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.

Guest post from Student Alex Martin on Kittybiome & Animal Shelters

We are nearing the end of our Kitty Kickstarter to fund research on the microbiome of cats (only three days left).  We have received some requests to learn more about our work with animal shelters. Here is a blog post by Alex Martin, a UC Berkeley junior who is working with us to study shelter cats in Berkeley.

---

The Berkeley Animal Shelter takes in all cats from within Berkeley city limits. Thus, cats who once varied markedly with regards to diet and home environment come to live under a fairly uniform set of conditions. It typically houses between fifteen and forty cats, but has held as many as seventy during the peak of breeding season. Recently we have begun collecting samples from cats at the Berkeley shelter in order to better understand their gut microbiomes.

A major dichotomy in the shelter cat population is the one separating house cats from feral cats. Both are considered domestic cats, members of the species Felis catus. If a kitten during its first few months of life is not exposed to humans, it develops behaviors to facilitate surviving in the wild, and grows up to become a feral cat. Some see feral cats as a nuisance, but the animals also tend to live difficult lives, enduring food shortages and a lack of medical care. Thus, a relatively new effort referred to as “trap-neuter-return”(TNR) aims to spay and neuter feral cats to slowly and humanely diminish the size and number of feral cat colonies. Differences in the gut microbiomes of feral cats versus their tamer counterparts is perhaps expected, as the two groups have vastly different diets and levels of environmental exposure. However, these differences have yet to be characterized.

In addition to the differences between feral and house cats, a small but important FIV(Feline Immunodeficiency Virus) population can potentially serve as an interesting point of comparison. Much like Human Immunodeficiency Virus, FIV attacks the immune system of infected individuals, making them markedly more susceptible to other infections. We think that this virus will affect the microbiome of FIV-positive cats in measurable ways. By identifying any differences, we will gain a better understanding of FIV as a whole and will hopefully be better positioned to one day develop more effective methods of treatment.

Geronimo is one Berkeley shelter cat whose gut microbiome will be analyzed. He was picked up as a stray just a few blocks from the shelter, and is three years old. Geronimo is exceptionally friendly, and loves playing with his wand toy and hiding in his cat tree to nap. He gets along well with other cats and was even introduced to a rabbit without incident. After spending about two weeks in the shelter, Geronimo was adopted into a loving home.

Koalas, Chlamydia, Antibiotics and Microbiomes - what else do you need?

Katie Dahlhausen, a PhD student in my lab, has become really really interested (perhaps a bit obsessed) with a really interesting case study regarding koalas, Chlamydia, antibiotics, and microbiomes.  Since we do not have funds to work on this in the lab, she has started an Indiegogo campaign to raise funds to work on this.  For more information on this project and how Koalas, Chlamydia, antibiotics and microbiomes are connected see "The Koala Project" page.

9 things PBS Newshour famously gets horrible wrong in story on fast food and microbiomes

Well, this is one of the worst microbiome news stories in a long time: Fast food kills gut bacteria that can keep you slim, book claims.  So many things wrong with it I don't even know where to go.  Here are nine:

1. The original headline: "Fast food kills gut bacteria that can keep you slim, study finds"

Here is the Tweet

Fast food kills gut bacteria that can keep you slim, study finds http://t.co/3fPIhJTuAB | @newshour

— PBS (@PBS) May 11, 2015

2. The correction:

is just completely lame and they should, as the New York Times does when it makes a correction, say what it used to say before they changed it

3. The sentence with the reference to Rob Knight is just bad reporting #1

Here is the quote:

Previous studies made similar findings: Professor Rob Knight of the University of Colorado Boulder, who collaborates with Spector, famously showed that transferring gut bacteria from obese humans to mice could make the rodents gain weight.

First of all - the paper they link to does include Rob Knight as a co-author, but the corresponding and senior author is Jeffrey Gordon and Rob is fourth to last (mind you I love Rob and his work, but in this case, saying this is something Rob showed without mentioning Gordon is just not right).

4 . The sentence with the reference to Rob Knight is just bad reporting #2

What the *$*$# does "famously showed" mean? Really.  What does it mean?

5 . The sentence with the reference to Rob Knight is just bad reporting #3

The statement "Previous studies made similar findings" is just so incredibly misleading.   It seems to be referring back to the previous sentences:

“What is emerging is that changes in our gut microbe community , or microbiome, are likely to be responsible for much of our obesity epidemic, and consequences like diabetes, cancer and heart disease,” he said. “It is clear that the more diverse your diet, the more diverse your microbes and the better your health at any age.”

This is just completely overblown.  The more diverse your diet the better your health at any age?  Oh #FFS that is just not based on any science.  And the "likely responsible for" is silly too.

