Tag Archives: microbiome

QS Radio Episode #1

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In our first episode of QS Radio we hit the ground running with a great pair of interviews and some super interesting news and discussion about exciting self-tracking projects.

In our show&tell segment, we hear from Shannon Conners, a self-tracking enthusiast who’s been learning amazing things from tracking her diet, exercise, and weight for over four years. Jessica Richman, CEO and co-founder of uBiome, joins us for a short Toolmaker Talk where we learn about the importance of the microbiome and citizen science. To wrap up, Ernesto and Steven share a few interesting tech and self-tracking stories in a segment we call “What We’re Reading.”

We hope you enjoy this inaugural episode. Make sure to check the show notes below for links to items we discussed.


Show&Tell
You can find out more about Shannon Conners and her self-tracking experience on the JMP blog. We spoke in particular about her excellent diet tree map visualization:
ShannonConnors_4yearsfood

Toolmaker Talk
You can find out more about Jessica Richman and uBiome on their website.

What We’re Reading

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What is in My Gut?

LesDethlefsenPostTop2

This past fall we learned about a unique study, conducted at Stanford University, designed to contribute to the understanding of the human microbiome. This study also has a component not common to academic research — data is being returned to the participants. Intrigued, I contacted the principle investigator, Les Dethlefson, to learn more.

Ernesto: Tell me about the Dynamics of Human Microbiota study.

les_dethlefsen_at_the_benchLes Dethlefsen: Since I joined the Relman Lab at Stanford, I’ve been looking at the human gut microbiota, focusing on what affects it and how it changes over time. In our study, we are looking at three different perturbations, deliberate changes to the gut ecology, to see how the microbiota population is affected.

We are very interested in the patterns that emerge. In people who have very stable gut microbiota, does their microbiota remain that way when they undergo diet shifts, a colon cleanout, or an antibiotic? Or maybe people who have a stable gut microbiota most of the time are the ones who are most affected by something unusual such as taking antibiotics. We just don’t know enough to understand these patterns right now. So, we’re really looking for basic ecological information.

Ernesto: If you look at the popular press, it seems the microbiome is the new golden child of biological life sciences. We’re even seeing companies in Silicon Valley get involved with this kind of work.

Les: It is broader than that. It really is a worldwide interest on the parts of both the scientific community and the public. And unfortunately, we are probably going to see some overhype, just as we did with the Human Genome Project. But I do believe this is a very important area. I think there will be a lot of payoffs and health impacts from this research, although it’s not going to be everything.

The shift that, I think, would be good for us to make intellectually is to get rid of the “us vs. them” thinking, because we are symbiotic organisms.

We have evolved with a native gut microbiota, and native microbiota is pretty much everywhere. We have evolved together, so it’s fallacious — an artifact of our past ignorance — that we don’t think of our microbes as part of our physiology.

Ernesto: It seems like exploring the deep sea, an unknown world that we’re just starting to peek into.

Les: It’s along those lines. You’re not wrong about that. But unlike, let’s say, the deep waters surrounding an undersea hydrothermal vent, we already know a lot about human physiology. There are a lot of molecular details and genetic pathways that we already have worked out. The context is somewhat understood.

And now, we have a reasonable start on the initial research: What microbes are present, and where? What’s the range of what we think is the normal distribution? We certainly don’t know enough, because we only know about people in the developed world. However, this may not represent all of human diversity or a very natural state of the gut microbiota.

Candida albicans

Candida albicans

Ernesto: Let’s get back to your study. You are asking participants to send microbiome data in the form of fecal matter and urine to your lab. What are you doing with those samples?

