Tag: Misc.

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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——–
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.

——–

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.

——–
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.

——–

Do preprints count for anything? Not according to Elife & G3 & some authors ..

Well, just got pointed to this paper: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms | eLife by Martial Marbouty, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, Romain Koszul.  Seems potentially really interesting.

It is similar in concept and in many aspects to a paper we published in PeerJ earlier in the year (see Beitel et al., 2014 Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. (2014) Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415 http://dx.doi.org/10.7717/peerj.415.

Yet despite the similarities to our paper and to another paper that was formally published around the time of ours, this new paper does not mention these other pieces of work any where in the introduction as having any type of “prior work” relevance.  Instead, they wait until late in their discussion:

Taking advantage of chromatin conformation capture data to address genomic questions is a dynamic field: while this paper was under review, two studies were released that also aimed at exploiting the physical contacts between DNA molecules to deconvolve genomes from controlled mixes of microorganisms (Beitel et al., 2014; Burton et al., 2014).

Clearly, what they are trying to do here is to claim that since they paper was submitted before these other two (including ours) was published, that they should get some sort of “priority” for their work.  Let’s look at that in more detail.  Their paper was received May 9, 2014.  Our paper was published online May 27 and the other related paper by Burton et al. was published online May 22.  In general, if a paper on what your paper is about comes out just after you submit your paper, while your paper is still in review, the common, normal thing to be asked to do is to rewrite your paper to deal with the fact that you were, in essence, scooped.  But that does not really appear to be the case here.  They are treating this in a way as “oh look, some new papers came out at the last minute and we have commented on them.”  The last minute would be in this case, 6 months before this new paper was accepted.  Seems like a long time to treat this as “ooh – a new paper came up that we will add a few comments about”.

But – one could quibble about the ethics and policies of dealing with papers that were published after one submitted one’s own paper.  From my experience, I have always had to do major rewrites to deal with such papers.  But maybe E-Life has different policies.  Who knows.  But that is where things get really annoying here.  This is because it was May 27 when our FINAL paper came out online at PeerJ. However, the preprint of the paper was published on February 27, more than two months before their paper was even submitted.  So does this mean that the authors of this new paper do not believe that preprints exist?  It is pretty clear on the web site for our paper that there is a preprint that was published earlier.  Given what they were working on – something directly related to what our preprint/paper was about, one would assume they would have seen it with a few simple Google searches.  Or a reviewer might have pointed them to it.  Maybe not.  I do not know.  But either way, our preprint was published long before their paper was submitted and therefore I believe they should have discussed it in more detail.

Is this a sign that some people believe preprints are nothing more than rumors?  I hope not.  Preprints are a great way to share research prior to the delays that can happen in peer review.  And in my opinion, preprints should count as prior research and be cited as such.  I note – the Burton group in their paper in G3 also did not reference our preprint in what I consider to be a reasonable manner.  They add some comments in their acknowledgements

While this manuscript was in preparation, a preprint describing a related method appeared in PeerJ PrePrints (Beitel et al. 2014a). Note added in proof: this preprint was subsequently published (Beitel et al. 2014b). 

Given that our preprint was published before their paper was submitted too, I believe that they also should have made more reference to it in their paper.   But again, I can only guess that both the Burton and the Marbouty group just do not see preprints as being respectable scientific objects.  That is a bad precedent to set and I think the wrong one too.  And it is a shame.  A preprint is a publication.  No – it is not peer reviewed.  But that does not mean it should not be considered part of the scientific literature in some way.  I note – this new paper from the Marbouty group seems really interesting.  Not sure I want to dig into it any deeper if they are going to play games with the timing of submission vs. published “papers” as part of how they are positioning themselves to be viewed as doing something novel.

//storify.com/phylogenomics/do-preprints-count/embed?border=false//storify.com/phylogenomics/do-preprints-count.js?border=false[View the story “Do preprints count?” on Storify]
——–
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.

——–

postdoctoral position openings in microbial evolution and ecology

Dear colleagues,

Below and attached is information about two new postdoctoral positions in my lab. Please help spreading the word to potential candidates.

Thank you,
Ramunas Stepanauskas

Two postdoctoral research scientist positions in microbial evolution and ecology

Summary
Two postdoctoral positions are available in Dr. Stepanauskas’ laboratory. One position is focused on the deep evolution of Bacteria and Archaea and the genome content of the “microbial dark matter”. Another position is focused on chemolithoautotrophy in the deep ocean and hydrothermal systems. The hired scientists will be engaged in large, collaborative projects, and will employ single cell genomics and other advanced molecular biology and biogeochemistry research tools. Anticipated employment duration: 2 years, with potential extension. Bigelow Laboratory’s new campus is located in scenic, coastal Maine with abundant opportunities for outdoor and cultural activities. It is about an hour drive from Portland and a 3-hour drive from Boston.

Responsibilities
Hired scientists will be responsible to lead computational analyses of large single cell genomics, community “omics” and biogeochemical data sets, prepare manuscripts, supervise undergraduate students, and assume gradually increasing responsibilities in project management. These positions also include opportunities for field expeditions and laboratory analytical work.

