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URMC / Education / Graduate Education / URBest Blog / May 2015 / The Best of Both Worlds—Insights Toward Establishing an Academic Center and a Biotech Company, from

The Best of Both Worlds—Insights Toward Establishing an Academic Center and a Biotech Company, from One Perspective

Career Story Blog Post By Joseph F. Petrosino, PhD, Associate Professor of Molecular Virology and Microbiology, Director of the Alkek Center for Metagenomics and Microbiome Research at Baylor College of Medicine, and Founder and Chief Scientific Officer, Diversigen, Inc.

In anticipation of my visit to UR, I’ve been asked to share my experiences in what brought me to where I am today as a director of a strategic research center at Baylor College of Medicine and as the founder and CSO of a metagenomics sequencing and analysis company, Diversigen, Inc.

It goes without saying that my experiences at UR had a direct impact on my career path on several levels. I entered the UR in 1989 with the idea that I wanted to be a biomedical engineer.  Like many, my focus shifted over my freshman and sophomore years. For example, I quickly realized that I wasn’t keen on the computer programming elements associated with engineering at that time, and for a while I thought I was going to go to medical school and become a clinician.  It wasn’t until I took my first microbiology laboratory course that I knew I wanted to pursue microbiology as a degree. I took advantage of the “Degree with Distinction in Research” program that was available to students at the time and developed an undergraduate thesis project in virology.  The cumulative experience: taking the advanced classes required by the program, executing a research project and writing a thesis, was very valuable in preparing me for what was ahead in graduate school.  I graduated with a B.S. in Microbiology and Immunology in 1993, and I have to give a ton of thanks to Dr. Alanna Ruddell, who was my undergraduate mentor, and Dr. William Bowers, a graduate student in the Ruddell laboratory who showed me the ropes and helped me with my project. While our paths diverged as I set my sights on a Ph.D. in Microbiology and Immunology at Baylor College of Medicine (BCM), Bill and I remain friends to this day. 

As a native Rochesterian, I never thought I would wind up in Texas, but BCM seemed to be the right fit.  BCM is in the heart of the Texas Medical Center—the largest medical center in the world--and that translates to having all of the collaborative support in the latest approaches within a mile or two away. Further, I found the faculty at BCM to be genuinely engaged with the students during the interviews, and I found many of the research projects in the department I was applying to very aligned to my interests.   At BCM, I trained in the laboratory of Dr. Timothy Palzkill studying the biochemical and genetic intricacies of antibiotic resistance.  Graduate school is where you develop the tools, skills, and scientific practices that you will carry forward into the next stages of your career, regardless of the direction you follow.  This is probably true in all fields, but clearly is the paradigm in the biological and physical sciences. Your prowess at the bench, ability to organize your thoughts and experimental data, ability to write scientific manuscripts, and much more are all developed during this important period of training.  Also, important at this time is the development of real world training on how to interact with his/her peers and deal with scrutiny and criticism.  With the current limited availability of federal research funding, competition for those scarce resources is as great as it has ever been, and how one responds to peer review critiques can be the difference between success and failure. There’s a balance to being open to criticism while also being able to articulate your position, and doing it in a way that isn’t defensive…or offensive, and that balance takes a while to master.

After I received my Ph.D. in 1998, and after much deliberation as to where to go next, I took a postdoctoral research position in the genetics laboratory of Susan Rosenberg, also at BCM. I then went on to spend two more years as a research associate, and two more as a non-tenure track faculty in the Human Genome Sequencing Center (HGSC) at BCM.  As one of the sites where the human genome was sequenced, the resources and environment in the HGSC are unparalleled. This was my first exposure to “Big Science” as the HGSC is like a company operating in an academic department.  Over 200 investigators, technicians, administrators, project managers, bioinformaticians, and engineers work in the HGSC.  Together, they operate the third largest genomic sequencing pipeline in the U.S.  My experiences in this unique environment helped me formulate the plan and vision for the center for metagenomics and microbiome research.  While staying at BCM for my postdoctoral training was a decision that many felt was unwise at the time, diversity in training background is often thought to be vital, the resources and environment at the college and in the Medical Center were the perfect environment to help me get to where I wanted to go.