6 . The sentence with the reference to Rob Knight is just bad reporting #4

Why exactly tell us he is collaborating with Rob Knight?  So some of Rob's good work rubs off?  I mean, Spector may do some fine work (and he has done some really good stuff).  But casually mentioning he collaborates with Knight who famously showed something (when actually it was more Jeff Gordon's work) which did not actually show what the article implies it showed.  Aaaaaaaaaaarg.

7. Good news.

Spector’s book claims that the diversity of microbes in the human body has decreased almost a third over the last century. But there’s also good news: Foods like dark chocolate, garlic, coffee and Belgian beer may help increase gut microbes.

Really?  Thinking about microbes MAY also increase gut microbes.  And so might listening to NPR.  Not something worth reporting here.

8. This sentence

This discovery suggested to his father that many cases of obesity may not simply be due to overeating.

That is right.  Looking at his son's poop and the microbes in it is the key to knowing that obesity might actually be fuc$*@#@ complex and not only caused by overeating.  Oh, that and 100 years of epidemiology and research.

9. This sentence

“Once on the diet I rapidly lost 1,300 species of bacteria and my gut was dominated by a different group called bacteroidetes. The implication is that the McDonald’s diet killed 1,300 of my gut species,” he said.

Sorry but that is NOT the implication.


UPDATE 1: May 11, 2015. 8:00 PM

Thanks to a Tweet from Jennifer Gunter I changed the title of my post from " 9 things horribly wrong with Newshour story on fast food and microbiomes" to "9 things PBS Newshour famously gets horrible wrong in story on fast food and microbiomes"

@PBS famously showed bad science reporting https://t.co/8VuGq5njWU

— Jennifer Gunter (@DrJenGunter) May 12, 2015

My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute

Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes.  My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology.  I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.

To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer.  And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes

 I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).

I got in pretty late and worked a little on my talk before going to bed.  I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did.  Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research.  I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture.  But once he suggested this notion my talk really congealed (in my head and on paper at least).  It is interesting to me how one simple suggestion from someone with vision and perspective can transform one's thought process so much ...

Anyway, the next day I headed over to the meeting venue (by the beach - life is rough in San Diego).  I got there in time to hear Francis Collins' talk.  I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there.  More about this later I hope.  Anyway - that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more.  And eventually went to sleep.  Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it).  And voila - only 30 minutes before the PM session was to begin I finished the prep.  I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).

I note - I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome.  Anyway, I gave my talk, and recorded the slideshow with Camtasia.  Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk.
As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people's pictures and names on all slides and references but I don't always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on ...

Here is a slideshow with Audio (which I recorded via Camtasia)



Here is the Slideshare posting of my slides

Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology from Jonathan Eisen

Another day, another microbiome journal ... alas not as "open access" as claimed

Just got this email

Dear Doctor Jonathan Eisen,

I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (http://www.degruyter.com/view/j/micsm).
As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems:
Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD "Invertebrate systems for hypothesis-driven microbiome research"
Amato KR "Co-evolution in context: The importance of studying gut microbiomes in wild animals"
Nelson DR, Tu ZJ, Lefebvre PA "Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production"
Rudlaff RM, Waters CM "What is the role of cyclic di-GMP signaling within the human gut microbiome?"
Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA "Genetically identical co-housed pigs as models for dietary studies of gut microbiomes"
MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.

Authors are offered a variety of benefits:
– transparent, comprehensive and fast peer review;
– language assistance for authors from non-English speaking regions;
– convenient, web-based manuscript submission and tracking system;
– efficient route to fast-track publication and full advantage of De Gruyter Open's e-technology;
– no publication charge in the first two annual volumes.

I look forward to your manuscript!
Please forward this invitation to any interested colleagues and associates.

Seemed right up my alley - an open access microbiome journal.  Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:

1. License
The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on http://creativecommons.org/licenses/by-nc-nd/3.0/., except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.

Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like "open access".  The no derivatives part drives me batty.  Also they write:

9. Scope of the Commercial License
The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows:
 to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article,
 to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same.
Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.

Well, no thanks.  Too many restrictions and not open access in my view.  If I had to choose a "microbiome" journal to publish in, I would choose "Microbiome" an actually open access journal, where papers have the following info on them:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Go Microbiome ...

