Janet Jansson

Spectrum

Janet Jansson is the Senior Staff Scientist in the Earth Sciences Division at Lawrence Berkeley National Lab. Her expertise is in molecular microbial ecology and “omics” approaches with a focus on soil, marine sediment and human gut environments.

Transcript

Speaker 1: Spectrum's next.

Speaker 2: Okay.

Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, [00:00:30] a biweekly 30 minute program, bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news.

Speaker 3: Good afternoon. I'm your host, Brad Swift. Today's interview is with Janet Jansen, UC Berkeley, adjunct professor of molecular microbial ecology. She is a senior staff scientist in the Earth Sciences Division at Lawrence Berkeley National Lab and president elect of the International Society of microbial [00:01:00] ecology. Her expertise is in the area of molecular microbial ecology and Omix approaches with a focus on soil, marine sediment and human gut environments. Today she talks about the human microbiome project, the Earth microbiome project and American Gut, a crowdsourced research project. Onto that interview. Janet Jansen, welcome to spectrum. Hi, what'd you give us a short description [00:01:30] of microbial ecology and give some examples of complex microbial communities.

Speaker 4: Sure. So microbial ecology is the study of micro organisms in the environment and their interactions with other microorganisms, plants, animals, that particular habitat that they happen to be living in. So it's really not just studying a single microorganism, but a community of microorganisms. Uh, so some examples [00:02:00] of complex communities. Well, the most complex ecosystem is soil and that's because it has such a diversity of microorganisms and it's really packed full of microbes. So there's so many microorganisms living in soil. So that combined with the diversity makes it a very complex system. The human ecosystem is very complex. Our own intestines have a very complex microbial community. [00:02:30] The oceans or other examples, sediments. So I think this is my community college that you had to think differently than one would when you study organisms in pure culture and their physiology is much more complex

Speaker 3: and microbial research seems to have jumped in stature in the past few years. You have a broader view of it than I do. What's your take on the trajectory of microbial research? I think

Speaker 4: [00:03:00] particularly the microbial ecology part has increased in stature recently. Microbiology as a field has been around for a long time. But the thing that I think has really boosted the field of microbial ecology is the advent of these new technologies, the new tools to be able to really look at these complex communities and understand them. Until I guess it was about the 1980s there wasn't [00:03:30] any way to really look at these micro organisms in soil. Again, I'll use that as an example, unless you cultivated them onto augur media or looked at them in a microscope. So when the field was limited to looking at what was possible to cultivate, that was only a fraction of the microorganisms that live in soil habitat. So probably fewer than 10% could be cultivated. So the majority of the organisms that were there, [00:04:00] nobody knew anything about them. Their identities or their functions were really unknown.

Speaker 4: So it was considered like a black box eco system. But after the late, I guess the 80s and into the 90s there were the developments in DNA extraction techniques. So it was possible to extract DNA from soil and then came PCR amplification methods and methods to be able to amplify specific [00:04:30] pieces of DNA that you had extracted that made it possible to actually study soil microorganisms without cultivating them. And now we have these deep sequencing technologies, so it's really made it much easier to do very deep analysis of these communities and not have to rely on cultivation.

Speaker 3: The human microbiome project is in its last year. What were the goals of it and can you speak to that about what the goals were and what you think [00:05:00] you've found out?

Speaker 4: The first stage of the h and p was to sequence different bodies sites and understand which micro organisms are residing in different sites in the human body. And so this was looking at a large cohort of humans, healthy humans, and just basically understanding who are the microbial inhabitants of the human body. So that part is winding down. We have that knowledge now. We know that there are different micro organisms that live on your skin, [00:05:30] then in in your gut for examples and also in the oral cavity. So these organisms are specialized to live in different parts of the human body and there are differences between different individuals though. So that means that each human has their own individual microbiome and it can almost be used as a fingerprint. So that was a successfully completed project. The next stage there has been a recent call too, I think it's even called h and p two [00:06:00] to go the next step. So to use other kinds of methods to look at not only which microorganisms are there, but what are they doing. So this would be looking at the functional capabilities of the human microbiome. Another thing that is still ongoing with the h and p is looking at how does disease influence the human microbiome and vice versa. What is the correlation with the microorganisms living with us and disease? And it seems like there are many different links between many [00:06:30] human disease that send the human microbiome

Speaker 3: [inaudible] [inaudible].