In the HGSC, I was able to start building a small reputation in the area of microbial genomics—studying the genetic similarities and differences between biodefense organisms of concern and then leveraging this information for experiments targeted toward the development of new diagnostics and therapeutics directed toward these pathogens.  This recognition led to me to a new position starting up my own laboratory as a tenure track faculty at BCM in the department of Molecular Virology and Microbiology, which happened to be the realigned/renamed department where I received my Ph.D.

I must say that while graduate school prepares you for the “scientific” challenges that lie ahead, in most cases, it does not prepare you for the business and managerial hurdles that one inevitably faces as the primary investigator in a research laboratory or a project director in industry.  Let’s face it, running a laboratory is much like running a small business: your success is tied to how well you publish and convey your research to others and how well you procure funding for your laboratory.  These are all forms of business communication: marketing, branding and sales.  Some may find this comparison to be a bit overstated, but there many qualities a successful business person possesses that would be/are vital for the success in a laboratory. Foundational to all other attributes is the ability to communicate one’s research to peers and, to an extent, the public.  Simplified, the need is to “sell” your research to journal editors, funding agencies and the reviewers these entities recruit.  Of course, scientific rigor and proper study design and execution are paramount to success, but if no one understands or is able to decipher your research, then it may as well have never been done.  Nowadays, there are courses and workshops that help students and faculty hone their scientific writing and presentation skills, and there are even companies that will help write/re-write your research manuscripts and presentations so they are more effectively communicated.  Institutions are now more sensitive to the training in communication that is needed, and it’s important for would-be scientists to leverage these resources whenever possible.

From a managerial perspective, no experience in graduate school can prepare you for what it’s like to run a research laboratory.  None of the seemingly simple concepts of effective communication, delegation of work, conflict resolution, etc. is taught in graduate school or postdoctoral training.  It’s learned on the fly, and those who have a natural talent in these areas have an advantage.  In my experiences, a happy, energetic laboratory is more productive over the long haul compared to an oppressed dysfunctional laboratory, and if an investigator is not able to effectively manage his/her team, problems will ensue.  In short, if you are not a people person, it would help you to become at least a little bit of a people person quickly!

Another front where we are poorly equipped when starting our own laboratory is in money management. Thankfully, in the academic world, we have administrators who help us with budget planning and forecasting.  Without this help, I’m sure I would have run out of money on a number of occasions, leaving the lab short on supplies when there was critical work to be completed.  Even with administrative support, it would have been beneficial to have had Business Accounting 101, or the like, in graduate school or as a postdoctoral researcher so that the budget side of running a lab came more naturally.

Soon after I started my laboratory, my research focus shifted toward study of the human microbiome. The National Institutes of Health was spearheading a large initiative in this area, the Human Microbiome Project (HMP), which would be largely driven through the large scale genome sequencing centers in the U.S., and BCM, specifically the HGSC, was going to play an important role in this program.  I was in the right place at the right time (another key factor in the development of a career) and was asked to help lead the BCM component of the project.  Over the next four years, I pursued leadership opportunities as they arose in the growing HMP consortium, and led and/or contributed to key projects within the overall study.  By 2010, I was a recognizable face in this exploding field.

It was at this time where I found myself at perhaps the most critical juncture for my career path. Our funding for the HMP was starting to wind down, and I very much wanted to pursue large scale studies in this field—engaging clinical and research collaborators who were interested in the microbiome’s role in their particular disease model and helping them translate their research from the bedside to the bench and back to the bedside again.  Rather than having to move elsewhere to pursue this vision, I was able to convince BCM leadership that this was an important area of research that should be invested in at the institutional level, and with their guidance and financial support we started the Center for Metagenomics and Microbiome Research (CMMR).  In 2011, we had fewer than 10 collaborative projects, and today we have over 260 with over 130 collaborators worldwide, all investigating how the human microbiome may be impacting, or be impacted by, a variety of human diseases.  The skills I acquired on the fly in communication and management were critical for our success.  I only wish I developed them a little sooner!