Buzzfeed includes microbiomes in "77 facts" but alas, gets the facts (and the math) wrong

Well, I admit it - I clicked on this Buzzfeed link someone posted on Facebook - 77 Facts That Sound Like Huge Lies But Are Actually Completely True.  There are some pretty funny and interesting things on the list.  However, I note - I did not click on the link per se for entertainment.   I clicked on it to see if there was anything about microbes on the list.  And happily, there was.  Alas, what there was, was, well, a bit wrong:

Let's start with #67.  "There is 10 times more bacteria in your body than actual body cells".  Well, alas, this is a nice bit of information.  But it is not based on facts.  See Peter Andrey Smiths wonderful article in the Boston Globe about this issue. The Buzzfeed article links to a 2010 Discover Magazine bit about this topic.  So they were trying to use facts.  But alas, that was not based on facts itself.

Then, let's go to #68.  "And 90% of the cells that make us up of aren’t human but mostly fungi and bacteria.".  So - I am at a bit of a loss on this.  First, isn't this really just rehashing #67 with the addition of fungi to the story?  Also - I note the math here is weird.  #67 would lead one to conclude that 90.9% of the cells in your body are bacterial (10:1 = 10/11 = 90.9%).  So then if one adds fungi to the picture the percent of cells in our bodies that are not human goes DOWN to 90%.  How does that work exactly?

So not only do they get the 10x as many cells fact wrong, they do something really weird by basically repeating #67 and then doing some weird math.

Oh well, glad they have something on microbiomes.  Too bad it came out a bit wrong.

New lab paper: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

A new paper out from my lab (with Jenna Lang as the 1st author and in collaboration with Angela Zivcovic from the UC Davis Food For Health Initiative and the Department of Nutrition):  The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types.  The work in the paper focuses on characterizing the abundance and taxonomy of microbes in food from three model diets.

Basically, Angela prepared meals for these three diets

Food was purchased and prepared in a standard American home kitchen by the same individual using typical kitchen cleaning practices including hand washing with non-antibacterial soap between food preparation steps, washing of dishes and cooking instruments with non-antibacterial dish washing detergent, and kitchen clean-up with a combination of anti-bacterial and non-antibacterial cleaning products. Anti-bacterial products had specific anti-bacterial molecules added to them whereas “non-antibacterial” products were simple surfactant-based formulations. The goal was to simulate a typical home kitchen rather than to artificially introduce sterile practices that would be atypical of how the average American prepares their meals at home. All meals were prepared according to specific recipes (from raw ingredient preparation such as washing and chopping, to cooking and mixing).

And then she blended them and we characterzied the microbial communities in the blended samples:

After food preparation, meals were plated on a clean plate, weighed on a digital scale (model 157W; Escali, Minneapolis, MN), and then transferred to a blender (model 5,200; Vita-Mix Corporation, Cleveland, OH) and processed until completely blended (approximately 1–3 min). Prepared, ready to eat foods that were purchased outside the home were simply weighed in their original packaging and then transferred to the blender. 4 mL aliquots of the blended meal composite were extracted from the blender, transported on dry ice and then stored at −80 °C until analysis. The following analyses were completed using these meal composite samples: (1) total aerobic bacterial plate counts, (2) total anaerobic bacterial plate counts, (3) yeast plate counts, (4) fungal plate counts, and (5) 16S rDNA analysis for microbial ecology.

And Jenna Lang coordainted the sequence analysis and then Angela and Jenna (with some help here and there from me) coordianted the analysis of the different microbial data and the writing of the paper.

Figure 5: Biplot of taxa in sample PCoA space.

Lots of interesting things reported in the paper (read it, I insist).  I note - this is a demonstration project in a way - trying to get the community and others to think about the source pools of microbes that come into our system from our food.  It is by no means comprehensive or conclusive (read the caveats section of the paper).  Congrats to Jenna and Angela for all their hard work. Anyway - the paper is Open Access in PeerJ.  Eat it up.

UPDATE: Some press and blog coverage

• Kevin Bonham on SciAM Blogs: The Microbes in Your Kitchen (Or in your Starbucks mocha)
• Maddie Stone on Motherboard: Here’s How Many Microbes You Eat in a Single Day
• “This paper will hopefully convince the powers that be that the next study, actually looking at how different foods or diets with differing microbes affect people, should be funded soon,” Zivkovic told me.
• Nathan Gray:  The microbes we eat: Study investigates bacteria in different diets
• Ross Pomeroy on Real Clear Science: This Is How Many Microbes You'll Eat Today
• Improbable Research: What’s Eating You, and/or Vice Versa: Microbes
• Marissa Fessenden at Smithsonian: You Eat Millions...Even Billions!...of Microbes Every Day

Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Sunday I gave a talk at the "12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference".  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:

The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.

It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things - diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:

Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:

UPDATE 10/16 -

I have scanned in my notes that I made in planning this talk.  Figured, why not post them.

Update: 12/10/2014 - just discovered a video of the talk was posted to Youtube