Speaker 5: Our guest today is microbiologists, Janet Jansen. In the next segment she talks about the microbiome and disease correlation. This is k a l x, Berkeley.

Speaker 3: Well, and often in science there's a lot of correlation [00:07:00] that goes on and sometimes you get fooled by the correlation. Sometimes you don't. Are there strategies you use in terms of validating what you think correlates?

Speaker 4: Oh, correlations are can be quite challenging. Definitely. So, um, that's an interesting question because then one of the things that is very tricky is if you find a difference in an environmental sample, for example, with the civic treatment or in a human with disease often all we have, [00:07:30] we can then say, well it's correlated to this organism that is higher in abundance or it's correlated to this protein that is higher or lower in abundance. That's a little frustrating. So that the next step, and we're not quite there yet in this field, would be then to say, okay, go beyond correlations and then actually do the proof, you know, to take that organism like Cox postulates, you then prove that this correlation that you see is actually [00:08:00] occurring. But it's difficult with these complex samples, like I was saying before, because you have to move away from the complex environment where you have all these different factors.

Speaker 3: So the complexity defeats you in a way because you can't isolate the specific from the general. Exactly. Exactly. And so within this correlation of disease, are there particular diseases that seem to be top priorities in a sense or are most likely to be effected by [00:08:30] the microbiome? An example of Crohn's diseases,

Speaker 4: Crohn's disease is the example. I would give us a very clear example and also other inflammatory bowel diseases where there has already been established a link between the gut microbiome and the disease. The details are still under investigation, but there is a difference in the micro organisms that inhabit the intestine in individuals that have Crohn's disease compared to healthy. [00:09:00] So that's known.

Speaker 3: And is that the case with ulcers as well? Or they were sort of one of the first, it seems that had this association with the microbiome in the gut,

Speaker 4: right. So systemic ulcers, there was a Nobel prize awarded for the discovery of [inaudible] go back to Pylori as the cause of ulcers in the stomach. And so that's a good example, this specific microorganism that can contribute to a disease. And then of course a lot of medications were subsequently [00:09:30] developed to dampen hillcoat back to pylori through new research. We know that there is a considerable diversity of microorganisms in the stomach that people weren't aware of before using these techniques and also in your teeth and then in the oral cavity. There's a very large diversity. I should mention that one of the things that is a really hot topic right now is the link between the brain and the human microbiome, including [00:10:00] the gut microbiome because it's known that some of the metabolites that are produced by these intestinal microbes can pass the blood barrier and then migrated essentially in impact the brain, so some current research is looking at the link between autism and schizophrenia, these kinds of things. Then I think that's really interesting. That's one future direction of the field.

Speaker 3: The new initiative in brain mapping exactly [00:10:30] now ties that together. That would be great. At least the findings here was just a new funding.

Speaker 4: Yeah, I know. I don't know if they've really decided to make that link for funding, but it probably will come.

Speaker 3: Can you talk a bit about American gut and how it's set up to help people figure out their own microbiome?

Speaker 4: Sure. So the American get is, it's a relatively new way of doing research [00:11:00] is crowdsourcing. And the idea is that if a person such as myself is interested in knowing quip, my gut microbiome is I can pay a small amount, it's like $100 to get my sample sequence. So that is the way that the project is funded. And so this project, it had a funding goal, I think it was $300,000 to be able to launch the sequencing. And so there was the campaign [00:11:30] and it was sent out to the community and through connections such as Facebook and another with this nice little carrot that if you pay $100 you can get your microbiome. And in addition to gut, it could be your skin sample, oral cavity, your pet. And so this idea really caught on and is a good example of crowdsourcing for funding.

Speaker 3: And how are people able to leverage that information? [00:12:00] Is there some characterization that you do as well?

