My Microbiome Experience from Start to Results

Everyday I'm Samplin'For the past couple of years my Twitter feed, Facebook wall, and this blog have been overrun with all things microbiome; however, until a couple months ago, I had yet to contribute my own microbial ecosystem to the growing dataset. While at uBiome, I joined the movement and quantified my own microbiome with their five site kit. My experience was not completely authentic since I missed out on the excitement of receiving the sleek, black kit in the mail and I gained the excitement of processing my own samples, but I still want to share and promote some citizen science at the end.

uBiome Kit

Sleek uBiome kit

 In the beginning…

Usually your sequencing adventure begins with ordering your kit online, but I sped up the process by bringing one home with me. When I opened the kit, the instruction card greeted me and directed me to register my kit online. Easy enough. With registration complete, I was ready to get started sampling. Not as easy. To get the most accurate representation of your microbiome, sampling should be done after about eight hours without microbial ecology disruption. This includes showering, brushing your teeth, kissing, swimming in a chlorinated pool, etc.

uBiome the Whole Kit and Caboodle

The whole kit and caboodle

As my friends will attest, I would gladly use sampling as an excuse to delay a shower, but I sleep less than eight hours a night and leave no extra time in my morning routine, so avoiding everything for eight hours is tough. I decided to stay up a little later than usual and do everything at once; except for the fecal sample, that would come in its own time (though we runners do have our tricks).

VirulentB skin sampling for uBiome

Let the swabbing begin!

The instructions on how to sample are both on the card and on-line but I found the Vimeo video demonstrating skin sampling far more fun and informative. Swabbing was easy aside from the issue of working in the small spaces of the nostril and mouth (I definitely got a tap of skin and teeth in the samples, respectively). The extra swab was appreciated to take a second tooth-biome free mouth sample.

Creepy nostril sampling

Oh yeah, this is creepy

When I ask my friends about their experience with swabbing, they unanimously complain about the nostril. Yeah, swabbing inside your nose is creepy, in a “send chills up your spin way,” but it isn’t painful. It just feels wrong.

No one ever mentions the fecal sample. It reflects our actual comfort with poop. If we are as bothered by poop as we assume we all are, diapers would never get changed and there wouldn’t be 14 “poop tracker” apps in the iTunes app store.

Usually the samples would be mailed back in the padded envelope provided, but I skipped USPS and brought them right back to the uBiome lab.

In the meanwhile…

 

Once in the lab, the samples are entered into the system and the processing begins. A DNews video gives you a behind the scenes look at this part of the uBiome experience. Once again, I deviated from the typical experience, and processed my own samples.

Processing my uBiome samples

Science is happening

As your samples make their way through the sequencing pipeline, you receive encouraging email updates to track your precious microbes. Eventually, you get the email you’ve been waiting for and your data are ready.

In the end.

Upon entering the data delivery site, my suspicions were confirmed: my microbiome falls outside the norm. I have far more Firmicutes and far fewer Bacteroidetes than the average Western population (and maybe would fit in better with the Hadza). This is most likely the result of my high fiber diet of fruits and vegetables. According to the Mayo Clinic, a woman needs about 25 grams of fiber per day, but Americans average 15 grams. I average 35-40 grams per day. My Firmicutes are well fed.

In addition to comparisons to the overall data set, there are other options on the uBiome site to play with your data, as well as phyla descriptions, but what I really want to know is how to apply this information. Unfortunately, this is where I hit a wall. Much of the research linking specific bacteria to conditions, like obesity, is based on correlative data and the findings from one study to another are often contradictory.

uBiome gut sequencing results

Never one for “average”

The young field of microbiomics isn’t ready to prescribe behaviors or lifestyle changes based on sequencing results now, but it will be. We can all contribute to this progress by acting as citizen scientists. If you start a new probiotic, decide to go Paleo, or start Couch to 5K, take the opportunity to advance microbiomics and sequence yourself before and after. uBiome is not the only option for sequencing your microbiome, but I would suggest that you pick one service and stick with it to ensure all results are comparable. Sequencing results can vary based on the methods used to generate the data. (Yes, this is problematic and groups are working to create a solution.)

