7/9 Why CroCoDeEL?

Manually searching for contamination lines in all sample pairs is:
⏳Time-consuming
❌Error prone

CroCoDeEL automates the process using:
📐Linear modeling
✔️Rule-based filtering
🧠ML model trained on an expert-labeled dataset

6/9 🧪 Our key finding

We compared species abundance profiles of a contaminated sample and its source.

This revealed a 'contamination line' formed by species introduced by contamination.

These scatter plots illustrate the before/after contamination, highlighting this pattern.

2/9 What is cross-sample contamination?

It’s the accidental transfer of material between samples processed together.

Common causes include:
💉Pipetting errors
💦Splashing following agitation

Extensive automation using plates increases this risk!

doi.org/10.1128/msys...

The LivinGut project addresses the challenge of understanding the human gut microbiome by integrating multiple scientific disciplines. By combining biology, social sciences, psychology and IA: build a holistic understanding of the norms and variables shaping the gut microbiome.

Transrationality is a less ideologic and biased approach. It can enrich each individual discipline.

Can social sciences and psychology help us understand the factors driving this trend?

How can we avoid reducing everything to biology?

How can we address freedom of people while managing all the layers of complexity?

Solution according to Béatrice de Montera: transrationality (from Bachelard)

Can we observe a collective trend toward less diverse microbiomes, particularly among young people in the US?

Can microbiome states be visualized as a subway map with hubs allowing transitions from one evolutionary line to another?

By analyzing 35,000 microbiomes, we can observe a form of evolutionary branching that helps us understand how microbiomes transition from one state to another. Leaves are less diverse, and some states are irreversible, acting as tipping points.

Many factors can affect the gut microbiome, leading to different states. But the question is: how can change occur?