Speaker 4: The data that they get back is, it's different kinds of information. So first which micro organisms do I have? That's kind of fun to know. It's sort of like 23 and me where you get information back about which genes you have in, which kind of markers for different things. So depending on your microbial community composition, you may have markers that are more indicative of health, certain kinds of diets like [00:12:30] vegetarian or a protein rich diet, even obesity, there's certain microbial indicators of obesity. So that's just interesting. Another thing that is valuable for the consumer, the person who does this is that you can compare your microbiome to everybody else's. It's all anonymous of course. And nobody knows who's this, who's, but you have your own data and can see how your microbiome fits into a pattern. So do you cluster [00:13:00] with obese people or with a disease type microbiome or a certain kind of eating pattern

Speaker 3: and are these online tools that you have available through American gut for people to do this kind of characterization?

Speaker 4: So the analysis has to be done by the actual scientists that are doing the samples because it's still quite elaborate and involves a lot of bioinformatics. So currently it's not possible [00:13:30] to do a lot of that on your own, but still to get an output, the actual data, the results of the analysis is what the individual can get through this project.

Speaker 2: [inaudible] you were listening to spectrum on a k a l x Berkeley. Our guest today is Janet Jensen. In the next segment she talks about the earth microbiome project.

Speaker 3: [00:14:00] Can you talk a bit about the earth microbiome project and maybe differentiate it from the human project?

Speaker 4: Yeah, sure. So the Earth microbiome project, which I'll call the emp, is, um, instead of just looking at humans, it's including basically all of earth. So it has a very lofty goal of understanding earth microbial diversity. That project also relies [00:14:30] on collaborators, so it's sort of a crowdsourcing project as well, but limited to the scientific community. So the way that Earth microbiome project works is if a collaborator has an interesting set of samples, for example, from the deep sea or from Yellowstone hot springs that have the required kinds of environmental data, so Ph, nutrients, things like that. Then they can [00:15:00] send an email to the steering committee and say, well, would this study be of interest to the earth microbiome project to the ENP? And then the steering committee looks through the data and decides whether the environmental data is sufficient and if the samples are filling a hole and providing novel information and if so the samples are accepted and the sequencing is done without any costs to the investigator. That's the win win scenario for the emp [00:15:30] because the investigator does of course provide the funding for the study and collection of the samples and the emp provides the funding for the sequencing. Now the funding for emp is also kind of fuzzy because it's through different kinds of companies that have supported by providing regions or equipment and then in turn they get advertisement through the emp that they're sponsors of the project. And so that [00:16:00] also seems to be quite successful.

Speaker 3: And the intent again to build a catalog

Speaker 4: basically, yes, to build a catalog to find out who's there and are there patterns. The nice thing about heading samples from so many different disparate environments is that you can see, well does this particular microorganism occur across different kinds of environments or is it really endemic only to one kind of habitat? And if you tweak the environment, [00:16:30] for example, with climate change to have increases or losses of certain members of the community that are predictive, one of the aims is to have something like a Google map and then you can highlight all of this sort of organism type in pink. If you click on a button and see where they are localized around the globe. But then if the climate increases by five degrees, then you can click another button and see what happens. Does that organism increase or decrease there? Does another microbial typing [00:17:00] green become more abundant?

Speaker 3: The methods you use that you apply to your research. So often we're results oriented with science or at least to the public, you know, what did you find out? It becomes more important than how did you find it out? Can you give us some sense of your methods to doing the research that you do?

Speaker 4: I think that the methods, as I mentioned earlier, that's been a limitation to my particular field, but that [00:17:30] also makes it kind of fun because we're always trying to develop better methods and new methods to be able to investigate these systems. And so it's quite challenging, which is something I like. So the method in my own lab that we're developing are different kinds of what I call omix quoting. Oh, mixed methods. So that's everything from sequencing everything, which would be metogenomic x to extracting RNA and [00:18:00] sequencing that. That would be looking at express genes. That's Meta transcriptomics or extracting all the proteins and looking at that. That would be metaproteomics. You can even do the metabolites metabolomics. So these are the current methods that are stated. The art right now for looking at these kinds of complex communities.

