The microbiome meta-analysis is published, Part 1: personal reflections

5 minute read


In all the excitement, I forgot to post about my microbiome meta-analysis getting published!

You can read the paper at Nature Communications (for free because open science is the way it should be!) I also wrote a blog post for Nature Microbiology’s Community Forum “Behind the paper” series.

Writing the “Behind the paper” post was really fun and helpful - it helped me think about how to communicate my motivation and findings to a broader audience, and was also really cathartic. For example, I got to mention some things that I believe to be true but which aren’t supported by the data we currently have and so couldn’t go in the paper. I also got to talk a little a bit about how hard it was to collect all the data - which feels really good because it can sometimes seem like collecting the data shouldn’t be the hard part, you know? (Obviously any data scientist and computational biologist will tell you how hard it is… It just doesn’t feel like a glamorous problem to have, unlike some hard scientific or statistical question or something.) And I got to step up on a small little soapbox and give a bit of editorialized perspective on doing reproducible science.

That said, there were still some things that were too personal or off-topic to include in the “official” blog post, which is what this personal blog is for! This post is mostly me being giddy and sharing my personal reactions to seeing this project come to fruition. I’ll write another post with some more thoughts on what I learned about data and doing reproducible science.

Personal reactions

The first thing that isn’t fully reflected in the blog post is how proud I am of this work. To be honest, I didn’t expect to ever publish in a journal like Nature Communications at any point in my PhD. But even with silly impact factors aside, I really feel like I contributed to the findings of this paper and that feels really good. The interpretation of the mostly-red vs. mostly-blue heatmaps is something I brought to Eric, and which he was super excited about. When I began this work, it seemed like a low-hanging fruit that anyone with enough persistence could do, but which didn’t really require that much “intelligence”. I’m a very stubborn person, so there’s no doubt that I was capable of slogging through the data collection and processing. But there’s always that doubt about the intelligence part… Not with this paper though. In no part of this do I feel like an imposter - neither with respect to the paper itself (“it’s not important enough to be in a journal like Nature Communications”) or with my contribution to it (“I’m a phony anyone could have done this”). No - this work is important, it represents a huge undertaking, I contributed meaningfully to the scientific takeaways, and it would have been a different (and likely less good) paper if I hadn’t been involved.

On a related note, I actually got my first dose of #validation when I finally got around to reading the paper that coined the term meta-analysis:

The best minds are needed to integrate the staggering number of individual studies… the integration of research findings is a scholarly undertaking requiring costly literature searches, extensive data analyses, and time to reflect and write.

Yes! This kind of work is hard and takes skill and should be respected! Let that be a lesson to us all that we should read foundational statistical papers more often, especially when our work is based on them! :P

The other fun and unexpected thing has been watching the responses to the paper on Twitter. It’s been retweeted and liked a lot - Rafalab friends even suggested I calculate my Kardashian index  (it’s 3.7). Twitter fame! Jokes aside, it’s been refreshing to see that people are actually excited about this work. To be honest, I think a lot of the excitement isn’t as much about the specific findings as it is a relief that finally someone did it (and that it didn’t have to be them!) It was also really nice to see the people who retweeted our finding that lots of bacteria respond non-specifically to disease in solidarity. Like “finally, someone showed this thing that is obviously true but people keep ignoring and instead publishing over-hyped papers. Amen.”

It was also really exciting to be highlighted as a Woman in STEM Doing Cool Stuff by an Important Woman who I have never met! I put the tweet in my happy folder, and will be revisiting it anytime I need a reminder that there exist supportive and uplifting communities on the internet and in STEM!

And a group in Canada read my paper for a journal club and posted a really great analysis of it with some questions that we were able to answer (the internet is great). I’ve reached journal club status! Wow!!

Okay, that’s enough giddyness for now. Read Part 2 for some more technical reflections…