UC Davis MARS Symposium Wrap Up #globalfood #UCDavisMARS

Yesterday I went to a symposium at UC Davis that was the launching of a new partnership between UC Davis and the Mars Corporation. I note - I have been collaborating with some people at Mars on multiple microbiome related projects and generally have had great interactions with the people there. I am not directly involved in the planning for this new partnership between UC Davis and Mars and thus I was interested in hearing more about it at the symposium.

The symposium was at the Mondavi Center on UC Davis campus and I zipped in on my bike through the cold (for Davis) air and got there just before they opened the doors to the main theater. I saw a few folks I knew milling around in the lobby and said hello and then went inside with some people from my lab for the "show".

 I will try to write more about this later but just one note - I found some of the big picture discussions about the importance of the nexus between food, agriculture and health to be pretty inspiring. For now - I hope the Storify I made and embedded below will give some idea as to the goings on of the symposium.

Surprise 28th

I've been meaning to write about my beautiful surprise birthday party for, oh, over a month now... but you know, busy-ness and the holidays and excuses excuses excuses. On this dreary Monday morning, however, I've finally gotten to it, and I'm having such a nice time reliving this oh-so-sweet evening.

On Decemeber 5th, I turned 28, which is weird all unto itself, seeing as how my twenties are creeping to a close and in some ways I still feel so young and others I feel so old. In some ways I feel so accomplished, and others I feel so panicky for not being further along. But that's another post for another day.

Also on December 5th, a few friends threw me a surprise birthday party, which was, indeed, an actual surprise!  In the last year or two, I've grown close to a beauty named Brittany who started her own event rentals company (Birch & Brass Vintage Rentals) here in Austin, of which I've helped to photograph the inventory over the course of many sweaty photo shoots and hundreds of beautiful pieces. Brittany is so, so good at styling perfect tablescapes and vignettes, and I always wished I knew her before our wedding or some other excuse to have her style an event for me.

Well now, thanks to her expertise and kindness, I have this incredibly perfect little party to look back on fondly, much thanks to Shalyn's gorgeous photos of the evening. I was so in shock that night, I barely took in all the details. Another reason that photography is so important: to capture and freeze time so you can go back and enjoy special moments over and over again.

There was fried chicken and other southern-style comfort foods (my absolute favorites), rum punch (another fave), cake and cupcakes and doughnuts (because you KNOW I love my sweets), a ridiculous piñata I had to whack about 47 times before it finally broke, and karaoke and quality time with sweet friends I was so grateful to for taking the time out of their Friday night to attend.

Thank you so much, Brittany, for one of the most thoughtful things anyone has ever done for me, and to Celine & Justin for hosting and for handling all of the mess that comes with that, and to Shay for taking the most beautiful photos and creating the most gorgeous little placecards, and to Kelsey & Jona, John & Kirsten, Kate, Emilie, Federico, and of course Matthew, all for attending.

Here's a few photos from the evening... thanks for stopping by today!

Postdoc position in Computational Biology / Infectious Disease w/ Ashlee Earl at the Broad

My friend, the brilliant Ashlee Earl is recruiting a post doc ... posting this for her.


POSTDOC – COMPUTATIONAL BIOLOGIST (INFECTIOUS DISEASE)
Requisition Number: 1571 http://www.broadinstitute.org/careers/job-openings/job-openings-0

The goal of the Bacterial Genomics Group at Broad is to develop and implement genomic and metagenomic methods to answer pressing questions related to bacteria and their role in human health. Specifically, we seek to understand the evolution and spread of bacterial pathogens (and antibiotic resistance) including the interactions that these pathogens have with their host and host-associated microbiota. We devise and carry out large-scale studies that employ genomic, metagenomic and transcriptomic data sets to understand human pathologies caused by e.g., Mycobacterium tuberculosis, carbapenem resistant Enterobacteriaceae, enterococci and uropathogenic Escherichia coli. We do this in close collaboration with clinical and academic researchers from across the Broad community and around the globe.