Speaker 6: [inaudible] [inaudible]

Speaker 5: this is k [00:18:30] a l x Berkeley. The show is spectrum. I'm Brad swift. Our guest is professor Janet Jansen, microbial ecologist at Lawrence Berkeley lab and UC Berkeley.

Speaker 3: In your experience working on these large projects and also then working in small projects, I'm curious about the, the idea of big science versus small science. You know, the individual scientists toiling [00:19:00] away versus the big group that gets together and decides what they'll do and [inaudible].

Speaker 4: So personally I, I'm a big science kind of person. I definitely appreciate the value of a small science than I do have some smaller targeted projects. I moved to Berkeley lab about five years ago. I was a professor in Sweden before that and my funding was more individual, smaller projects in Sweden. But uh, one of the reasons I came to Berkeley lab was because of the big team science. I really [00:19:30] like that I'm a super collaborator and I can see the value of having people with different skills working together to tackle some really big problems. [inaudible]

Speaker 3: and I suppose the culture then becomes really important to the group, the dynamics, the sharing, the openness. And how does that happen, do you think? Have you seen it work well and work badly?

Speaker 4: Oh, it's very important. So you had to choose your collaborations as well and sometimes if they, the dynamics [00:20:00] aren't working, then it might be time to rethink the collaborations and revise it in a certain way. But ideally you have people that are so motivated that they are, I know that start delisting, but in the best case situation you have people that are so motivated towards a specific goal that it works quite well. There is an example of one project that is ongoing right now at the lab. It's called the next generation ecosystem [00:20:30] experiment in the Arctic, which is looking at the impact of climate change on permafrost communities. And that's the big doe funded project that involves probably hundreds of researchers at different laboratories, different doe laboratories and universities that are all focusing on one location in Barrow, Alaska, using all of the different tools available at the national labs and expertise at universities as well.

Speaker 3: [00:21:00] And how long has that been going on?

Speaker 4: It's been about a year and a half. It's a new project, but I'd like it because it has the necessary funding. Of course, when you spread it out, you know, everybody gets a little chunk of it, but it enables incredible things to be done at that site. It's just so much fun to go to these meetings and hear about the lidar sensing team and the modeling team and the hydrology team with their sleds and the geochemists go [00:21:30] in and my part is the microbial ecology. We get deep cores and we extract DNA and sequence them. It's just really a lot of fun

Speaker 3: and there's a lot of emphasis on trying to encourage young people to get into science, technology, math. Is there really an opportunity in this field for, for people?

Speaker 4: I have to say that right now it's a huge opportunity and there aren't enough persons educated in this field [00:22:00] to be able to fill these growing companies that are starting up. I'm getting several calls from companies that are asking for postdocs from my lab if they're interested in joining and if I were starting right now as a biologist, I would definitely look into bioinformatics and also the metagenome mix fields because these are the sorts of persons that there aren't that many yet. It's not that widespread yet [00:22:30] and there are companies that really need that expertise.

Speaker 3: Would you characterize both of those briefly?

Speaker 4: The bioinformatics would be more of generation of software algorithms, ways to look at these big data that are generated from different kinds of biological samples

Speaker 3: and that might include visualization as well as other normal text output kind of a thing.

Speaker 4: Yeah, absolutely. Everything from the database [00:23:00] management to the visualization of the data and things in between. The statistical analysis, that's a huge growth area and I predict this is going to continue because the data is just getting bigger. It's not going away from that a genomics and these other kinds of omix areas. I think that that would also involve some computing skills, but in addition to differentiate it from bioinformatics, more of the combination with lab skill.

Speaker 3: [00:23:30] Janet Johnson. Thanks very much for coming on spectrum.

Speaker 4: Thank you. I really enjoyed it.