In the meantime, I’ll stick with my fiber and exercise and quietly keep quantifying myself until science catches up and tells me how to live better through bacteria.

Microbiomics for Everyone from “Gut Check: Exploring your Microbiome”

Gut microbiome from Scientific American

Scientific American image

For all the microbiome scientists, aficionados, and dabblers out there, I would highly recommend “Gut Check: Exploring your Microbiome” on Coursera. Developed and presented by American Gut researchers Dr Rob Knight, Dr Jessica Metcalf, and Dr Katherine Amato, the six module course opens with, “What are microbes?” and continues through the development of and applications of microbiomics. The course covers all the usual uses of microbiome data for health, such as autoimmune disease and obesity research, but also stretches into less widely known applications like forensics. The liberal incorporation of interviews with field experts gives the course vitality and lots of directions for “independent study”. (Speaking of independent study, I would suggest Jeff Leach’s engaging and blunt blog posts for his The Human Food Project here.)

“Gut Check” is perhaps more academic than necessary in presentation style, a little more animation from the presenters would have been appreciated, and many of the slide deck snippets from the interviewees are above the level of a general audience; but the beauty of an on-line course is the ability to pause, fast forward, and skip at will.

The data analysis-heavy nature of several of the modules may surprise some students. Microbiomics is not just cool bugs but is actually a big data field. We must make sense of the deluge of data pouring out of the sequencers to unlock the health and wellness potential of our bacterial ecology. The sections are presented in simple terms with plenty of visual aids (and generous use of Giant Microbes) so invest the time in these modules.

Michael Pollan's American Gut DataWeek 6 focuses on the American Gut project and walks you through the process of participating, which is much more fun than an instruction sheet. They also guide you through interpreting the data you receive, including how to compare yourself to Michael Pollan. I don’t know if American Gut is suggesting he is a super-human prototype, but it is a fabulous idea that everyone gets to see how he or she stacks up against the famously omnivorous author.

If after joining the American Gut Project and acing Gut Check you still want more microbiome, check out Bik’s Picks: MicrobiomeDigest for a clearinghouse of microbiome news and research. TED has several excellent talks such as those from Jonathan Eisen, Joe DiRisi (infectious disease detection), Jessica Green, Jeroen Raes, and Rick Stevens.

There is a glut of information out there so happy hunting and remember to feed your gut-brain axis frequently.
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Five Networking Tips for Graduate Students and Postdocs

Metazoan signaling network

These are not the only networks (Korcsmaros, et al., PLoS ONE, 2011)

As PhDs prepare to leave the hallowed halls of academia, most are immediately confronted with the glaring fact that they have absolutely no idea how to find a job. We were told it’s all about the network, but we didn’t need to network, we were busy for the last five to ten years building all these amazing skills and now industry is going to fall over itself to recruit us, right? Perhaps, but it will be a slow fall that takes many months and a lot of pushing.

There are clear reasons for this lag that may not be obvious to the academic. First, most of your skills were developed using the cheapest, most MacGyver-ed method possible that your PI perfected 30 years ago. These methods are probably carried out on the the same equipment he used, too. This is because he refuses to admit someone developed something better in the intervening decades and he has one R01 for 15 trainees. Second, you chose your project, (insert crazy-specific thesis title that only you, your PI, and maybe one other person cares about), based on your passions and not on developing the skills that industry needs.

My thesis on IMC proteins in Toxoplasma gondii

A little casual reading…

There was no reason to consider industry, though, because you were going to be a PI, just like the 60 other students who started grad school with you and the thousands across the globe. Third, you know no one outside of academia and have no “real world” experience (pre-grad school counts very little). Even those PhDs lucky enough (or prescient enough) to work with current generation equipment and the most up-to-date methods in the sexiest fields may have trouble overcoming the lack of experience. Finally, get ready to fight the stereotype. Employers have assumptions about the PhD personality and the ability of PhDs to assimilate into cooperate culture.