We are seeking a creative and highly motivated postdoctoral researcher in Computational Biology.  The ideal candidate should be broadly conversant with bioinformatics techniques for genomic data analysis including metagenomic analysis. They should also be familiar with microbial ecology principles, statistics and have made significant contributions to their area of study.

Responsibilities include:

• Developing data analysis strategies, writing algorithms and deploying computational tools for the exploration of large genomic, metagenomic and metatranscriptomic data sets
• Collaborating closely with experimental and computational researchers to interpret analytical results for publication
• Communicating scientific findings in writing and orally

A Ph.D. in Computer Science, Bioinformatics, Biostatistics, Physics, Biological Sciences or a related field

• Must be proficient in working in the Unix environment.  Solid coding proficiency in some combination of Python, Perl, Scala, Java, C/C++ and R. Experience with cluster computing and parallelization preferred.
• Comfort and experience with programming for biological data analysis
• Demonstrated ability to analyze and interpret metagenomic data
• Excellent ability to communicate scientific material
• Excellent collaborative skills and unrelenting enthusiasm for genomic science

EOE/Minorities/Females/Protected Veterans/Disabilities

Haloferax volcanii, model archaea, and me

When I was a graduate student I was looking around for an extremophile - especially an evolutionarily novel one.  And I settled on this species Haloferax volcanii - a model halophilic archaeon largely because Ford Doolittle and colleagues had started to turn it into a genetic model organism (and because Patrick Keeling, from Ford's lab convinced me it was a good thing to do).  So I started work on this species - doing DNA repair studies in the lab.  See my PhD thesis for some of the work I did which I never published outside of the thesis for multiple reasons.  But I continued to be interested in this species.  And when I was working at TIGR, an NSF Program Officer approached me asking me to help get the genome sequencing done for this species.  So, well, I did: The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.  And I became interested in other haloarchaea and eventually started working with Marc Facciotti, in the lab next to mine, in sequencing from across the diversity of the haloarchaea: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response.

Anyway - enough about me.  The whole point here is to point people to a new paper:  BMC Biology | Abstract | Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery.  Further evidence for the use of Haloferax volcanii as a model species.  Tools continue to become available for genetic and experimental studies in this species.  So - if you are looking for an unusual and interesting organisms to work on - consider working on this species ...

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus

Well, this press release is from October:Study Suggests Altering Gut Bacteria Might Mitigate Lupus But I just discovered it and it definitely deserves an award.  An Overselling the Microbiome Award.  The PR, sadly and amazingly from the American Society for Microbiology which should know better, discusses a paper from the ASM Published journal Applied and Environmental Microbiology.  The PR does an OK job discussing what was in the paper - a study of the microbiome in mice including those that are a model for lupus.  The researchers characterized the microbiome is mice with and without the lupus model disease and also compared over time and between sexes.  And they found some interesting correlates of microbial patterns that are found during flare ups of lupus for example and also in drug induced worsening of symptoms.  But they never showed ANY causal connection between any of the mcirobes and the lupus like disease.  And the never showed ANY benefit of treating the lupus-like symptoms in the mice.  Yet amazingly they go over board in making such claims including

Title: STUDY SUGGESTS ALTERING GUT BACTERIA MIGHT MITIGATE LUPUS.

No - the study did not suggest that at all.  The authors suggested that, yes.  And the study is consistent with that.  But it is also consistent with altering gut bacteria having NO EFFECT on lupus.  So this title is simply deceptive.

In the text other statements are like this:

These results suggest that the gut bacteria may contribute to lupus.

Stunningly, the PR includes some really inappropriate comments including:

Nonetheless, Luo suggests that people with lupus should eat Lactobacillus-containing probiotics, such as live culture yogurts, to reduce lupus flares.

Seriously?  Shame on ASM for allowing this garbage to be in the PR. No evidence at all is presented that this is helpful.

