Tag Archives: 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 builtmicrobiome@nas.edu
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).
AGENDA
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

Time for #DegreeMadness – where we rank people’s statements by what degrees they have not by science

10/19 in #DavisCA: 1st Quarterly Food and Agriculture Roundtable

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

Jonathan Eisen

1st Quarterly Food and Agriculture Roundtable

Discussion of Microbes in Food and Agriculture
including a discussion of glyphosate and microbiomes

Eisen Roundtable Flyer .pdf

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.

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

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 

What the fungi do I do with my ITS library? (Part 2)

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…

What the fungi do I do with my ITS library?

Originally posted on jennomics.com May 21, 2014

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:

Bioanalyzer trace for my first fungal ITS MiSeq run

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…

 

Storification of my notes/tweets from #UCDavis CLIMB Symposium "The infant gut microbiome: prebiotics, probiotics and establishment"

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. 


Anyway – here is the storification:

http://storify.com/phylogenomics/climb-symposium-at-uc-davis.js&amp;amp;amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/climb-symposium-at-uc-davis&#8221; target=”_blank”&amp;amp;amp;amp;amp;amp;gt;View “CLIMB Symposium at UC Davis” on Storify&amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;gt;