Slides for talk: Marine Host-Microbiome Interactions: Challenges and Opportunities

Posted slides for a talk I gave at Scripps Institute for Oceanography last week.

Kisaco Research – sponsoring YAMMMM – yet another mostly male microbiome meeting – again – not their first biased rodeo

Well, sadly, I am not shocked by this. Disappointed, yes.  But not shocked.  Just got an announcement sent to me for this meeting: Animal Microbiome USA 2019 | Kisaco Research

Happening next week in Kansas City.  Run by Kisaco Research.  I have written about their propensity to have meetings where most of the speakers were white men previously.  See
People from the company claimed they were going to do better in the future.  And maybe they have for some meetings.  But alas not for this one.  By my estimate the speakers are ~ 85% male.  15% female.  Grrr.  Not good.  Not representative of the field.  Most  likely some sort of implicit or explicit bias going on.   

Frustrated by YAMMMMs: Yet another mostly male microbiome meeting

UPDATE 3/9/2018 - See Comments.  Carly Rosewarne coined the term last year ...

A while back I coined the term "YAMMM" - yet another mostly male meeting - to reflect my frustration in seeing meetings where most of the presenters were male:

What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?

I have since written dozens of posts about such meetings.  Sadly this is not an unusual thing.  Fortunately there has been a growing movement in many communities, including in science, to critique and not support such "MANELs".  Progress is definitely being made.  But it is piecemeal and in my opinion we must still keep up the fight for meetings and conferences to better reflect the diversity of people doing interesting and important work that should be heard.  I am sure many fields still are seeing slow progress in this area but one that frustrates me personally is the microbiome arena.  So today I am coining a new term - YAMMMM (note the extra M).  Yet Another Mostly Male Microbiome Meeting.

I decided to update my mini image about this so I went to world and entered some common male names and some numbers for them.

Charles: 10
Robert: 20
Joseph: 20
David: 5
Doug: 20
Michael: 5
James: 20
William: 10
Jake: 5
Sam: 5
Richard: 10
Chris: 20
Paul: 5
Mark: 5
Donald: 10
Brian: 5
Kevin: 10
Edward: 10
Timothy: 15

And Voila:

I then added a little header

So if you see a YAMMMM - please feel free to use this image.

Storify of #UCDmicroBOOmes Halloween Symposium at #UCDavis on #microbiomes

Microbiomes of the Built Environment NAS Meeting Webcast 4/11 10:30-5 EST

This may be of interest:

Microbiomes of the Built Environment: From Research to Application

The National Academies of Sciences, Engineering, and Medicine are conducting a consensus study that will examine the formation and function of microbial communities in built environments, the impacts of such microbial communities on human health, and how human occupants shape complex indoor microbiomes. This study is intended to provide an independent, objective examination of the current state of science regarding built environment microbiomes and their impacts on human health, and then attempt to bridge gaps in moving this research to an application stage, in which building materials and architecture will be designed with microbiomes in mind. The study is being conducted by a committee of experts and the consensus report is expected to be released in 2017.
The study’s first public meeting will be held on April 11, 2016 in Washington, DC. You may view the webcast of the public sessions, to be held from 10:30am – 5:00pm EDT by clicking here.
Please direct any questions or comments to
This study is sponsored by the Alfred P. Sloan Foundation, U.S. Environmental Protection Agency (EPA), National Aeronautics and Space Administration (NASA) and the National Institutes of Health (NIH).

Monday, April 11
10:30am Welcome Public Observers and Study Sponsors Committee Member Introductions
What are microbiomes of built environments and why is the study topic a compelling one to address?
Joan Bennett, Committee Chair
10:45 Discussion of Statement of Task with Study Sponsors
Sponsoring organizations will provide perspectives on the context for the study, how the study relates to their missions, and what they see as key needs and challenges for understanding microbiomes in built environments. Invited speakers will each provide 10 minutes of opening remarks.
Paula Olsiewski, Alfred P. Sloan Foundation
Tina Bahadori and Laura Kolb, Environmental Protection Agency David Tomko, National Aeronautics and Space Administration Lisa Chadwick, NIEHS, National Institutes of Health (remotely)