PhDs increase while the number of academic positions stay the same

There are more PhDs for a stagnant number of academic positions (Schillebeeckx , et al., Nature Biotechnology, 2013)

Based on my observations, postdocs are averaging a year or more to find their first industry position. Under- or unemployment for more than a year is common. Here in the San Francisco area, many PhDs go to startups that are willing to take a risk and then find themselves jobless again within a year or two.

However, this is a hopefully and encouraging blog post! There are simple things graduate students and postdocs can do to expedite the future job search, protect against fluctuations in industry, and show themselves to be more than the stereotype. The most important is networking. It takes time, but it’s an investment that will pay off.

Increasing number of life science PhDs unemployed

The red line is on the rise. (Jordan Weissmann, The Atlantic, 2013)

Below are my top five networking tips, from one PhD to another.

  1. Attend networking events outside your comfort zone and network

Conferences and meeting in your field of expertise are important, but will not suffice. You must leave your comfort zone and diversify your connections. Start by taking a tour of events, attending several types of events hosted by different groups. Try happy hours, talks, and short courses by societies, meetups, and companies. Pick the ones that you enjoy and are most productive for your goals and then become a regular. People should start to recognize you.

In general, the events you pay for are higher quality and will bring in more people from industry. Free events draw people on a budget, i.e. graduate students, postdocs, and the unemployed. You can make great connections at these events but remember, investing in your network is investing in your future so pony up the registration fee.

At first it is ok to just show up. This is a tough first step for most people. After a few, though, don’t just grab a drink and try to blend into the wall. People are all at these events to mingle so pick a group and introduce yourself.

If this is particularly difficult, considering volunteering with a professional organization. It will provide a purpose for your interactions, will not feel like shallow small talk, and will give other members a sense of what you are like to work with, which is important for future recommendations and introductions.

  1. Talk to everyone

When out and about, make an effort to strike up conversations. You never know who is on the yoga mat next to you or in line behind you at the grocery store. This has the added benefit of making you more open and your conversational manner more natural at professional events.

For the same reasons, accept all networking meetings that your schedule and energy will allow. Prepare for meetings and come with an agenda. Be ready with enough information to engage in deeper conversations and to make efficient use of everyone’s time. At the end, “get to the next person” by asking for specific introductions to expand your network.

  1. Don’t over do it

You are now attending events and meeting with contacts and it is very easy to get overwhelmed. When I started building my network I was attending events and taking meetings everyday and sometimes twice a day. The burnout was quick and defeating. I learned my magic number is three career-building activities per week. It forces me to prioritize and allows me take full advantage of the most productive activities.

  1. Build a brand 

In order to increase networking efficiency, you need something accessible where contacts can get a sense of who you are before they meet you. It should also allow potential connections to evaluate if you are worth their time (it’s harsh but true). It’s an added bonus if this presence brings people to you.

LinkedIn is the most common first step for professional brand building, but it’s more stagnant and dry than Twitter and Facebook (see Belle Beth Cooper’s Fast Company article here).

Social media use statistics

The majority of LinkedIn users are inactive (Belle Beth Cooper, Fast Company, 2013)

To build a brand, start tweeting and making public Facebook posts based on your passions. Focus on the field you plan to build your career in and maybe a hobby or two. For example, I’m a molecular biologist interested in infectious disease, microbiomics, and next-generation sequencing, so my tweets and public posts are focused on industry news, research findings, and media related to these areas. To prove I’m still human, I toss in yoga and fitness tidbits, as well.

Blogs are an excellent tool, too. They come in all flavors and can be as focused as you desire. I use this blog to record my professional growth and share my current professional interests and thoughts. However, do keep personal and professional blogs separate. Updates on your toddler’s potty training show your humanity but do little to promote future employment.

  1. Follow up

This is the most important tip: follow up on every discussion. Your network will cease to grow if the people that make up your nodes do not feel appreciated or respected. After every event, reach out to the people you met; LinkedIn connections are the easiest. Try to include some reference to your discussion to show you were invested and not just collecting business cards.