Requirements
Candidates must have a PhD degree in microbiology, evolutionary sciences, bioinformatics, computational biology, or a related field. Prior experience in computational analyses of large microbial genomic data sets will be necessary for this opportunity. Candidates interested in these positions must be highly motivated, willing to learn and demonstrate initiative in assigned tasks. Excellent written and verbal communication skills and willingness to work in teams composed of field, laboratory and computational scientists are crucial.

Research overview: Deep evolution of Bacteria and Archaea
Hired scientist will be engaged in a major effort to improve our understanding of the genealogy of the Bacteria and Archaea by a large-scale genomic analysis of those deep evolutionary branches (phyla) that contain no cultivated representatives. Popularly referred to as Microbial Dark Matter (MDM), these enigmatic limbs near the base of the tree of life constitute a large fraction of biological diversity on our planet; yet, we learned of their existence only in 1990’s. Current knowledge about MDM is mostly limited to sequences of its small subunit ribosomal RNA genes, primarily due to former technology limitations. Recent advances in single cell genomics technology, however, have enabled us to bridge this knowledge gap – one that is essential to the genealogy of life – by providing access to the complete genomic blueprints of microorganisms without the need for cultivation. The following, general hypotheses will be tested: 1) The extant number of major (phylum-level) evolutionary branches of Bacteria and Archaea is significantly greater than the current consensus; 2) Extant cellular life forms three distinct domains: Bacteria, Archaea and Eukaryotes; 3) The early evolution of Bacteria and Archaea followed a progression of bifurcating divergences rather than a single radiation from the last universal common ancestor; 4) Inter-domain and inter-phylum horizontal gene transfer (HGT) had a significant impact on the early evolution of Bacteria and Archaea; 5) Evolutionary divergence in the early history of Bacteria and Archaea co-occurred with the colonization of and adaptations to novel environments; 5) The habitable subsurface is a repository for early evolutionary history of Bacteria and Archaea. Primary field study sites include the Kaapvaall Craton of South Africa; the Sanford Underground Research Facility in South Dakota; and the Death Valley Regional Flow System in Nevada.

Research overview: Chemolithoautotrophy in the dark ocean
An increasing body of evidence suggests the significance of chemolithoautotrophy in the dark ocean water column and hydrothermal systems. However, the specific energy sources, metabolic pathways and microbial taxonomic groups remain poorly understood. The hired scientist will assume a leading role in a) A global inventory of chemoautotrophs in the dark ocean water column; and b) An integrated study of energy metabolism, carbon fixation, and colonization mechanisms in chemosynthetic microbial communities at deep-sea vents. The following general hypotheses will be tested: 1) Multiple prokaryote taxonomic groups found in the dark ocean contain chemoautotrophic metabolic pathways; 2) Both known and previously unrecognized chemoautotrophy pathways are present in dark ocean’s prokaryotes; 3) Dark ocean chemoautotrophs are broadly distributed around the globe, with biogeographic patterns determined by the isopycnal movement of water masses, water mass age, and the downward flux of organic matter; 4) Diverse chemoautotrophy pathways are expressed in the dark ocean. During the course of the project, single amplified genomes (SAGs) will be generated from several diffuse-flow hydrothermal systems and from all major intermediate and deep water masses around the globe, representing most major taxonomic groups of bacteria and archaea that are known to be present in the dark ocean. Whole genome sequencing will be performed on a subset of SAGs, enabling detailed annotation of chemoautotrophy pathways. Metagenomic and metatranscriptomic fragment recruitment will be used to determine global patterns of chemoautotroph distribution and chemoautotrophy pathway expression.

How To Apply
Please visit www.bigelow.org for more information and method of application, position reference # PD-2015-1 for the Ecology position and PD-2015-2 for the Evolution position. Application deadline: February 1, 2015.

—
Ramunas Stepanauskas, Ph.D.
Senior Research Scientist
Director of the Bigelow Laboratory Single Cell Genomics Center

Bigelow_Postdoc_ad_2014.pdf

Crosspost – papers for sale

Crossposting from ICIS Blog (even though this is short – always good to reveal where things are posted first).

Well, this is much more elaborate than I could ever have imagined: For Sale: “Your Name Here” in a Prestigious Science Journal – Scientific American. Seems that there are services out there to help people write, in essence, bogus scientific papers filled with pithy somewhat reasonable sounding phrases about certain topics. Seems we could all use some more comprehensive full text analyses of papers to try and flag such activities.

——–
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.

——–

Wanted – info on workshops in and around Northern California on bioinformatics & genomics

I have been asked by multiple students about this topic and figured I would just put it out there.  I am trying to compile information  on workshops and short courses on topics relating to genomics or bioinformatics that are in the general area of Northern California (you know, Davis, Sacramento, SF, Berkeley, Stanford, Santa Cruz, etc).  This would include using specific tools (e.g., R, Galaxy, QIIME, and more) and specific fields (e.g., ecology, microbiology, genetics, plant biology).  Any information would be appreciated.

