Throughout my PhD, I rely on my experience in the lab on microbial communities to address philosophical issues.

• First, by investigating a widely used approach by scientists, amplicon sequencing, I suggest a novel definition of samples, a category overlooked by philosophers compared to data.
• Then, I took a more historical approach by delving into the records of Serguei Winogradsky, opens an external URL in a new window, a founder of microbial ecology, to back up my thesis that current microbiome research practices are divided. This division can be traced to their medical and ecological scientific lineages, affecting explanations in this discipline.
• Lastly, by using the ideas of model-based accounts of measurement, I thought of analysing the species concept used in microbial ecology in the context of diversity-as-a-measurement. I investigate the potential implications of such analysis for the practical, epistemological, and theoretical dimensions of the well-known biological and philosophical species problem.