Speaker 3: Well, we'd like to mention a few of the science and technology events locally over the

Speaker 7: next two weeks. Rick Karnofsky joins me for the calendar. The Saturday the science of cow lecture will be given by Dr Nadir Mirabal Fathi. The lecture is entitled, connecting infant decimal to infinity, the search for dark matter. [00:24:00] He will speak about a new class of elementary particles known as weakly interacting massive particles or Wimps to resolve inconsistencies in our understanding of the nature at both extreme, large and small scales and how they are connected together. He will also explore the experimental efforts to detect these particles. Interest real laboratories. Nadir r Mirabal Fathi earned Phd in elementary particle physics and cosmology at the University of Paris. He did his postdoctoral [00:24:30] studies at UC Berkeley and has been an associate research physicist at UC Berkeley since 2008 the lecture is Saturday, May 18th at 11:00 AM in room 100 of the genetics and plant biology building. Makerfair. The self-proclaimed greatest show and tell on earth is this weekend, May 18th and 19th at San Mateo fairgrounds.

Speaker 7: We talked last year with Tony to rose and Michelle, who? Bianca. Two of the founders of young makers about [00:25:00] the maker fair. Find our interview with [e-mail] slash calix spectrum one day prices range from $15 to $30. Highlights of this year's maker fair include KQ [inaudible] kitchen sisters with their new radio series, the making of what people make in the bay area and why NASA makers with astronauts, John Grunsfeld, Dennis Bartell's discussing building the new exploratorium, [00:25:30] how to tie a perfect neck tie with Nobel prize physicist Arno Penzias, DIY research with Tekla labs and amazing science. Tornadoes, smoke rings and more. For more information, visit makerfair.com that's maker F A I r e.com the long nose Stuart brand. It's presenting on reviving extinct species on Tuesday, May 21st [00:26:00] at the San Francisco Jazz Center, two Oh one Franklin Street at 7:30 PM tickets are $15 he'll summarize the progress of current de extinction projects including the Europe's Oryx Australia is gastric brooding frog and America's passenger pigeon.

Speaker 7: He'll also discuss some of the ancient ecosystem revival projects such as Pleistocene Park in Siberia. New Genomic technology can reassemble the genomes of extinct species [00:26:30] whose DNA is still recoverable from museum specimens and some fossils. Sorry. Jurassic Park fans. No dinosaurs. It is hoped that the jeans unique to the extinct animals can brought back to life in the framework of the genome of the closest living relative. For more information, visit long now.org now Rick Karnofsky and I present to news stories. Alberto Saul from Brown University and colleagues [00:27:00] published an article in science on May 9th that suggests the water that is on the moon came from Earth. The team measured the relative abundance of deuterium that is heavy hydrogen that contains an extra neutron to hydrogen in the water, found in small bubbles of volcanic glass and Melt inclusions in moon rocks. They found the ratio was very similar to the ratio found on earth and from carbonaceous chondrites meteorites that are thought to have supplied [00:27:30] the earth with water.

Speaker 7: Higher. Deuterium levels were expected by some who had hypothesized the comments from the Kuyper belt in Oort cloud could have been the source of the Moon's water. If the moon's water did come from Earth, it is likely the earth already had this water when the moon was formed. Some four and a half billion years ago when the earth and another Mars sized planet collided. However, such a collusion may have been hot enough to vaporize the lunar water. There is sir now [00:28:00] debating whether it may have been retained because of the earth's gravity or because the moon shared some of the earth's high temperature atmosphere when it formed pregnant mothers exposure to the flu was associated with a nearly four fold increased risk that their child would develop bipolar disorder in adulthood. In a study funded by the National Institutes of health. The findings add to mounting evidence of possible shared underlying causes and illness processes [00:28:30] with schizophrenia, which some studies have also linked to prenatal exposure to influenza, principal investigator Allen Brown and MD mph of Columbia University says prospective mothers should take common sense preventative measures such as getting flu shots prior to and in early stages of pregnancy and avoiding contact with people who are symptomatic in spite of public health recommendations, only a relatively small fraction of such women [00:29:00] get immunized.

Speaker 7: The weight of evidence now suggests that benefits of the vaccine likely outweigh any possible risk to the mother or the newborn. Brown and colleagues reported their findings online. May 8th, 2013 in the Journal of the American Medical Association Psychiatry

Speaker 2: [inaudible]. The music heard during the show is written and produced by Alex Simon. [00:29:30] Thank you for listening to spectrum. Had comments about the show, please send them to us via email or email address is spectrum dot k a l [e-mail] join us in two weeks at this same time.

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