Meeting announcement: “Modeling the Spread and Control of Ebola in W. Africa”, Atlanta, GA, Jan 22-23, 2015

Of possible interest:

Modeling the Spread and Control of Ebola in W. Africa
Historic Academy of Medicine @ Georgia Tech
Atlanta, GA, USA
Jan 22-23, 2015

Website: bit.ly/ebm_gt

Please see attached for an image and pdf meeting flyer. The organizing committee includes Pinar Keskinocak and Fred Vannberg from Georgia Tech, as well as Rustom Antia (Emory), John Drake (UGA), Jonathan Dushoff (McMaster), John Glasser (CDC) and Lauren Meyers (UT-Austin).

The meeting will begin at 8:30am on Jan 22 and conclude by 1:30pm on Jan 23. Note that there is a $50 registration fee for all participants before Jan 8, 2015. This fee includes access to all events, as well as breakfasts, lunches and coffee breaks for the 1.5 day meeting.

We have a maximum capacity of 200 individuals on-site. We also expect to be able to offer travel awards targeted to young researchers and participants from developing countries – preference will be given to those who intend to present a poster at the meeting.

Please distribute to colleagues, questions should be addressed to:

ebola-modeling-workshop

eb_mod_workshop_poster_v2.pdf

Great idea from Nicole King – Lists of Women Speakers – more examples wanted

Just been pointed to this compilation from Nicole King (a brilliant professor at Berkeley): Lists of Women Speakers | The King Lab.

She has put together a collection of a few links:

As a resource for those who are interested in increasing the number of female speakers at their scientific conferences, seminar series, etc., I offer here a compendium of female speakers from diverse fields.  I’ve started with lists that I could find easily, but if you know of additional lists, please feel free to send along the links.  I would also be happy to maintain similar lists for underrepresented minorities if any such lists exist. 

These are the lists she maintained:

General
Field-specific lists
Are people aware of any other relevant lists like this?  Please share I will compile …

Some responses from Twitter

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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.

——–

Call for Participant Applications: Sustaining Biological Infrastructure

Of possible interest …

SBI_Banner.jpg
Dear NSF Division of Biological Infrastructure Principal Investigator:

The Ecological Society of America (ESA) announces the training course “Sustaining Biological Infrastructure (SBI): Strategies for Success – A Short Course for Project Directors.” Please see the call for applications below for more details about the course and how to apply. We hope that this course will be of particular interest to you and your colleagues. If you have any questions please contact us!

Sincerely,
The SBI Team
sbi

Cool opportunity: Postdoctoral Scholar: Disease transmission in societies

http://www.cidd.psu.edu/jobs/postdoctoral-scholar-disease-transmission-in-societies

Postdoctoral Scholar: Disease transmission in societies

Campus/Location: University Park Campus Date Announced: 11/27/2014

Work Unit: College of Agricultural Sciences Job Number: 54802

Department: Entomology

The laboratories of Drs David Hughes, Ephraim Hanks and Matt Ferrari are seeking a Postdoctoral Scholar. This position is in collaboration with the lab of Dr Shweta Bansal at Georgetown University, another position is available at Georgetown University, and funded by the NSF-NIH-USDA-BBSRC Ecology and Evolution of Infectious Disease (EEID) Program. The position is available in the Centre for Infectious Disease Dynamics (www.cidd.psu.edu), The Pennsylvania State University, University Park Campus.

The Postdoctoral Scholar position at Penn State involves the development of mathematical models to understand the transmission of diverse agents inside ant colonies. These agents range from beneficial agents such as food to agnostic agents like beads to detrimental agents such as parasites. The position is a mixture of both theoretical work and empirical work (with ant colonies in a lab setting). Possibilities for both field work and molecular work exist. We are seeking expertise in compartmental models of disease spread and statistical and agent-based models of animal behavior. Candidates should demonstrate a track record of publication; have strong organizational, written, and oral communication skills; and be able to work both independently and as part of a collaborative team. For further information, please feel free to contact Dr Hughes (dph14; +1 814- 863-6073). Interested applicants should submit a curriculum vitae, a 1-2 page statement of research interests that explicitly describes professional qualifications for this position, and contact information for three referees. Review of applications will begin immediately, and continue until a suitable candidate is found.

David Hughes: Hughes, is a behavioral ecologist who has studied social insects and their diseases in 11 countries on 5 continents. He has worked with diverse diseases as well as the behavior of healthy and infected ants under field (rain- and temperate forests) and laboratory conditions. www.hugheslab.com

Ephraim Hanks: Hanks is a spatial statistician and has worked extensively in the modeling of animal movement and connectivity. He has studied the spatial spread of disease in black spruce and mule deer, and the spatial properties of random walk models on networks. http://sites.psu.edu/hanks/

Matt Ferrari: Ferrari is a computational epidemiologist and statistician who has worked extensively on the analysis of time-series surveillance data to predict epidemic dynamics and evaluate management interventions. http://theferrarilab.com/

Shweta Bansal: Bansal is a network epidemiologist and has worked extensively on the effects of immunity on network structure and disease dynamics. She is studying infectious disease-related network structure in several wildlife populations including Australian bottlenose dolphins and Mojave Desert tortoises. Bansal is based in Georgetown University which is 3.5hrs drive away.http://bansallab.com/