Anyway – we ended up talking about microbes and animals and I told him about a project my lab was working on on tracking the microbes after ileal transplantation in people (see our paper on this here – the result of a collaboration between Amber Hartman in my lab and the lab of Michael Zasloff’s at Georgetown). We then discussed probiotics and he then told me an amazing story about how the old school farriers used a special method to treat horses if they were sick with some sort of gastrointestinal distress (e.g., colic). They would make the sick horse “poo tea” by taking feces from healthy horses and making it into a tea of sorts and then they served this to the sick horses. Anyway – the flight ended and he told me I should talk to some of the old school people in the Vet School at UC Davis and they might know more about it.
And then a few months later I had an interesting conversation with someone from the UC Davis Vet School – Jonathan Anderson – about horses. And as part of the conversation I told him of the discussion with Mike Lagrone and Jonathan told me there was a method called “transfaunation” which was analogous to the poo tea treatment – and was used for cows and horses and possibly other animals. Jonathan suggested I talk to Dr. Nicola Pusterla at UC Davis about this … but alas I never did.
And so – the seed of “transfaunation” and “poo tea” faded. And some things that should not have been forgotten were lost. History became legend. Legend became myth. And for four and a half years, the idea passed out of all knowledge.

But like the ring of power, transfaunation and poo tea could not be suppressed forever.  And magically, people began to talk about it over the last four years.  The human microbiome became hot.  Fecal transplants became a topic of conversation (with a little help from Carl Zimmer).  Even Colbert covered the topic.  And the final straw for me to get me to write about Mike Lagrone was when a few days ago my mom showed me an article in Scientific American by Maryn McKenna entitled “Swapping Germs: Should Fecal Transplants Become Routine for Debilitating Diarrhea?”  I knew then that the time had arrived for me to write about Mike Lagrone.  So I have.

I note, one reason I wanted to write up the story of meeting Mike Lagrone was because I personally had not noticed much in the coverage of human fecal transplants discussing the animal side of things.  This seemed a bit odd as transfaunation and poo tea and such are clearly closely connected in concept to fecal transplants in people.  A little digging (well, actually, a few Google searches) showed that many in fact have made the connection.  See for example these stories/articles:

To help those who might be interested in the animal side of “fecal transplants” I have made a mini-Mendeley collection of papers on the topic:

http://www.mendeley.com/groups/1716865/_/widget/29/10/

It is interesting to me how what goes around comes around (literally and figuratively).  This is probably a very ancient methodology – trying to move microbes from healthy individuals to sick ones to help treat them for various GI ailments.  And lets not even start talking about coprophagia which almost certainly has some “microbial colonization” component.  Thus, I conclude that, though fecal transplants in people may seem gross, it certainly makes a lot of sense that it could provide some benefits.  Not saying we know how to do it best or that it can cure everything – but it certainly seems worth pursuing in more detail.

Stay tuned – it seems very likely we will here much more about this in people over the next few years.  For some of the latest on the human side of things see
Fecal Transplants: They Work, the Regulations Don’t – also by Maryn McKenna.

Seems that medicine is catching up to what animals (and their caretakers) have known for some time …

UPDATE 1/16/2003 – Embedding my Ted talk on a related topic here

http://embed.ted.com/talks/jonathan_eisen_meet_your_microbes.html

More on fecal transplants and bacteriotherapy from my blog can be found below:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Important paper on annotation standards for bacterial/archaeal genomes – readying for the "data deluge"

Interesting paper in the journal “Standards in Genomic Sciences” that is worth checking out for anyone interested in genome sequencing and annotation. The paper is “Solving the Problem: Genome Annotation Standards before the Data Deluge” by William (aka Bill) Klimke et al.

It discusses the development of international annotation standards at NCBI (The National Center for Biotechnology Information) in collaboration with others. Note – the paper is Open Access.

Their abstract:

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.

The paper refers extensively to workshops held by NCBI on genome annotation and gives a link to a page from NCBI with additional information about these workshops.

Now – never mind the extensive use of the term prokaryote in the paper … the paper has got a wealth of information and tidbits worth checking out.

For example the paper has a nice table on annotation tools and databases and resources.

Among the other sections worth checking out
* Discussion of pseudogene annotation and identification
* Discussion of variation in structural annotation
* Evidence standards
* Functional annotation and naming guidelines

For anyone interested in annotating a genome – and more and more people are these days with the decrease in sequencing costs – this is a must read.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Arrived at Sacramento Airport to witness nice welcome for troops returning from Iraq

P92 P90 P91 P93 P89

See the full gallery on Posterous

p94.mov Watch on Posterous

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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My brother Matthew, a UC Irvine grad. student in sound engineering, takes on the pepper spray issue

My younger brother Matt is a sound engineering student at UC Irvine. As I did with my post: Top 10 reasons to still consider attending #UCDavis #OccupyUCDavis he has tacked the UC crisis with humor … Check out his radio spot:

https://player.soundcloud.com/player.swf?url=http%3A%2F%2Fapi.soundcloud.com%2Ftracks%2F29593375&show_comments=true&auto_play=false&color=ff7700 Radio Spot by mattglenn

