Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu

I could spend a lot of time on this website: Bioart and Bacteria – The Artwork of Anna Dumitriu.  I found out about it from a Tweet from Dumutriu:

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And it is right up my alley (being interested in the interface between art and science, especially in relation to microbes).  Lots of interesting sections here including:

Sequence
Super-organism
Don’t Try This At Home
[micro]biologies: the bacterial sublime

Modernising Medical Microbiology

And many more.  I do not know much about the artist but really glad she pointed me to this.  

A long (and I think good) listen: Tim Ferriss podcast on "the microbiome"

So – I have been travelling a lot lately.  On one of my trips – to Las Vegas and neighboring areas – I was interviewed by Tim Ferriss for his blog.  Jessica Richman of uBiome was also interviewed – she was in SF, Ferriss was somewhere else, and I was on the phone in Vegas.  As soon as it was over I got caught up in the work I was doing there (field work for a new NSF Funded Project on “microbial dark matter”.  Anyway – the interview was entertaining and I think interesting.  And then it came out while I was on the road again for another trip.  So I am just getting around to posting about it now.  Anway – here are some links for the podcast.

Ferriss’ blog post about it: Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome…

Direct links

I note – I have never done such a long interview for a show before (it was about two hours) but Ferriss was remarkably adept at making it relaxing and fun (for me at least).  Even the part about Jim Watson …

Open Faculty Position, Asst. Professor Microbiologist Plant-Soil Systems

Bayer Crop Science in West Sacramento hiring a Bioinformaticist …

Just got this email

Dear Dr. Eisen

I am a Sr Bioinformatics Scientist working within the Biologics Division at Bayer CropScience. We are looking to fill a Bioinformatics Scientist position here in our West Sacramento facility. We are interested in hiring someone with either a MSc and relevant years of experience or someone with a PhD and 1-3 years of postdoctoral experience. I would greatly appreciate it if you could circulate the attached job position or forward the attached job ad to the appropriate candidate(s).

Many thanks.

Best,
Dilara Ally
Senior Bioinformatics Scientist

Biologics

BioinformaticsScientistII_2014.pdf

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.

EvoDevo meeting, Clark Kerr, Aug 5-9, 2015

Just got this email from friend and colleague Nipam Patel at Berkeley:
I wanted to bring this meeting to your attention.

Registration is now available for the Evo Devo meeting that will be held at Clark Kerr (Berkeley Campus) from Aug. 5-9th, 2015.

http://www.evodevopanam.org

http://www.evodevopanam.org/meetings–events.html

Registration and abstract deadline is April 1st. People can register now, and abstract submission will probably be available in about a week or so. There will be plenty of slots for students, postdocs, and faculty to speak (chosen from submitted abstracts) and there should be a great poster session as well.

Please pass this information on to anyone else you think might be interested.

Cheers,

Nipam

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

Rob Knight at #UCDavis 1/5

The 2015 Hurley Distinguished lecture will be held on Monday, January 5th. Dr. Rob Knight will be presenting a talk on “Dynamics of the Human Microbiome.” This event will be held in Genome Auditorium, 1005 GBSF, from 12:10-1pm.

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

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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.