Also in the PR:

More generally, "The use of probiotics, prebiotics, and antibiotics has the potential to alter microbiota dysbiosis, which in turn could improve lupus symptoms," says co-principal investigator Husen Zhang. Ultimately, says Luo, fecal transplant might prove valuable as a treatment for lupus.

Again, shame on ASM.  No evidence is presented for this either.

And then the PR ends with

"We were inspired in part to perform this research by a study on type 1 diabetes, which found that that disease is dependent on gut microbiota," says Zhang. "Like type 1 diabetes, lupus is an autoimmune disease that is even more prevalent [than type 1 diabetes] in women."

What?  I know of no research that shows that type 1 diabetes is dependent on gut microbiota.  I really don't even know what to say here.

This is one of the worst Press Releases I have ever seen in terms of misleading statements about microbiomes.  And ASM should be embarassed about it.  And ASM should retract it.  And ASM should never ever put out something like this again.  And for this, I am awarding a coveted "Overselling the Microbiome Award" to ASM for putting out this inappropriate press release.  If any with lupus goes out and gets even remotely worse from taking such probiotics, prebiotics, or antibiotics, ASM will bear some of the responsibility for their problems.  Shameful.

---

UPDATE 1: Jan 2, 2015

I did some searching for "probiotics" and "lupus" and found some much more tempered claims from other places. For example in "Lupus Studies Point to Gut Microbes, Epigenetics"

 "The long-standing anecdotal patient reports of certain diets worsening or improving flares might be more real than we thought. They should be studied more systematically, now that we know that almost any dietary component acts on the gut microbiota, [which] in turn has profound effects on the immune system," Dr. Kriegel said. He also warned that patients should not assume that the various "probiotic" products now available to consumers would have a beneficial effect in lupus. "Probiotics could theoretically even worsen a disease state, since it is possible that physiologic immune responses against benign commensals could fuel autoimmune responses via cross-reactivity (as we hypothesize) or other mechanisms," he said.

Dr. Kriegel concluded, "I think the best will be to wait until we have a better understanding of which commensals or commensal-derived products might be driving which autoimmune disease and then target those with a diet that is known to modulate these strains or products. Ideally, the field will also develop eventually novel types of antibiotics or vaccinations against certain commensals. Such approaches would allow us, in the future, to more specifically modulate the gut microbiota in autoimmunity." 

Now that is responsible commenting on lupus and the microbiome.  Too bad ASM allowed complete BS to get into this PR instead of more reasonaed statements.

See also

@phylogenomics Sure! BTW you may be interested in a blog post I wrote on hype in PRs: http://t.co/GlbF7wWs9n pic.twitter.com/Kfk4p3W6bF
— Freya Harrison (@friendlymicrobe) January 2, 2015

Quick post: Viruses - don't forget about the viruses

OK OK.  Everyone, everywhere keeps telling me "Viruses - don't forget about the viruses" whenever I talk about microbial communities or discuss work we are doing in my lab.  Yes, I say "I know, I know" but then I panic and think "We can't even deal with the diversity of bacteria and archaea out there.  We generally ignore the microbial eukaryotes.  How the hell are we going to include viruses too?"  But, in the end, if we are going to study microBIOMEs (as in, ecosystems that include viruses), then, well, we need to include all the players.

(I note - as I am writing this, my son asked me what I am doing and I said I am writing about viruses.  He got excited and sad "Write about Ebola").

What got me on my viral kick today?  Well, I have been thinking about viruses a lot recently.  And then I saw this paper: The ISME Journal - Diversity of viral photosystem-I psaA genes.  And it reminded me of the largely unknown diversity of viruses out there in the world.

Anyway - I was going to write a longer post about viruses, but I have to go and do something with my son.

Paper of possible interest: Exploring interactions of plant microbiomes

Just got alerted to this new (open access) paper that seems like it should be of interest to those working on plant microbiomes Scientia Agricola - Exploring interactions of plant microbiomes. It has some useful summaries of work that has been done on plant microbiomes.