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Two #UCDavis Academic Senate Ballot Initiatives related to #OccupyUCDavis Pepper Spray Incident

Just got this email and thought it would be of interest to some

Colleagues,

This message provides notice of two impending ballots, as required by Davis Division Bylaw 17:  http://academicsenate.ucdavis.edu/cerj/manual/dd_bylaws.cfm#17-.  You have received this notice as a voting member of the Davis Division of the Academic Senate.  The Davis Division received at least 50 valid signatures with each petition, requiring initiation of a formal notice and electronic ballot.  More information, including the method for gathering pro and con statements and the voting period, will be distributed on January 9, 2012.  The petitions are summarized below:

1) Petition received on December 6, 2011, requests a vote regarding a lack of confidence in the leadership of Chancellor Katehi, with the result of the vote to be communicated to the Board of Regents and UC President.

2) Petition received on December 15, 2011, requests a vote regarding 1) condemnation of both the dispatch of police and use of excessive force in response to non-violent protests on November 18, 2011; 2) opposing violent police response to non-violent protests on campus; 3) demanding that police deployment against protestors be considered only after all reasonable efforts have been exhausted and with direct consultation with Academic Senate leadership; 4) acceptance of Chancellor Katehi’s apology; 5) expression of confidence in Chancellor Katehi’s leadership and efforts to place UC Davis among the top public universities in the nation.

Sincerely,
Ines Hernandez-Avila
Secretary, Davis Division of the Academic Senate
Chair, Native American Studies

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Butterfly exhibit at the Smithsonian Museum of Natural History

Some pics from the butterfly exhibit at the Smithsonian Museum of Natural History

 

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Maybe the next thing is animal fecal transplant toys? #poop

OK – this is a bit gross – but whatever.  At the National Zoo the other day at the store my kids pointed out these “Pooping Animal Key Chains”.  Wonder what is next?

IMG_0061.MOV Watch on Posterous
Img_0059
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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My twitter notes from the #NASOneHealth meeting via Storify

I am posting here a wrap up of my notes from the National Academy of Sciences Institute of Medicine Forum on Microbial Threats meeting on Improving Food Safety Through One Health I just attended. I made a little “story” via Storify and that is what I am embedding below. More comments to follow I hope but wanted to get this out there.


http://storify.com/phylogenomics/tweets-and-notes-from-nasonehealth.js<a href=”http://storify.com/phylogenomics/tweets-and-notes-from-nasonehealth” target=”_blank”>View the story “Tweets and notes from #NASOneHealth” on Storify</a>]

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Very nice new #PLoSGenetics paper on "Functional Phylogenomics" of Seed Plants

Update2 – 12/22 – Data available here.  Thanks to the authors for clearing things up quickly.

Update1 –  12/19 – Data for this paper seems to be unavailable – not sure why – but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there.  Note – this is one reason that all data sets should be made available at the journal or third party sites.

Original post:

OK never mind that the terminology of “functional phylogenomics” is a tiny bit vexing to me (long story – some other time perhaps). The paper behind it – PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.

Here’s what the authors did (a very coarse summary)

1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)

2. Constructed a “total evidence” phylogeny for these taxa (using a few approaches) 
3. Use this phylogeny to reinterpret some general features of the evolution of plants 
4. Searched for gene ontology categories (in annotated genes from these organisms) that agreed with the phylogeny. In essence, this seems to be a search for shared-derived traits (i.e., synapomorphies) in particular clades. 
5. Generated hypothesis about functional evolution in particular clades.
Overall, there is a lot that is really fascinating in here and this approach seems very powerful (though I note – I think something akin to this though not as comprehensive or as careful has been done for other groups but not sure).  Check out the paper for more detail …
Lee EK, Cibrian-Jaramillo A, Kolokotronis S-O, Katari MS, Stamatakis A, et al. (2011) A Functional Phylogenomic View of the Seed Plants. PLoS Genet 7(12): e1002411. doi:10.1371/journal.pgen.1002411
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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NSF Cyber-Enabled Discovery and Innovation declares success, terminates self

Just got this email.  On the one hand it is nice to see that NSF is not keeping around programs when they may no longer be needed.  On the other hand, this somehow seemed melancholy …

Dear Colleague,

The Cyber-Enabled Discovery and Innovation program has demonstrated the value of interdisciplinary computational and data-enabled science and engineering.  Increasingly, this research approach is being integrated into new and continuing NSF programs and solicitations.  As of fiscal year 2012, proposals will no longer be accepted by the CDI program.

Investigators are referred to related NSF funding opportunities, which are listed on this web page (http://www.nsf.gov/cdi).  Please check for updates on this page as new opportunities are announced, and follow the links for program information and program officer contacts.

This is a one-time e-mail being sent to all PIs and Co-PIs of CDI proposals.

Tom Russell, Eduardo Misawa, and Ken Whang
CDI Co-chairs

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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