After meetings send thoughtful thank you’s. Again, include something that shows you were engaged and internalized the conversation. Provide any additional information discussed during the meeting and ask for introductions to the next person or people.

Networking is a skill and it takes practice to get comfortable, efficient, and effective. Even if you stay in academia, with academic-industry collaborations becoming the standard a diverse network is priceless. Furthermore, the interpersonal skills you exercise through networking will translate into your personal and everyday life.

It’s a win-win investment so get out there and meet people.

Why I Love Contract Science Writing, an Evaluation

Science Writing for Everyone

As an engineering consultant, I knew I was busy, solving problems, slogging through tedious environmental regulations (CFR Title 40 still gives me the willies), and enduring round after excruciating round of report editing; but I never considered why I was doing these things or what skills I was gaining. I did not appreciate the value of my circumstances. Years later it become obvious that what I was really doing as a consultant was developing amazing technical writing skills; acquiring a keen attention detail; learning to manage projects, teams, and clients; learning how to sell products; and, this is the big one, learning how to take relentless critical feedback and integrate it without any sense of personal attack. If I had realized this at the time, how much more could I have grown? How many opportunities did I waste?

I like to think I learn from my mistakes, and since I prize the efficient use of time, it is now standard practice to reflect on any project and evaluate: 1) what am I learning, 2) what skills am I developing, and 3) how can I gain as much transferable experience as possible?

Over the last two years, I have taken on several technical writing contract projects and love them. Below are my reflections on the “why” and the general criteria they meet:

1) Exercise an existing skill: technical writing skill

Neglected skills atrophy the same as unused muscles, regardless of the number of years invested in developing them. I spent five years learning Italian and how much can I speak now?- nada..or is it niente? Contract writing for multiple companies provides excellent skill reinforcement since each project is different. It hinders recycling a formula from project to project and requires active thought and growth.

2) Expand an existing skill: scientific communication to a broad audience

Scientists talk a great deal about the importance of communicating science to the general population, but most of us never do. A poster or a talk at a general interest conference doesn’t count. The closest I had come was writing due diligence reports to business people with Oxbridge Biotech Roundtable (OBR).

This is not Science Writing

Tucker Martin, Worchester Polytechnic Institute

When I started writing service descriptions for Science Exchange (SE) I learned what it meant to write for anyone. Describing “science for the people” forced me to distill concepts to the basics and to ask for feedback from naïve audiences. It became clear that examples of when to use a service are most important and reinforced the idea that analogy is usually the best tool for disseminating knowledge to uninformed audiences.

3) Develop new skills: learn novel techniques and fill-in knowledge gaps

Writing service descriptions and especially grants for different companies requires learning about new fields and techniques outside the narrow focus of my research. It forces me to stay up to date on current science and technology trends. Contract writing can bring to light any gaps in knowledge, as well. I have had to fill-in plenty of holes in my areas of expertise.

4) Lead to additional opportunities: other contract projects

Learning the theory behind new fields helps me find opportunities to gain technical experience in areas outside my existing expertise like next-generation sequencing. It also provides conversational knowledge for conferences and networking events. Through engaging people in deeper conversations other opportunities arise that allow me to stay on that exciting slope of the learning curve and keep cycling through the list above.

Deer Mountain: the basis of my first writing contract

My first paid writing project in 2nd grade entitled “3 miles that became 6″ tells the harrowing tale of my family’s hike on Deer Mountain. Critical acclaim has been slow in coming.

Perhaps these general criteria will provide something to mull over the next time you evaluate a project and consider stepping a little outside your comfort zone. Always keep asking, “what am I gaining and could I grow more?”

