Learning about the Human Microbiome

The following was written by Nur Majida Shahir, graduate student, Bioinformatics and Computational Biology at the University of North Carolina at Chapel Hill.

Mur Majida sitting in the lecture room

Nur Majida Shahir at the Microbiome workshop at SAMSI.

This past month, I had the opportunity to attend a workshop at the Statistical and Applied Mathematical Sciences Institute (SAMSI) on the human microbiome. While I was only able to attend the first day, the information and insight I gained over the course of the day was amazingly useful.

Dr. Susan Holmes gave the first talk of the morning session on Multi-Table Data Analysis. While the talk itself was interesting, the thing that stood out most to me was being introduced to an R package that was created by Dr. Holmes’ group called phyloseq. Prior to this workshop, the only downstream analysis program I knew of was Explicet but after being exposed to the flexibility of phyloseq, I have a feeling that I may be using the latter more in my research.

two people sitting by the SAMSI sign

Bill Shannon (L), Washington U. at St. Louis, and Timothy Randolph, (R) Fred Hutchison Cancer Center

Dr. Vanni Bucci gave the second talk of the morning on predictive modeling of microbiome dynamics. In contrast to the previous talk, this was approaching the microbiome from an applied mathematics perspective with a focus on creating and using a minimal model to study microbiota dynamics in enteric infections. I found this talk particularly fascinating in part due to my background in mathematics as well as the fact that looking at the microbial community dynamics in the gut makes sense due to the transient nature of some of the flora seen in the gut.

people sitting around a table

Nur participates in her first breakout working group session.

After the morning sessions and lunch, I had my first experience with a working group breakout meeting at this workshop. On one hand, it was a good experience to hear what people were thinking with regards to various datasets and the analysis of said dataset. There were many concepts and approaches that were thrown around that I honestly hadn’t thought of. On the other hand, I found it disorienting because I had a very superficial idea of what they were discussing. It would have been more beneficial if I had access to the data or at least the papers to which they were referencing prior to the working group breakout meeting.

One of the things that I enjoyed about this workshop was the varied backgrounds of the presenters. While the majority of the presentations were focused on statistics approaches and problems regarding the analysis of the microbiome, others approached the microbiome from a much more theoretical perspective as seen in Dr. Giseon Heo’s talk, which if I recall correctly, approached it from the perspective of knot theory.

four people in front of two posters

People discussing their work at the poster session.

The poster session was held at the end of the day. Reflective of the talks, the poster session content was fairly diverse content-wise as well with posters ranging from the “standard data analysis + results + future directions” to more methodology oriented approaches regarding how to approach the data. I personally enjoy poster sessions because they allow me to approach the material at my own pace and to interact with the presenter in a more direct manner.

All in all, I left the workshop very content. I’ve attended a few conferences where halfway through I’m utterly exhausted and dreading the next 4 hours. At this workshop, I felt that my time there was both well spent and informative.

Leading a SAMSI Working Group: One Size Does Not Fit All

The following was written by Paul Brooks, Associate Professor, Department of Statistical Sciences and Operations Research, at Virginia Commonwealth University.

I came to SAMSI to get “real” statisticians to look at data that my microbiologist/clinical colleagues were generating to discover new patterns related to human health. Whenever I work with colleagues in the biomedical arena and they learn that I am a quantitative person, they automatically assume that I am a statistician and can help them with all of their statistical needs. They lump all of us applied math people together (I was happy to return the favor in my previous sentence). The experience depicted in this video rings all too true:

I watched this with some of my colleagues and we laughed until we cried because we have had nearly the same conversation several times over the years.

Last year, we were working on a grant proposal that asked for outreach to the community to make data available to analysts and train people on best practices. I had heard of SAMSI from a statistician in my department who had been urging us all to get involved. Then I discovered the \research program” concept that SAMSI has and further, that a theme for this year was Beyond Bioinformatics. The stars aligned. After speaking with Snehalata Huzurbazar, Deputy Director of SAMSI at the time, we agreed that I could lead a working group during the Beyond Bioinformatics program. Several other things fell into place, and I am now a visiting research fellow at SAMSI and leading two working groups.

Coming into the year, I was excited about the concept of a working group adding all kinds of new expertise to our ongoing projects. But I am a bit of an anxious person. Perhaps a nicer way to put it is, I am a planner. I like to have my stuff together well ahead of time. I met some SAMSI postdocs over the summer at a conference and asked them for advice on a successful working group. They said it takes a leader to assign tasks and hold people accountable for getting things done. Okay, I would need to learn how to do that.

When I arrived at SAMSI, I attended the opening workshop on ecological modeling and spied on them and how their working groups formed. Some of the working groups that formed there were huge! There were 35+ people in most groups, and many people were in multiple groups. How was I going to find enough ideas for that many people to work on? One group seemed to have a pretty good approach: they first brainstormed general topics of interest, then they collected whose to form article topics, then they began to work on what their paper titles would be, and even discussed target journals. That seemed pretty good for the first two days. I would try that. But of course it didn’t go quite as planned. Around 200 people attended the Beyond Bioinformatics opening workshop, and there were about 10 working groups proposed. The working groups formed after lunch on Thursday, but many of the people left right after lunch. The initial working group meetings were not as big as anticipated, and many of the working groups met in the same room.

working group meeting

MCDC group meeting during the Beyond Bioinformatics workshop.

My proposed working group, MCDC (Microbiome Community Dynamics and Complexity), was sort of split into two and one was merged with another working group and would be complementary to one or two others. Plans went out the window. One of the working groups started with about 5-6 people on site and about 25 people attending online via WebEx. For the first few meetings, we agreed on papers to read, and someone would lead a discussion of the analysis methods used. For a while, it seemed like only 2-3 of the 20-30 in attendance participated in the discussions. Some of these discussions were somewhat heated because of disagreements about appropriate modeling strategies. Perhaps people new to the held and graduate students/postdocs did not feel that they could weigh in on the issues yet. But they kept coming back.

The meetings reminded me of my early experiences with microbiome conferences. When I first started attending microbiome conferences, there was a group of postdocs who would microblog every slide from every presentation. They would describe what the speaker was presenting, then offer their opinion. They often disagreed with the presenter and with each other. Observing these discussions was incredibly helpful to me to understand a new field and to understand what the big questions were. Perhaps that’s the kind of service/entertainment we were providing with our working group meetings.

Fast forward to today. We still have 15-25 people at each meeting. Many more people are actively participating in the discussions than when we started. We have some subgroups who are working on different parts of a paper that we hope to write together. And we are laying the foundation for two additional papers to write together.

Each working group is a unique experience. Be flexible and know that different approaches to leading a working group can lead to fruitful collaboration.