Les: We ask participants to provide both stool and urine samples. With the stool sample, we apply four different methodologies to turn it into data. One is the very common 16S ribosomal RNA (16S rRNA) gene sequencing approach. It’s relatively standard and inexpensive. It acts like an ID card for microbial taxa — telling us approximately what strains are present and in what relative abundance. We have a lot of data like that already for comparison.

sequencerThe second approach we will be applying is metagenomic sequencing, wherein we will be sequencing a random selection of all the genomes of the microbial types that are present. We can’t take this to completion, even with the dropping cost of sequencing, especially because there are some very, very rare microbes that we barely even have the chance to see at all. But we can get a pretty good swathe of genetic sequence data from all the microbes.

The third approach is even more ambitious. It’s called metatranscriptomics. Genes can be carried by any critter, you and I included, but not expressed. Knowing which genes are turned on, and to what extent they’re turned on is a better measure of the biological activity that is actually happening. The metagenome is a measure of potential activities, what the bugs can do. The metatranscriptome shows what the microbes are actually doing. Metatranscriptomics is even more challenging than metagenomics partly because of the nature of messenger RNA (mRNA). It’s a highly unstable molecule. There are technical challenges, but we’re ambitious enough to try to collect information on gene expression.

The fourth approach is not based on gene sequences, but on chemical composition. Metabolomics is the name given to a number of these approaches that are not directed to a specific chemical. These are techniques that try to measure a broad swathe of chemicals present in the environment and their relative abundance. This is a technology that we, in the Relman Lab, know very little about. We’re collaborating with the Nicholson Lab in Imperial College in London, and they will be doing the metabolomic analyses on the stool samples. That may be even closer to where the rubber meets the road — knowing not just the gene expression but also the resulting chemical changes that are happening in the environment.

MicrobeHeatMapMetabolomics takes us to the other type of sample we’re collecting: the urine samples. We aren’t doing this because we have an interest in the urinary microbiome itself, but because, as the Nicholson Lab suggested, the urine provides a more complete, integrated picture of the co-metabolism between the human host and most of the gut microbiota. So while metabolomics for the stool samples would primarily measure the gut microbial activity and what they contribute to the host’s physiology, the urine provides a more integrated picture about how the host metabolism works in concert with the gut microbiota.

Ernesto: If a participant is going to be contributing all of that data, will they have access to it?

Les: As someone with similar interests, I certainly knew that a huge motivation for people to join the study would be the access to their own data. We offer monetary compensation, but for the amount of time that will be spent in contributing samples, it is probably trivial. We knew we would attract the curious, scientifically inclined, and practising scientists. Of course, they would want to see their data.

The Institutional Review Board (IRB) was quite open to us sharing information with the participants about their own microbiota. It probably helped that there’s publicity  about ways people can get this information. There is the American Gut project, offering an assessment of your microbiota for a donation, and uBiome, a private company offering the same kind of service.

I, or another staff member of the study, are going to share this microbiota data with each participant in a conference call. So in effect, I’m going to be a microbiota counselor. It’s nowhere near as high-stakes as sharing genome information. We don’t know enough to say, for example, that this microbiome is definitively healthy, or that it’s unhealthy, or what the exact risks of diseases are due to this particular composition. So we will be putting this information in context, and we will be available as interpreters of the scientific literature. We may be able to say that there is a statistical association between a particular microbial group that someone may have in their gut and some health-related outcome.

sequence_data3

Microbiome sequence data

Ernesto: Will participants be getting a copy of their data as well?

Les: Yes, we will provide that. I have an open source mentality. Added to that is the fact that there are many practicing scientists signing up for the study and saying they want data, not just a PDF summary. I am happy to provide the data in as raw a format as people want. They can get the raw sequence information, a low-level summary (which is the result of the first pass of data processing), or the final summary. I have permission and full intention to share all the data derived from a person’s samples with that person.

Ernesto: Do you think we will see this happening more in the future?

Les: I think we will probably see more of it in the future. We’re moving in the direction of access to information. The open source movement has reached the health and medical realm from its origins in tech and computing. I think the participatory nature of access to data and scientific information is a good thing. It has started, and I don’t see any way of reversing the trend. I would hope that it becomes the norm that there is some appropriate level of sharing, that research participants have access to their data if they wish, and in a way that lets them interpret that data appropriately.