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Too hot to hold?: “Hot Trends in Life Science Tools” event reflects competition in biotech

Biotech is on fire with new tools

The October 1, 2014 “Hot Trends in Life Science Tools” event at Bio-Rad hosted by the Women in Bio San Francisco chapter highlighted the excitement of emerging biotech resources and profiled some of the women that are pioneering these technologies. However, each of the panelists has challenging competition to consider, as the scary side of great ideas is that they rarely come from only one source. The approaches these companies are taking, or will take, to carver out their niche in the rapidly growing biotech market should provide good parables for anyone considering entering the biotech startup world.

Dr Rachel Haurwitz, President and CEO of Caribou Biosciences, was the panelist that most represented how a hot idea in biotech spreads like wildfire and how focusing on a specific application of your tool can keep you relevant.

Caribou is in the CRISPR system genome editing game. When the CRISPR system was first described in Science in 2007 it was esoteric and best left to PhD molecular biologists. However, people wanted it and the demand sparked a race to simplify the system into a tool for anyone. Today, a search on Science Exchange brings up ten providers offering CRISPR contract services. To do-it-yourself, Addgene provides extensive resources and kits are available from Clonetech, OriGene, System Biosciences, Life Technologies, and more.

As a small startup, Caribou is avoiding being engulfed by the CRISPR blaze by focusing on a narrow market in a sexy field: epigenetics. Modifying epigenetic markers adds additional complexity to genome editing that the large kit makers are not ready to address, but that academic and industrial researchers need. This niche is giving Caribou time to grow and evolve. It also may make them attractive to those big companies.

Jessica Richman, President and CEO of uBiome, may face a similar challenge. uBiome is in the hot field of microbiomics and companies are popping up all over to stake early claims. Microbiomics is so nascent that the majority of these companies are in extreme stealth-mode; however all biotech startup expositions and competitions seem to include at least one, if not several. Watch closely, the microbiomics explosion will soon provide plenty of marketing and business development lessons.

Microbiomics and Dr Natalie Wisniewski’s PROFUSA, Inc., which is focused on implantable devices for monitoring tissue oxygen levels, also brought to mind the issues with “quantified self” product competition. Quantified self is commonly associated with “wearable” devices, like FitBit, Nike Fuel, and old-fashioned pedometers, but it can encompass any type of self-monitoring. Buy-in for these products is extremely low outside of tech bubbles like San Francisco according to TechnologyAdvice but more and more continue to flood into the market. Furthermore, NBC News reports consumers bore of them quickly with 40 percent of owners abandoning the product. This does not bode well for products that rely on a consumers attention span.

As an implantable device, PROFUSA is, according to Wisniewski, “what comes after wearables.” It has a medical application, but they will still face the wearable challenge of making continuous monitoring records useful to doctors. A The Daily Beast article highlights how these devices can be valuable tools, but concedes that most doctors have no interest in the data, which can come in an indigestible deluge. Without the acceptance of the medical community, and until doctors and insurance providers start requesting this information, self-monitoring devices may struggle.

As the title “Hot Trends in Life Science Tools” suggests, biotech is full of scorching new ideas; but it never hurts to remember that to keep a company vibrant takes as much innovation as that first idea.

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The world of fecal microbiota transplants

Poop pills or bacteria pills

Not to be confused with these poop pills, FMT requires transplantation directly into the colon

This is the link to my most recent post for uBiome on fecal microbiota transplants (FMT).

A little taste:

Fecal microbiota transplant (FMT) is the therapeutic process of transplanting feces from a healthy individual to an ailing recipient. Despite the obvious “ick” factor of receiving healthy poop from your sister, husband, or friend, people suffering from debilitating Clostridium difficile bacterial infections are overlooking the ick in hopes of a C. difficile cure. Currently the only indication for which FMT is approved by the FDA is C. difficile colitis and there is contention as to the efficacy of FMT for C. difficile treatment.”

Thank you from California Academy of Sciences

Oral swabbing for uBiome by Cal Academy

Angus Chandler, Academy postdoc, and Sean Edgerton, graduate student at SFSU, demonstrate oral swabbing

Check out my blog post on the wonderful thank you letter we received at uBiome from the California Academy of Sciences.  Visit both uBiome and the Cal Academy at Bay Area Discovery Days November 1, 2014.