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Microbial Diversity Course Alumni 2013- 2019 Testimonial of Impact of techniques, skills, mini project research, and professional development networking (Please note this questionnaire was recently deployed and still receiving responses).

Alumni / Questions Please share any examples of how your mentored research experience (i.e., the miniprojects) or any other techniques you learned in the course impacted your ongoing research while back at home, impacted the scientific questions you now pursue, or became a part of research labs you have gone on to launch? Are there any examples where the course impacted your professional development (publications, introduced you to a scientist you went on to work for, made a connection that helped advance your career, etc)?
Lynn Kee, Assistant Professor of Biology, Stetson University MicDiv has been a great opportunity for me to learn microbial and genomics techniques, expanding my toolbox from my graduate training in molecular and cell biology. I had the opportunity to attend as a student in the summer prior to a tenure-track faculty position at a PUI, and have returned two times during the summer in subsequent years as a Whitman fellow to continue working on my mini project. I’ve been fortunate to be housed in the MicDiv space in those two summers, to continue learning from the expertise of instructors from the course and utilizing the resources that the course provides. Two publications in Microbial Resource Announcement of microbes isolated from the course have contributed to my tenure portfolio. The knowledge and skills I have gained have helped me tremendously with my teaching of undergraduates and scholarship.
Alex Villarreal (2019) Ph. D candidate University of Minnesota-Twin Cities Medical School My mentorship and mini project taught me many skills that I still use in the lab today. A specific example is that I became very familiar with Fluorescent In-Situ Hybridization (FISH) as part of my mini project. When I returned to my home lab, I was able to volunteer to complete FISH on tissue samples for an Achromobacter mouse model project. I was the only one in the lab that was familiar with the technique, I was able to complete the protocols well, and my contributions are leading to my authorship on an upcoming publication. The microbial diversity course profoundly impacted my professional development. It got me excited about science again and helped me solidify the decision to see my graduate program to the end. The course also led to a second author publication from the techniques I learned, as well as a first author genome announcement from the data I collected during the course. Additionally, my professional and social network of scientists has greatly expanded. I have no doubt that this will be beneficial to me in the future.
Guillaume Urtecho (2018) Postdoctoral Researcher Columbia University As a synthetic biologist by training, the course allowed me to transition to a postdoctoral career studying microbial ecology in the mammalian gastrointestinal tract. Several years later, I am still using the experimental and computational methods taught during the course in my research. Furthermore, the concepts and questions I learned during this course have been a guiding light as I formulate my own research plans in preparation for my future career goals. In addition, the course directors allowed me to continue developing my miniproject after the conclusion of the course. In collaboration with other affiliates of the Microbial Diversity course, we produced a publication describing a new species of bacteriophage and its molecular relationship with its bacterial host, Phaeobacter inhibens (10.1128/ mSphere.00898-20).
Indu Sharma (2017). Assistant Professor Department of Biological Science Hampton University I was able to develop a course in Microbial Ecology and have been successfully teaching this course for the past 3 years. I was able to network and collaborate with Dr. Mark Saito, WHOI, whom I met during the course. He is also a collaborator in of the proposals submitted to NSF with anticipated funding in the fall of 2021. I connected with Dr. Kyle Costa (was one of the TIA for the course) and visited University of Minnesota for a diversity conference. Informal discussions with Kyle helped me to develop extended Curriculum - based Undergraduate Research Experience.
  The techniques learned though the course allowed me establish a vibrant research program at my home institution. We successfully cultured Cyclobacterium marinum from near benthic water, sequenced genome, and currently studying ecophysiology. I was able to apply and receive the E.E. Just fellowship at the MBL summer of 2021. I will bring two students of color to MBL and engage them in cutting edge research.
Michael J. Braus (2016) Postdoctoral Scholar Idaho State University I wrote another paper measuring the relationship of bacterial communities and soil pH (exploring this property as hydrogen activity) across Wisconsin. This should be published in Soil Biology and Biochemistry in a couple weeks. This work, largely stemming from my training, conversations, and experiences at MBL in the summer of 2016, helped me land my current position at Idaho State University, working on a $6 million NSF project investigating the microbiology of intermittent streams across the West and Southwest USA. I recently published a paper in Journal of Microbiology and Biology Education with an improved diffusion microchamber device (aka "ichip") for cultivating soil microorganisms, intended for research laboratories and microbiology classrooms.
