This may be of interest:
For those in or near Davis, CA
Block the date – this will be awesome
October 19, 2015
1:00 to 3:00pm
Student Community Center, Multipurpose Room
1st Quarterly Food and Agriculture Roundtable
Discussion of Microbes in Food and Agriculture
including a discussion of glyphosate and microbiomes
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 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
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:
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:
I have scanned in my notes that I made in planning this talk. Figured, why not post them.
What the fungi do I do with my ITS library (Part 2)
Originally posted on jennomics.com on May 22, 2014
Previously, I expressed some concern about size variation in my environmental fungal ITS PCR libraries. I’m still concerned about that, but I have an additional concern. The ITS region can’t be aligned, and I’m partial to phylogenetic approaches to pretty much everything. So maybe ITS is not for me?
So, I asked Twitter again…
In summary, I don’t think that I can use ITS given the size variation that I see, and I’m not sure that I want to, given the fact that you cannot align it to do phylogeny-based analyses.
28S (or LSU) is a reasonable alternative to ITS that has two big downsides: 1) the reference database is much smaller than the ITS reference database and 2) it does not provide the fine-scale taxonomic resolution that ITS does.
Rachel Adams referred me to Amend et al, in which they use both. I’ll have to look into this approach…
It’s been about 8 years since I started working on my first 16S rRNA PCR survey (of Drosophila gut microbes). At that time, I was occasionally asked, “what about Archaea or what about microbial Eukayrotes?” Then, and ever since, my reply has been that it’s hard enough to get a handle on what’s going on with the bacteria – I don’t need to make my life more challenging by broadening my scope.
But, finally, this month, I’m making my life more challenging. As part of my new Seagrass Microbiome Project, I’ve decided to tackle the fungi. As far as I can tell, ITS is the “barcoding” marker of choice for fungal types. For many reasons, it’s best to follow the herd when doing this sort of thing: 1) someone else has already designed, tested, and published results with these primers, 2) there is a reasonably large database of ITS sequences available to compare my sequences to, and 3) I lack the interest and personnel to explore an alternative approach.
So, I just plunged right in. At first, I tried some new primers designed by Nick Bokulich, but he warned me that they were “finicky” and he was correct. I got no amplification with my seagrass samples, and the positive control I had only worked about half the time. I know some other fungi people, well, I know Jason Stajich (@hyphaltip), so I asked him which primers I should use, and I decided to go with the primers set used in a cool paper by Noah Fierer’s lab, in which they looked at fungi in rooftop gardens in New York City.
Those worked, and a few days ago I got word that my sequencing run was in. It looks like crap. We typically get about 12 million sequences from our MiSeq runs, but this time, I only got 4 million. I was also told that the reverse reads looked much better than the forward reads.
So, now, in addition to working with a new “barcode,” I have to troubleshoot a crappy sequencing run. In many ways, it’s nice to have undergrads and a technician in the lab who do all of my lab work for me these days, but it sucks when it’s time to troubleshoot because I’m so far removed from the bench that I have no idea what’s going on anymore.
So, the first thing I asked for was the Bioanalyzer trace that’s always run before the library goes on the machine. It looks like this:
I had been told that there was size variation. I had even seen some of the PCR gels. But, still this is not what I expected to see. Upon seeing this, I am concerned about two things. 1) If there is strong preferential amplification of smaller DNA molecules during the bridge PCR on the flow cell, then will I even see DNA from those larger peaks? 2) With our 300bp reads, for sure the amplicons in the peaks <400 will have overlapping forward and reverse reads, but for sure the 676bp amplicons will not. What effect will these two things have on my analysis? How do I accommodate this size variation? One of the reasons to follow the herd with these methods is that other people have probably already encountered and dealt with exactly this issue, so I turned to Twitter…
There are some great resources suggested here. I know what I’ll be reading this weekend…
I made a Storify posting for the CLIMB Symposium I participated in yesterday. First I am reposting my summary of what the symposium was about which I posted the day before the meeting:
There is a symposium tomorrow at UC Davis organized by a undergraduates in the CLIMB program. CLIMB stands for “Collaborative Learning at the Interface of Mathematics and Biology (CLIMB)” and is a program that emphasizes hands-on training using mathematics and computation to answer state-of-the-art questions in biology. A select group of undergraduates participate in the program and this summer the students had to do some sort of modelling project. Somehow I managed to convince them to do work on human gut microbes. And they have done a remarkable job.
As part of their summer work, they organized a symposium on the topic and their symposium takes place tomorrow. Details are below.
The Infant Gut Microbiome: Prebiotics, Probiotics, & Establishment
- Jonathan Eisen, UC Davis “DNA and the hidden world of microbes”
- Mark Underwood, UC Davis “Dysbiosis and necrotizing enterocolitis”
- Ruth Ley, Cornell University “Host-microbial interactions and metabolic syndrome”
- CLIMB 2010 cohort “Breast milk metabolism and bacterial coexistence in the infant microbiome”
- David Relman, Stanford University “Early days: assembly of the human gut microbiome during childhood”
- Bruce German, UC Davis
The only major issue for me is I am losing my voice. So we will see how this goes. Though I note I have gotten some very sage advice on how to treat my voice problem via the magic of twitter. If I do not collapse I will also be tweeting/posting about the other talks during the day.
http://storify.com/phylogenomics/climb-symposium-at-uc-davis.js&amp;amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/climb-symposium-at-uc-davis” target=”_blank”&amp;amp;amp;amp;amp;gt;View “CLIMB Symposium at UC Davis” on Storify&amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;gt;