History of SPAAM

by James A. Fellows Yates

As one of the founders, I would like to give a short(ish) background of how the SPAAM community came to be. By doing so, I hope to provide some context and share the original motivation of establishing this community but also maybe provide inspiration to others in similar situations who might be interested in setting up their own similar communities.

2015-2016

The ability to study whole microbiomes has only been made possible very recently (in the last 10-20 years), and ancient microbiomes even more recently, making it a very exciting area of research to start my metagenomics career in. I began my PhD in 2015 and I was essentially the only person in our department working on ancient microbiomes - my supervisor (Tina Warinner) had not yet arrived at the MPI, Jena. When I started my PhD, there were people in the department who had experience researching ancient microbes focusing on a single-genome of well-characterised bacterial pathogens. In comparison to this, microbiome research was a whole other kettle of fish, both from the perspective of modern biology but also ancient DNA - where at the time there were a very small handful of studies on the topic - due to the sheer number of well- and uncharacterised taxa (emphasis on the latter) that must be analysed all together. Due to the daunting task ahead of me, and with limited direct support and expertise, this ended up being a rather lonely period with a lot of wild stabbing in the dark. In contrast, my colleagues working on human population genetics were working at breakneck speed (albeit in a highly competitive environment), with exciting new results being presented every month.

Fortunately, in 2016, Alexander Herbig and Johannes Krause (both then at an MPI in Jena, and now in Leipzig) hosted a workshop with the fantastic name ‘Standards, Precautions and Advances in Ancient Metagenomics 2016: 1st INTERNATIONAL WORKSHOP’, a.k.a ‘SPAAM’ for short¹. This was an interesting workshop where some key players in (ancient) metagenomics came together to talk about the current state of the art of ancient metagenomics, spanning from lab-based protocols to taxonomic profiling to functional profiling. While a really nice publication (disclaimer: I’m a co-author) eventually came out from the discussions of this workshop (Warinner et al. (2017) Annu. Rev. Genom. Hum. Genet), we never heard from ‘SPAAM’ again.

2019

By 2019, I was well into my PhD and now within a well-established group with more experience under my belt as well as talented colleagues making a much less lonely working environment. As we had been gaining this expertise, more and more groups from around the world were wanting to work on ancient microbiomes and microbial genomes. We were often contacted by various PhD or MSc students who often were ‘alone’ in their own groups - e.g. embedded in ancient human population groups - without much domain-specific expertise around them to help them establish their projects. Often these people had been left to ‘fend for themselves’ even though they had well-meaning supervisors. Given my early PhD experiences, I empathised with these researchers - I didn’t want anyone to have to repeat the lonely experience I had at the beginning of my PhD. I also thought it was frustrating that often not even very basic knowledge was available for these students to absorb themselves e.g. from reading the literature and so on.

At the same time, as my PhD had progressed, I had shifted more into bioinformatics topics, and as a part of this I started helping out with a re-write of the aDNA pipeline ‘eager’ - which was being developed within the ‘nf-core’ initiative of community-curated and best practises for bioinformatic pipelines. As I worked and more on nf-core/eager, I got deeper and deeper into the community of more than 2000 people. It was a massive eye-opener to me on how friendly, collaborative, and helpful an online community can be, despite being dispersed across the entire world! I became rather envious of the bioinformaticians having this space where they could ask diverse questions, get feedback, share knowledge and, due to the online nature of the community, in almost real time. I started to think how great it would’ve been to have such a community for ancient microbiomes and even ancient metagenomics, to break down walls and work collaboratively rather than in the very competitive fashion that aDNA generally has operated in in the past (see Elizabeth Jones (2023) Ancient DNA: The Making of a Celebrity Science for a nice summary of particularly the earlier days of the aDNA field).

In May 2019, I was writing a PhD progress report when I remembered of the original SPAAM back in 2016, and thought it was such a shame the name (which still amuses me to this day) hadn’t been re-used. It was this, in combination of my feelings for the students contacting our group, and my experiences in nf-core that made me think “why not do another SPAAM workshop?”. This way I could both find out about the latest developments in ancient metagenomics but also start building a support network for PhD students and postdocs who were having to operate alone!

I brought the idea up in one of our group meetings, and it was well-received - particularly by the resident postdocs Alex Hübner and Irina Velsko, who fortunately agreed to help me set up the ‘SPAAM2’ meeting, given I had never actually organised a scientific event before. At the same time, the ninth edition of bi-yearly International Symposium for Biomolecular Archaeology was scheduled for the September 2020 in Toulouse, so we wondered if we could make SPAAM2 in-person via a satellite event to ISBA9. We contacted the main organiser - Ludovic Orlando - who passed us on to Clio der Sarkissian (Centre for Anthropobiology & Genomics of Toulouse, Toulouse) who also agreed to be the ‘on-the-ground’ co-organiser. Finally, to make sure we had a diversity of knowledge and expertise across as much of ancient metagenomics as we could on the organizational committee, I contacted Åshild Vågene and Anna Fotakis (both of the GLOBE Institute, Copenhagen) who both agreed to also help organise and coordinate the event. Thus, by September 2019 we had established the first SPAAM Workshop committee!

2020

In February 2020, again taking inspiration from nf-core, we decided to also set up a Slack workspace for the community. This ended up being a pivotal moment in SPAAM history as since then this online chat platform has become critically important as the focal point and impetus for the sure and steady growth SPAAM has enjoyed. This open workspace allowed people from many different labs, institutions, and countries to discuss any topic they wished (as well as helping the organisers coordinate amongst themselves).

