Blast from the not so distant past – special issue of JMBE on Scientific Ethics

So _ picked up my new issue of Microbe in the mail today and I saw something in it that seemed very intriguing.

A whole section of JMBE – the Journal of Microbiology and Biology Education dedicated to Scientific Ethics.  Sounded intriguing.  So I looked it up.  Took a bit to find it but there it was from December 2014 – Volume 15 number 2

I don’t know about the specific articles but the whole collection seems definitely worth a look and of potentially many uses.

So I have listed the individual papers below.  Kudos to ASM and JMBE for putting this together.  Now off to read some of the papers.

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


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


No #AAAS and ASM you do not deserve good PR for freeing up a few papers on Ebola

Saw a PR from AAAS about how they were freeing up all of ~ 20 papers on Ebola

In light of what has become the largest Ebola outbreak on record, Science and Science Translational Medicine have compiled over a decade’s worth of their published news and research. Researchers and the general public can now view this special collection for free.

OK. More access is good. But alas, they did not even free up all papers in #AAAS journals with Ebola in the Title or Abstract.

And then I started thinking. What about HIV? TB? Malaria? And as I started Tweeting about this, I saw that ASM also was hopping on the “free Ebola” bandwagon (actually I do not know who did it first).

And so I got angry and started Tweeting away. The Storify below sums up most of the details.

//[View the story “#AAAS and ASM free up Ebola papers show they don’t care about HIV, malaria, TB, etc.” on Storify]
UPDATE 9 AM 8/21

Great.  And now the Lancet has joined the bandwagon.

They write
“The current outbreak of Ebola in west Africa constitutes the largest and most complex to date. Declared a public health emergency of international concern by WHO, the outbreak of a disease with no known treatment or vaccination is proving difficult to contain given the already fragile and under resourced health systems in the affected areas.
The Lancet wishes to assist health workers and researchers working under difficult and dangerous conditions to bring this outbreak to a close. This Ebola hub contains all related resources from The Lancet family of journals offered with free access to support their vital work.”
Since they do not make papers available on TB, malaria, AIDS, cancer, etc does this mean people working on those are not doing vital work?
UPDATE 2: 8/21 5:45 PM
Wiley also trying to get some PR for making papers available.

UPDATE 3: 9/3
Oh look.  ACS cares about Ebola too.  They are making 18 papers available for free.  How generous. Oh and only until February 2015.  After then, they don’t care about Ebola.  Oh and before then, they apparently don’t care about any other affliction affecting the world.  Ebola is the only thing important enough to make freely available.

UPDATE 10/17

As the Ebola situation worsens, journals and publishers are still trying to get props for making certain papers freely available.  For example, AAAS continues to do this – (see this news story here which ends with a statement about a collection of free ebola papers).  Alas they are being sadly selective in what papers they make available.

Here are some that are not available

What a joke.  If #AAAS really cared about infectious diseases and human health and making papers available, they would stop being one of the most anti-open access publishers out there.

If you want consistently #openaccess papers about Ebola, go to #openAccess journals or do a search in Pubmed Central with a “limit” for Open Access papers:

mBio – home of some really cool, #openaccess microbiology papers

Am really enjoying the suite of papers coming out in mBio – the Open Access PLOSOne like journal from the American Society for Microbiology.  Here are some examples of recent papers that caught my eye:

And many many more.  Kudos to ASM and mBio.

Worth a look: American Academy of Microbiology report on the Human Microbiome

Definitely worth checking this out: FAQ: Human Microbiome, January 2014. It is a report from the American Academy of Microbiology and it is really well done.  In addition to the report itself there is also and Infographic and a nice little handout.

The report was based on discussions with a collection of Human Microbiome Gurus:

And it was written  by Ann Reid and Shannon Greene. It has a variety of useful tidbits and has a reasonable number of caveats – such as “it should be noted, however, that at this point, most studies, even in mice, are looking at correlations between gut microbiome composition and factors like weight, insulin sensitivity, and other metabolic measures.”

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note – I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad – covering all microbes – all the time – everywhere. But much of it is due to a growing interest in the microbes closer to us – those that live in and on us (the human microbiome) – those that live in and on plants and animals and other organisms we care about – and those that live in the places where we spend much of our time (the microbes of the built environment). I mean – come on – everyone is talking about fecal transplants now in public – in cover stories of the NY Times Magazine and in Ted talks.

  • Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too. 
  • The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology. 
  • Citizen Science is growing by leaps and bounds in other areas (e.g., check out 
  • Crowdsourcing (not the same thing as Citizen Science – more on this another time perhaps) is also growing in leaps and bounds. 
  • Crowdfunding is providing new ways to fund scientific activities. 
  • Sensors of all kinds are getting cheaper and easier to use and are being deployed widely. 
  • Many people are becoming more and more interesting in recording information about themselves and sharing it with others. 
  • The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research. 
  • Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used. 

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include 

  • Germophobia is rampant and fueled by media hype and marketing forces. 
  • We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on 
  • Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know – claiming that probiotics will cure all ailments for example. 
  • Some information about microbes that is out there on the web is, well, less that ideal 
  • The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most. 

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

  • Ethics 
  • Funding 
  • Openness and sharing 
  • Visualization 
  • Analysis tools 
  • Communication 
  • Outreach 

And of course – the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project – well – why not? Get your act together.

Anyway – got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.