Student Alumni Microbial Diversity Course 2017 By training, I am a structural biologist. My experience with the MD course allowed me to pursue a postdoc where I focused on microbial physiology of mycobacterial secretion machines. Based on what I learned about the environment of bacteria I was able to uncover new ways of asking questions with the secretion system, ESX-1 in Mycobacterium smegmatis, and this has been my main postdoctoral research for the past 4 years. I have found my experience definitely opened doors, and laid out common ground with many scientists across a variety of fields.
Emily Fogarty (2019) UChicago I am continuing (slowly!) to analyze the data that I collected during the course, and I'm hoping it may eventually turn into a small publication. I just had a postdoc interview with a speaker from the course.
Elizabeth Archie (2019)Associate Professor Behavioral ecology and disease ecology, University of Notre Dame In my case, the skills I learned led to a new R01 award to my lab to understand patterns of functional aging in primate gut microbiomes. Invited to guest speak at Dartmouth School of Medicine through George O’Toole 2021/2022.
Lev Tsypin (2017) Phd Candidate in the Newman lab at Caltech. NSF Graduate Research Fellow In brief, I'm currently a PhD student, and my dissertation is directly based on a miniproject from the course. My time at the MBL, and the support that I and my colleagues received for the work we pursued there, has directly led to one publication already (and another under review) and lifelong connections that I'll appreciate wherever my career takes me. I hope to return to the MBL someday to help teach the course myself.
Emily Cardareli (2013) Ph.D candidate in Francis Lab, Stanford University My mentored research experience while at the MBL exposed me to some of the pure wonders of microbial ecology and taught me how to identify microbial diversity in the field. This course forged my love for microbial ecology and developed relationships with my colleagues that almost 10 years later I still treasure. The resources both financial and advisorial and freedom from my course directors lead me to complete a mini-project that changed the course of my PhD from studying denitrification in estuaries to studying AOA in alluvial subsurface environments. Microbial Diversity allowed me to literally have dinner with legends who pioneered fields archaeal fields of study [Rolf Thauer] and share small talk with the discoverer of quorum sensing [Woody Hastings]. It also connected me with outstanding scientists from around the world and equipped me with the fundamentals of Microbial Ecology. I learned from the course instructors and TAs but also from the other tremendous course participants. I cannot underscore how necessary, fundamental, and impactful this course was in my education and career. The relationships and connections I built almost a decade ago, continue to open doors to learning new techniques [ex. BONCAT FISH] from other course members and to seminar speaking engagement invitations [@ Caltech].
Student Alumni Microbial Diversity Course 2013 The insights and techniques that I learned during the course had a big impact on how I view and study microbes. My background is in bacterial pathogenesis, and this course helped me put in perspective my own field. Outlooks and skills learned from the course allowed me to develop an ecological approach to natural product antimicrobial discovery and molecular biochemistry, that is based on interspecies interactions.  
Analissa Sarno (MD-2014) Arizona State University The mini project was really impactful for me because it led to me presenting the work from the project at the American Society for Microbiology Conference in New Orleans, 2015. Many of my peers from the course were co authors so that was great too. Here is the info from the poster. A. F. Sarno, B.R.K. Roller, A. Bose, S. Bhatnagar, S.C. Dawson, J. Korlach, M. Boitano, D.K. Newman, J.R. Leadbetter, Poster Presentation. The Isolation, Sequencing And Transposon Mutagenesis of a Newly Isolated Janthinobacterium sp. from Woods Hole, MA during the MBL Microbial Diversity Summer Course 2014; American Society for Microbiology General Meeting 2015.
Student Alumni Microbial Diversity Course 2019 The course served greatly to expose me to different culture and sequencing techniques available that end up helping me to optimize several procedures for my thesis projects experimental design, including collection and isolation of microorganisms associated techniques for microbiome studies. Additionally, the viral enrichment lessons provided me new ideas to study the role of the microbiota in my model organism. Meeting many scientists from around the world encouraged me to think about moving to study in other countries that I never thought about. One of my classmates is working in a lab where they are currently studying one of the topics I’m most passionate about and I’m looking to apply there for postdoctoral opportunities. Nevertheless, I am looking forward to collaborating in the future with the Microbial Diversity course, as well as with the Woods Hole Marine Biology Labs, bringing my research work and expertise back.
Student Alumni Microbial Diversity Course 2017 It's my honor to be a student of MD course 2017. Attending the course is a good experience and memory for my career and life. From the course, I learned a lot of techniques (i.e. cultivation, PCR, sequencing), especially the idea of miniprojects. Later, I combined what I learned with my scientific research direction, and carried on the study on the diversity and functions of petroleum reservoir microorganisms with some publications. I really enjoyed and benefited a lot from the course as much as I have.