I realized soon after we started the CMMR that commercial applications for metagenomic studies were in high demand. And, seeing that commercial needs operate at a different scale and time frame than is typical in academia, and that commercial projects are not ideal for graduate student and postdoctoral research projects, I approached the college with the idea of commercializing our metagenomic pipelines.  Like a number of institutions, BCM has a commercialization program that includes the creation of incubator companies (PodCo’s is the local term at BCM) that leverage the academic expertise and pipelines for the purpose of commercial development when appropriate.  As a blossoming PodCo gets rolling and grows, subsequent phases of implementation hopefully will follow that include an independent bricks and mortar expansion to enable the company to stand on its own and develop as a unique entity.

It is exciting to start a company as an academic investigator.  It’s like having your research program give birth to a unique life form that you are responsible for nurturing and developing into a self-sustaining being.  Of course, as you can guess from my statements earlier, few scientists are trained to be able to handle the business side of such an endeavor.  Fortunately, the commercialization process at BCM and other institutions includes bringing in the business expertise to handle those elements of the company’s development.  In the process, I have received a lot of on the job training on how to build a business (hint: start with a business plan).  So, with these valuable resources (and the college) in place to support me, I founded Metanome in August 2013. We have since renamed the company Diversigen to reflect the importance of diversity in the human microbiome as well as in the processes used to study and analyze it. And, we are off and running.

As thrilling as it is to start a company, I would be lying if I didn’t say there were growing pains.  When I am particularly frustrated, the analogy of building a airplane as we are flying it is often invoked…this doesn’t help.  One quickly learns just how much academia and corporate needs and expectations differ.  Companies exist to make money, and as we’ve heard, time is money.  Therefore, if you are assisting a company in developing a product, and you are perceived to be not moving as fast as you could be in generating data for that project, you will hear from the contracting company.   You quickly learn where the weak points are in your processes, and if you are good, you adapt and evolve to meet the demands of the business. The side benefit is that your academic strategies are simultaneously improved as well.  Growing pains aside, if you are an adrenaline junky, you’ll appreciate the thrills of seeing your company grow-the first contract, the first invoice, the first successful study, the first repeat customer… It’s an experience relatively few get to have as an academic faculty, so I try to savor each moment I can.

While this is going on, our academic center continues to grow. Part of my vision of being the first fully translational microbiome research institute in the U.S. includes the hiring of a cadre of tenure track faculty with expertise in a variety of microbiome related fields. We were fortunate to hire three assistant professors and a full professor last year with more to hopefully follow soon.  And, we are off and running on this front too.

If it isn’t clear by the end of this narrative, and from the other entries collected here, the one important lesson in life (not just in a career) that I think everyone should keep in the back of their mind is that everyone has their own path, and no two paths are the same.  And sometimes, the path you wind up on or choose is one that is rarely followed, or even usually avoided. For example, not going to a different institution for my postdoc was something that was frowned upon by my thesis committee. One member of my committee told me that it would stunt my career and that I would likely not be competitive for postdoctoral fellowships in the years ahead (it turns out that I was awarded three). Another lesson that I found incredibly valuable is to have a vision.  A five-year plan gives you focus and direction.  There will many roads to reach or achieve that vision, but having that fixed point on which to base and justify decisions in life and/or your career is very beneficial I have found.   Finally, it’s important to embrace what comes and not try to fight the detours, pit stops, and forks in the road that appear along the way.  In the end, they help you develop and mature. You may not reach the exact destination you envisioned, but it’s likely you will be much happier and successful because of it.

Global Administrator | 5/4/2015

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