UPDATE: Notes from the Session Added 5/23

Here are some notes from the meeting:
Meeting Report: ASM 2013 in Denver, Day 1
ASM 2013, Day 1: From Oceans to Guts
Citizens doing Science, or Science on Citizens? (ASM 2013: Post 1)
Symbionticism: ASM 2013 LINKS
Storify by SPONCH

My storify embedded below

Come all ye Citizen Microbiologists – to Denver 5/19 for ASM Meeting – abstracts due 1/15

This is going to rock.  Citizen microbiology – highlighted at the American Society for Microbiology Annual Meeting in Denver in May.  The details on the session are below.  Sunday May 19 at the American Society for Microbiology General Meeting in Denver.  If you are interested in attending Register here.  If you work on some aspect of Citizen Microbiology please consider submitting an abstract for a talk or poster. The deadline is January 15.  We will highlight ALL accepted abstracts in some way both during the session and in blogs, tweets, interviews, etc.  So please consider participating.
Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public OralAbstract Image
3:00 p.m.- 5:30 p.m.
JONATHAN EISEN; Univ. of California-Davis, Davis, CA
DAVID COIL; Univ. of California-Davis, Davis, CA
Invited Speakers:
GRAHAM HATFULL; Univ. of Pittsburgh, Pittsburgh, PA
   Carski Foundation Distinguished Undergraduate Teaching Award and Division W Lecturer
DARLENE CAVALIER; Sci. Starter, Sci. Cheerleader, Philadelphia, PA
ROB DUNN; North Carolina State Univ., Raleigh, NC
Citizen Science is a valuable way to both generate scientific data and to engage and educate a broad audience. Some areas of biology such as astronomy and ornithology have conducted multiple successful citizen science projects over the years. Surprisingly, there are not many citizen science projects in microbiology even though microbes are of interest to the majority of the public, as well as being tractable for these kinds of studies. This session will focus on citizen science in microbiology. This session will examine the diversity of Citizen Science projects, outline what makes a successful project, and highlight examples of past, current and future Citizen Microbiology projects. Speakers will also provide details on overcoming challenges in Citizen Science (e.g., visualization, permissions, privacy, standardization, informed consent). Our belief is that more projects, throughout the different domains of microbiology, could benefit from incorporating a citizen science component. Having this session at the General Meeting will help bring together people interested in this topic, as well as fostering collaboration on existing and future citizen science projects.
Sunday May 19 at the American Society for Microbiology General Meeting in Denver.  Register here.

ASM Career Development Grants for Postdoctoral Women

American Society for Microbiology:Career Development Grants for Postdoctoral Women.

Career Development Grants for Postdoctoral Women

The Membership Board is pleased to announce that the Career Development Grants for Postdoctoral Women Committee is accepting applications for its 2013 grant program.

Three grants ($1200 each) are given annually to advance the careers of postdoctoral women with outstanding scientific accomplishments and potential for significant research in the area of microbiology.  The fields covered by the award are any of those represented by the scientific divisions of the American Society for Microbiology (ASM).  The grants support the career development of the winning candidates by providing funds to attend a meeting (other than the ASM General Meeting or ICAAC), to visit another laboratory, to take a course in a geographically distant place, or for other travel to advance the candidate’s career.

To be eligible for this program, a woman scientist must hold a doctoral degree and have no more than five years of relevant research experience since receipt of her most recent doctoral degree.  Candidates must currently be performing postdoctoral work in microbiology, at an institution in the United States.  The candidate must be a member of ASM.  A letter of support must be provided by a nominator, who should be the candidate’s research project director, Department Chair, or Center Director.  The nominator must be a member of ASM and may only support one candidate for this award per year.  (Other guidelines exist – please check the website cited below for more details.)

Deadline for applications is February 1, 2013.

For more information on the program and the application process, go to on the Membership section of the ASM website, or contact Anne Dempsey at ASM Headquarters by email ( or telephone (202-942-9381).

ASM Exchange Program for Early Career Scientists

Just got this e-mail – if anyone’s interested in an overseas jaunt!

Dear ASM Member,

Are you interested in traveling to the U.K. to expand your scientific network? Apply for ASM’s Heatley-Payne Exchange Program for Early Career Scientists before November 15, 2012!

This program, offered jointly with the Society for General Microbiology (SGM), provides up to $4,000 in funding for U.S. members, who have received their PhD within the past 5 years, to travel abroad to present their research at the SGM’s Annual Spring Meeting in Manchester, UK, March 25-28, 2013 and spend up to three weeks at a nearby research laboratory in the UK or Ireland.

The grant is designed to benefit young scientists by giving them the opportunity to present their work overseas and experience the best of microbiology in the partner countries.

For more information, please visit

ASM is pleased to offer these exciting opportunities; if you have any questions please Good luck!

Best Regards,

May Chu
Chair, International Board (IB)

Coming up at the #ASM2012 mtg. "The Great Indoors: Recent Advances in the Ecology of Built Environments"

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there.  These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM – 5:30 PM

Session Room: Esplanade Ballroom 300

Description: Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors – microorganisms – and their interactions with humans.


  • Jonathan Eisen microBEnet: the microbiology of the built environment network
  • Nicholas Be: Examination of the environmental air microbiome using deep sequencing
  • Katie Kirsch: A microbial analysis of environmental surfaces in hotel rooms
  • Mark Hernandez: Stability of airborne microbes to master environmental variables
  • John Senko: Microbial communities associated with flue gas desulfurization systems
  • Kimberly Ross: Drinking water delivery networks as microbial ecosystems
  • Jordan Peccia: The effect of environmental conditions on the allergenic potency of Aspergillus fumigatus spores