Rebecca L Mickol Ph.D. (2016) ASEE Postdoctoral Fellow Center for BioMolecular Science and Engineering I was introduced to metagenomics at MBL, and I was able to change research paths in my subsequent postdoc position having been introduced to the topic previously. As part of the course, I became friends with Dr. C. Titus Brown, who was also taking the course at the time. He and his TAs, (Harriet Brown and Lisa Johnson) who came to assist with portions of the course, helped me develop a project sequencing a unique organism that I isolated from the river/ocean interface at Trunk River. I was also awarded a post-course research grant to travel to UC Davis to spend a week with Titus to analyze the sequencing data. This resulted in a publication in Microbiology Resource Announcements, titled, "Draft Genome Sequence of the Free-Living, Iridescent Bacterium Tenacibaculum mesophilum Strain ECR." Further, as I was working with Titus, I graduated with my PhD and was seeking a postdoctoral position. Titus put me in touch with Jeff Gralnick, who didn't have an open position at the time, but who put me in touch with Sarah Glaven at the Naval Research Laboratory. I then went on to conduct a 3-year postdoc with Dr. Glaven on metagenomics and metatranscriptomics, to which I was first exposed at the MBL Microbial Diversity course. I have now moved into a temporary Federal employee position in the Glaven lab at NRL.
Pedro Junger, (MD-2019) PhD student in Ecology and Natural Resources Laboratory of Microbial Processes and Biodiversity (LMPB), Universidade Federal de São Carlos (UFSCar) The Microbial Diversity Course has certainly been a key step for my career as a Microbial Ecologist. The excellence of the lectures, workshops and laboratory facilities were beyond my expectations. I have extended my experience with molecular methods, which I am using extensively in my PhD project. I have also been trained to use state-of-the-art microscopy to record amazing images, which I have used in my mini-project. This has made me realized the great importance of such resources in microbiology research – which is not always taken into account. Moreover, I had the opportunity to improve my skills using bioinformatics, particularly to analyze (meta)genomics data. These skills have been key to the development of my thesis (publications in preparation). I have been able to conduct my project in the Sippewisett Salt Marsh, which is a new type of ecosystem for me since it is not common in my home country (Brazil). The Microbial Diversity Course also provided a friendly atmosphere to build longstanding networks with both faculties and students from all around world. We came up with some ideas of cooperation to continue some of the work we started during the course, which we intend to develop over the next years (but interrupted due to the covid-19). I have no doubts that the Microbial Diversity Course has been a milestone in my academic career. I am extremely grateful to have been part of it and I always recommend it to my colleagues.
Student Alumni Microbial Diversity Course 2017 The project I have worked on resulted in the isolation of a new strain of bacteria able to oxidize phenazines. My initial work was continued by Lev Tsyipin at Dianne Newman's lab, and was recently published. The project helped me gain valuable experience in anaerobic cultivation of bacteria, experience which I used when consulting in various ongoing projects in my lab. The connections I have gained in the course were super helpful for my career. I still keep in touch with some of my peers, and that has opened up many doors for me in the American academia. There were some scientific ideas which I learned about during the course that led me to come up with research proposals that won awards in the institute.
Aspen Reese, (MD-2015) Assistant Professor, Section of Ecology, Behavior and Evolution, University of California San Diego In the microbial diversity course, I was introduced to and gain expertise in new technical skills (microelectrode use and FISH) which I went on to use in my dissertation research. The FISH I knew would be helpful, and so I picked a miniproject that would allow me to practice it, but the microelectrodes were not something I had considered before. Using microelectrodes ended up being instrumental in a project that we were otherwise stuck on. We will continue to use these techniques and consider similar questions about how the environment shapes microbial communities in my lab at UCSD. Methods I learned at MBL Microbial Diversity course were used in two of my dissertation chapters and the subsequent publications (Reese et al. 2018 eLife (PMID 29916366) and Reese et al. 2018 Nature Microbiology (PMID 30374168)). I cannot quantify it as explicitly, but I also believe connections I made at MBL have helped advance my career including building connections with collaborators and colleagues at my new institution.
Lot van der Graaf,(MD-2019), Masters of Science, Department of Agrotechnology and food services, Microbiology, Wageningen University and Research By exposing us to many different techniques in a short period, the Microbial Diversity Summer School helped me approach my own research with more 'daring' and creativity. Specifically, using different microscopy techniques (brightfield, fluorescence, SEM, TEM) translates well to my PhD thesis work. Furthermore, the workshops on bioinformatics analyses gave me tools and protocols I have been able to apply on multiple occasions in my own research. I would also like to mention that overall, the tight link made between the laboratory practicals and our immediate surroundings (many sampling trips to the beach and the salt marshes) really rekindled my fascination with the bigger picture in which my research fits. This is sometimes easily forgotten when spending most of your time in the lab, on a small taxonomic/ metabolic group of microorganisms. I feel enormously privileged to have been a part of this course. I do not have measurable output of the summer school, in terms of publications, but I am 100% convinced that the fellow students I met in the course, as well as the lecturers and teaching staff are an invaluable network that I can contact in the future. Furthermore, the enthusiasm and dedication with which the teaching staff and lecturers ran the course provided wonderful role models of how to conduct myself in the future, if I am ever in such a position.