Committee Discussion with Sponsors
12:15 Lunch
1:30 Setting the Stage for the Study
Presentations will highlight developments and challenges in several background areas. Invited speakers will each give 15 minute presentations.
1:40 Built environment microbiome interfaces: Why is improving our understanding of these interactions an exciting topic and perspective on the eld?
Gary Andersen, Lawrence Berkeley National Laboratory and University of California, Berkeley
2:00 Understanding and modeling building systems: What’s known and how might these parameters impact indoor microbiomes?
Jelena Srebric, University of Maryland
2:20 Example of built environment microbiome studies and their potential human health links
Benjamin Kirkup, Naval Research Laboratory
2:40 Understanding microbes in water systems
Amy Pruden, Virginia Polytechnic Institute and State University
3:00 Committee Discussion with Speakers 3:30 Break
Light snack will be provided
3:50 Further Discussion: Major Issues Relevant to the Study
Opportunity for committee members, sponsors, speakers, and meeting participants to further
discuss points raised during the presentations and to identify additional topical areas, gaps, or needs that may be relevant to the study’s statement of task.
4:30 Public Comment Period
Opportunity for meeting participants to share additional information or ideas they would like the committee to consider.
5:00 Meeting Adjourns

Storify of the IFAL Roundtable on Microbiomes in Food and Agriculture

Here is a quick roundup of the Roundtable discussion I was involved in on Microbiomes in Food and Agriculture run by the IFAL at UC Davis.

Microbiome Evolution, Molecular Recognition and Interaction Webs: the PLOS Comp Biol July Issue

Here are our highlights from July’s PLOS Computational Biology   Neutral Models of Microbiome Evolution There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes) and how they correlate with host health, disease, phenotype, physiology and ecology. However, few … Continue reading »

The post Microbiome Evolution, Molecular Recognition and Interaction Webs: the PLOS Comp Biol July Issue appeared first on PLOS Blogs Network.

Spinal Cord Injury, Gut Microbiome, and White-Plague Coral Disease: the PLOS Comp Biol June Issue

Here are some highlights from June’s PLOS Computational Biology   Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome The community of bacteria that live in our intestines (called the “gut microbiome”) is important to normal intestinal function, … Continue reading »

The post Spinal Cord Injury, Gut Microbiome, and White-Plague Coral Disease: the PLOS Comp Biol June Issue appeared first on PLOS Blogs Network.

Guest post by Katie Dahlhausen on her project on "The effect of antibiotics for chlamydia on koalas and their microbiomes"

This is a guest post by Katie Dahlhausen, a PhD Student in my lab.

Koala populations across Australia are on a rapid decline due to many culprits including habitat loss, being hit by cars, attacks by dogs, and the Chlamydia infection. Yes, that’s right, Chlamydia. And when koalas are brought into wildlife hospitals, they are treated with antibiotics to cure their Chlamydia infection. Although ridding koalas of Chlamydia, the antibiotics also kill off important gut microbes that are essential to the koala’s life biology. Koalas eat a diet solely of eucalyptus leaves, which would be poisonous to the koalas if it wasn’t for the tannin-protein-complex-degrading enterobacteria that break down the toxic components of the koala’s diet. Brace yourself, because the koala’s biology gets even more interesting! Mother koalas feed their young joeys a substance called pap, a fecal matter more concentrated in nutrients and microbes than normal feces. This form of a natural fecal transplant allows the joeys to colonize the critical gut microbes necessary for them to eat noxious eucaplytus leaves. But what does this mean for joeys whose mothers have been administered antibiotics?

My name is Katie Dahlhausen and I am A PhD student in Jonathan’s lab. I am crowd-funding a project to study this fascinating koala biology, as well as investigate alternative infectious disease treatment where antibiotics are not a viable option. Want to help out these adorable critters? You can support the Indiegogo campaign here, which is live until June 16, 2015. More information about the project is available on the crowdfunding page, and in these recent articles published in Scientific American and the Washington Post.

So how did I get into this project? Well, When I was at the Australia Wildlife Zoo in Australia last September, there was a sign next to the koala exhibit with picture of a joey whose mouth was covered in a brown substance. The sign read something like "It's not chocolate!" and explained the pap part of the koala's biology.

The moment I read this I knew there was some fascinating microbiology questions that were begging to be answered. While researching the microbiology behind this behavior, I found a study the recorded the detrimental effects antibiotics had on a koala's eating habit and inability to maintain weight, but the question of how antibiotics were effecting the microbial composition of koala's guts remained unsolved. That is how this whole project started. Like most people, I think koalas are cute and appreciate how iconic they are to Australia. Otherwise, I'm not very attached to koalas - they are actually quite mean and antisocial! But koalas are a fantastic model system - one food source, plenty of sampling opportunities (in Australia at least), frequently given antibiotics, and clear mechanism of the transfer of microbes from mother to offspring. The implications of the study are vast, but are aimed at the care for animals in captivity and foster changes in how/when we administer antibiotics.