Galaxy of sourdoughs: exploration of twinkling microbial constellations
Dear Sourdough Enthusiasts,
As the year winds down and the days grow shorter here in Zurich, the city comes alive with sparkling Christmas lights, casting a warm glow over the streets. But this year, it’s not just the festive decorations brightening the season - your sourdough samples are stealing the spotlight! Our HealthFerm sourdough analysis is picking up pace, uncovering fascinating insights into the microbiomes hidden in your homemade fermentations. Let’s have a look together at Mathilda’s (and Every Other Sourdough’s) journey through the Bioinformatic Analysis Pipeline:
Mathilda’s (and Every Other Sourdough’s) Journey Through the Bioinformatic Analysis Pipeline. After extracting DNA (as detailed in our KingFisher blog post) and sequencing it, each sourdough sample - Mathilda included - embarks on a fascinating analytical journey. This involves several intricate steps: transferring and cleaning the data, comparing sequences to specialized databases to identify the microbial species present, and performing advanced statistical analyses. The goal? To uncover why certain species thrive in specific sourdoughs, which microbes tend to team up, and how these microbial communities are influenced by factors like sourdough ingredients, geography, or insights from the sourdough questionnaire responses. It’s a deep dive into the secret lives of sourdoughs!
Having collected an incredible number of unique sourdoughs from all over Europe, we dove into the genetic information of the yeasts and bacteria calling your sourdough(s) their home. After retrieving the unique DNA sequences of these microorganisms, we can match them to fungal and bacterial databases to uncover their identities. It’s just like detective work to discover the names of your sourdough's microscopic roommates!
But before we can get to the good stuff, there’s some tidying up to be done. Think of it like cleaning up after a big Christmas party - there’s wrapping paper everywhere, and we need to sort through it to reveal the gifts. In our case, we clean the DNA data to remove low-quality or irrelevant sequences, leaving us with the true treasures: the sequences that help us obtain the exact names of the microbes living in your sourdough.
And now that we’ve unwrapped the gift (sticking with the analogy), we’re diving into the most exciting part! We’re not only studying the microorganisms living in one specific sourdough but also comparing all 660 sourdoughs to uncover what shapes their microbial communities. Is it the temperature at which the sourdoughs are stored? Could it be the geographical origin of the samples? Or perhaps the type of flour used?
While we can’t provide a definitive answer just yet, we’re making strides in unraveling these mysteries - so stay tuned! For now, let us give you a sneak peek into our ongoing work by introducing you to the fascinating Sourdough Microbiome Galaxy:
The Sourdough Microbiome Galaxy. Curious where your sourdough star shines within this galaxy? So are we - and more importantly, we’re exploring why it’s there. Our mission is to uncover why some sourdoughs cluster together in the same spiral arm (meaning they share similar microbial communities), while others drift into completely different, or even opposite, spiral arms (indicating distinct microbial compositions). To create this galaxy, we followed the process outlined in the previous figure. By mathematically comparing the presence, absence, and abundance of microbial species in each sourdough, we projected the entire galaxy into a two-dimensional space. Then, with a touch of scientific magic, we added glowing halos around the most similar sourdoughs to highlight their connections - bringing this dazzling sourdough star-map to life!
In the Sourdough Microbiome Galaxy, each star represents a single sourdough starter. Some “stars” cluster together, forming groups - or, as we’d call them in galaxy terms, "Spiral Arms". Sourdoughs within the same spiral arm have more in common in their microbial communities compared to those in different spiral arms. In simpler terms, these clusters reveal which sourdoughs host similar microbes, while those farther apart showcase unique microbial compositions.
Now, here’s something to ponder: which cluster do you think your sourdough belongs to, and why? Are these groups related to differences in ingredients used in different starters? Or differences in baking practices? These are exactly the kinds of questions we’re exploring right now.
And doesn’t it all look a bit like twinkling Christmas lights? To us, it’s like the festive sparkle of the holiday season - but in the microbial universe of sourdough! ✨
What’s Next?
Right now, we’re swimming in a sea of data (just imagine how long it took you to fill out that questionnaire - and now multiply that by around 660! And then multiply it by an extremely large (but yet unknown) factor to account for all the diversity within each single sample 😉). To uncover clear connections between all the different factors, we’ll need to keep digging deeper.
We’re diving deep into graphs like the one above, analyzing a variety of parameters like ingredients, fermentation methods, geographic origins, and more. By running statistical tests, we aim to determine whether the differences we observe are truly meaningful. It’s a challenging task, but the reward is worth it: uncovering a clear and comprehensive picture of sourdough diversity across Europe and understanding how this incredible variety comes to life.
With that, we wish you all a joyful and peaceful holiday season and a wonderful start to the new year! May your days be filled with happiness, inspiration, and perhaps even the delightful aroma of freshly baked sourdough (bread). Cheers to a year full of exciting discoveries and delicious creations!
Your ETH-Sourdough-Microbiome-Team