Rachel Hestrin, (MD 2014) Postdoctoral Researcher,Nuclear and Chemical Science Division, Cornell University - Will be starting a new faculty position at UMass Amherst in 2022 The 2014 Microbial Diversity course was my first introduction to many of the fundamental approaches that I use in my research today culturing, sequencing, and imaging organisms—in order to understand how plants and microbes interact with each other and their environment. The course (thanks to the intellectual curiosity, generosity, and expertise of the instructors, TAs, and my fellow classmates!) helped me build the foundation of knowledge and technical skill necessary to pursue the research questions that I am interested in. I look forward to continuing to apply these to my work at UMass-Amherst, where I will be starting a faculty position in 2022.
Danielle E. Campbell, (2018), Postdoctoral Researcher Baldridge Lab, Washington University, St. Louis Microbial Diversity overall made me a much more confident and capable microbiologist, even as someone from an established microbiology PhD program and who has taught microbiology labs to undergraduates for several semesters. In particular, the course introduced me to the use of flow cytometry and cell sorting on complex microbial samples. When I later was searching for a lab to do my postdoctoral training, I happened upon one that was exploring this technique. I have since joined that lab as a postdoc and am now refining flow cytometric approaches to study bacteria-virus and human cell-virus interactions. Without the Microbial Diversity course, this would not have been an avenue of research of that would pique my interest, and I am happy to now be a on this new innovative path. I was fortunate to be invited back to the Microbial Diversity course the year after I was a student as a research facilitator. This led to me being involved in the completion of my former course mate’s project, and resulted in a publication (Urtecho, et al. 2020, mSystems). As a research facilitator, I personally coordinated, planned, and piloted a student-led project studying the eukaryotic algae Chlorella and its viruses. Becoming a research facilitator with Microbial Diversity has expanded my view of microbiology, allowed me to be more innovative and creative in the research I pursue, and helped me to be a more capable leader in guiding rigorous research. In my lab as a first-year postdoc, my PI asked me to lead a small group of researchers (two graduate students, one research fellow, and myself) using a combination of techniques to understand phage-host interactions in the human gut. Because of my experiences with Microbial Diversity, I feel well-equipped to take charge of such a large research project and feel these both will be invaluable experiences as I move on to applying for faculty positions in the future.
Achala Chittor(MD 2017). Molecular biologist, Ph.D., IMolecular and Cellular Biology Department in the lab of Dr. Karine Gibbs, Harvard University. As part of my PhD, I led a collaboration project with Dr. Colleen Cavanaugh to whole genome sequence bacterial isolates and also phenotypically and experimentally characterize bacterial physiology and behavior. Coming from a more molecular/cellular background, the Microbial Diversity course was the first time I was really introduced to the broad swath of tools available for comparative genomics and metagenomics. Titus Brown, especially, was an incredibly patient and insightful instructor for this part of the course. I felt much more confident in my ability to use these tools and think about genomics. I think this is why I was able to not only work on this interdisciplinary project with Dr. Cavanaugh's group, but I took a leadership role on the research and a manuscript in preparation.
Student Alumni Microbial Diversity 2018 Prior to the Microbial Diversity course, I considered myself a chemical oceanographer with interest, but lack of skill, in microbiology. The techniques I learned at MBL and through my miniproject have been integral to developing my skills and confidence as a microbiologist and in facilitating collaborations with biological oceanographers. I am currently applying to postdoctoral fellowships and each proposal entails techniques I learned in the Microbial Diversity Course, including viral, bacterial, and eukaryotic culturing methods, amplicon and RNA sequencing, and microscopy. I cannot emphasize enough the positive and transformative impact that the microbial diversity course has had on my career and in developing my curiosity and knowledge of microbial systems. The rigorous and thorough nature of the microbial diversity course at MBL is well-known, thus my completion of the course opened the door for my discussions with marine microbiologists including Kay Bidle, Jeff Bowman, and Liz Harvey. Thus, the microbial diversity course has unequivocally impacted my career as I am bridging my research across the fields of chemical and biological oceanography.