The timing was also good fortune, as it coincided with the outbreak of the COVID-19 pandemic. One month after the set up of the SPAAM Slack channel, much of Europe went into lockdown and then 5 months later ISBA9 was postponed to 2021. On one hand, this was quite a disappointment as we were excited to meet a lot of ancient metagenomic researchers, however, on the flip side, we had already filled up our 30 person room rapidly, and were quite oversubscribed. So we decided to follow the rest of the world and forge forward and adopt an online meeting - allowing for more people - and at the same time as originally planned to ensure we didn’t lose our momentum.

As Alex, Anna, Ash, Clio, Irina and myself were re-doing all our plans, another milestone hit. Around June/July 2020 I was asked by my supervisor Tina Warinner if I had a list of all published ancient microbiome samples with basic time and location metadata, as she was working on a review paper that was to act as a major overview ‘primer’ paper for ancient DNA. While I had been tracking the ancient microbiome field during the 4 years of my PhD at that point, I was well aware that I definitely had not been able to keep up with everything (a quick literature review confirmed this), and I definitely would not be able to aggregate all of these myself. I was also very reluctant to do something as a ‘one off’ - such a database would be useful over many years for many researchers, it wouldn’t be worth doing if it wouldn’t be maintained. Then, inspiration struck! When faced with a large task, the best way to tackle it is to break it into small pieces and ideally split it up into smaller tasks amongst a lot of people. What better team would be, than people who would directly benefit from such a database? And who was currently chatting away on a Slack channel - the SPAAM Community! Fortunately, Tina allowed me to somewhat drop everything I was doing to get this going. So at the end of July 2020 I set up the GitHub repository for AncientMetagenomeDir, and I sent out an email to all the registrants of SPAAM2 if they would be interested in helping out. On Friday 31st of July 2020 we ran the first of many training and hackathon events (that were still going in 2022!). The AncientMetagenomeDir community project went so well we already had a preprint on bioRxiv by the beginning of September with 17 co-authors. Which was just in time for SPAAM2!

SPAAM2 was held online on Zoom on 21-22nd September 2020. With 63 attendees from 15 countries, spanning 6 sessions and 11 independent speakers, we covered everything from laboratory protocols, to challenges in genotyping, to aDNA authentication, and what methods to do next (the slides and nodes of which can by found on the spaam-event-notes repository). It was a great success, despite the long days to account for large timezone differences across the attendees.

At this point I had had great fun discussing stuff with people on Slack, coordinating the AncientMetagenomeDir project, as well as organising and listening to all the talks at the SPAAM2 workshop. So at the end of the event, I asked everyone if they were interested in ‘doing it’ again in the future, and was anyone interested in organising the next meeting. Fortunately, 5 (crazy?) people even volunteered to be on a commitee for SPAAM3!

The Future of SPAAM

Since SPAAM2, we’ve had two further editions of the SPAAM workshop (SPAAM3 in Sept. 2021, and SPAAM4 in Oct. 2022), established a Summer School, a monthly get-together of SPAAM members (SPAAMTisch), this blog, as well as a variety of cross-institutional collaborations and projects. And at long last, SPAAM will meet again in person at [SPAAM5] (https://www.spaam-community.org/events/2023/04/26/news_SPAAM5-registration/) in September 2023!

I’m pleased to say that at the end of SPAAM4 we set up the first official SPAAM Steering Committee to guide the future development of SPAAM, and I’m very happy to ‘hand over’ the reigns of SPAAM to them, and wish Miriam Bravo, Aida Andrades Valtueña, Maria Lopopolo, Shreya Ramachandran, Ian Light, Gunnar Neumann, and Kadir Toykan Özdoğan good luck in their endevours. I look forward to seeing what the ancient metagenomics community will collaborate on next!

Post Script

I would like to briefly end on a few thanks and acknowledgments to a few people who inspired and supported both myself and others during the early days of SPAAM. Firstly, thank you to Tina Warinner for giving me the freedom to veer off from ‘standard’ academic work to spend time on various aspects of SPAAM including until today. I would also like to thank Irina, Alex, Clio, Ash and Anna who agreed to co-organise and ‘babysit’ the over-enthusiastic PhD student who had no idea what he was doing throughout the set up and execution SPAAM2. Thanks also to the SPAAM3 (Aida, Kelly, Miriam, Betsy, and Stirling), SPAAM4 (Nasreen, Abby, Gunnar, Pooja, and Shreya), and SPAAM5 (Sierra, Meriam, Alina, Alice, Megan, Zoe, and Olivia) commmitees for continuing the crazy idea. I would would like to acknowledge Alex Peltzer for intorducing me to nf-core, and the nf-core community who remains to be one of my ‘happy places’ to meet lots of lovely people. Finally, thanks to Alexander Herbig and Johannes Krause for coming up with the original name for SPAAM and letting me re-use it for my own purposes.

Alexander Herbig was tasked with one for ancient microbes, but got stuck on a good name. Most of the other names/acronyms they thought of were already taken. Then at one point in the department group leader meeting, they were discussing how many bad ancient microbe papers were being sent out of review and landing on their desks, and one of the group leaders mentioned ‘it’s like your inbox is being spammed’ by them, and Alex thought it was a funny name, setting up a meeting to stop the (inbox) spam. So he worked around it trying to make a name that fit the acronym. What I find really funny to me, as a Brit, is that there is a canned processed meat food-thing, also called spam. Which is considered to be a bit …‘low quality’ (even if popular) because it’s lots of mixed up processed meat but you’re never entirely sure where from. And I thought it was also a fun representation of the field at the time somewhat - lots of people trying to make a nice dish but not doing it well and rather formulaic, but also a great representation of an ancient metagenome - a big mish-mash of we aren’t really sure into one unknown mass. I even spent an embarrassingly long amount of time looking for spam food custom emojis for it). So it was a great name! But the funny thing was - Alexander had never even heard about spam (the food) until 2 months ago at the end of the second summer school, 7 years after the first SPAAM!