I believe that people have a right to that level of knowledge about their bodies, and if we, scientists, are generating that knowledge, there’s no reason not to share it with the individuals.


The Dynamics of Human Microbiota study is currenlty recruiting participants. If you’re interested in learning more about the ecosystem within read more about the study and check to see if you’re eligible to participate here.

We invite you to share your data access stories, and this article with the #qsaccess hashtag and follow along on quantifiedself.com and @quantifiedself.

 

 

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QS Access: Data Donation Part 2

In our Access Channel we’re trying to expose ideas, efforts, and insights about personal data access and it’s role in both generating personal and public insights. The last time we wrote about data donation we mentioned a few different projects that allowed you to collect and/or publish your self-tracking data for others to view and access. Today we’re going to showcase a few research-focused projects that collect personal data, but also allow participants to access the data they contribute. This seemingly minor addition, participant access to data, is actually a process not commonly employed by research studies. We’re very interested in new participatory models of research that respect participant’s rights to fully understand and access the data they contribute. If you know of others please get in touch and we’ll add them to the list.

Personal Genome Project: Harvard
Probably the most well-known of these research projects is the ongoing Personal Genomes Project based at Harvard University (PGP). Led by George Church and an outstanding team, the PGP is an ongoing research project recruiting participants to “share their genetic, health, and trait data in a public and non-anonymous manner. Participation is free.

American Gut
Much like the project above, the American Gut project is an open call for participant to collect and share their data. In this case it is human microbiome data. Although enrollment is not free (they request donations starting at $99 to participate) data is returned to participants. (If you’re interested in participating in microbiome research, but live in Europe see the British Gut project)

Dynamics of the Human Microbiota
This new project, based out of Stanford, is also exploring the human microbiome. This study includes a variety of different perturbations and longitudinal data collection. Participants are compensated for their participation, their data is made accessible to them, and they have the opportunity to discuss their results with the study staff.

For those of you interested in research methods and ethics we recommend reading this brief article by Jeantine E. Lunshof, George M. Church, and Barbara Prainsack: Raw Personal Data: Providing Access

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Conference Preview: Tracking our Bacterial Buddies

bacteria-600x381We are not alone. No, there haven’t been any extraterrestrial sightings lately, but there have been many advances in understanding the organisms that make up the ecosystem of ourselves. Did you know that you are supporting almost 10 times more bacterial cells than human cells? These bacterial collaborators have a profound affect on health and wellbeing. Jessica Richman, co-founder and CEO of uBiome, will be leading a breakout session at our upcoming QS Europe Conference on understanding the microbiome.

Access to microbiome data outside the official research and clinical context is bound to ruffle feathers, just as access to genomic data has created controversy for 23andMe and other companies. While the regulators argue, we’re keenly interested in finding out how microbiome info can be useful and interesting in our own tracking projects, and there is nobody better to work on this with than Jessica. Please join this session if you share our curiosity.

 The QS Europe Conference is just a few weeks away; come if you can!

 

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What would you do with your microbiome sequence?

If you had access to free microbiome sequencing tests, to detect and analyze bacteria living in the nose, mouth, skin, gastro-intestinal, and/or urogenital areas of the body, what experiments would you think up?

Would you compare oral bacteria in people with lots of cavities vs. people with no cavities, look for differences between people with clear skin and acne, or sample your gut flora as you travel or change your diet? These are just examples — there are countless ideas.

As it turns out, we DO have up to 100 free microbiome profiles being offered to the QS community, thanks to Pathogenica and QS sponsor Autodesk.  Now we just have to think up some cool experiments to do.

So the challenge is on – propose an experiment in the comments, and the top experiments will be done with some of the free tests. The deadline for submitting ideas is August 31. Also, all the data will be made openly available.

Check out some background reading on microbiome sequencing at the Human Microbiome Project website and Wikipedia.

Let’s come up with awesome ideas!

 

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