Beyond consumer–resource models: Decoding the natural growth habitats and habits of Escherichia coli to reveal physiological adaptation

To thrive in their natural habitats, microbes must adapt their behavior, tightly matching their cellular processes to environmental conditions. Yet deciphering this adaptation and predicting microbial growth in natural settings remain challenging, requiring models that integrate cell physiology and ecology beyond simple resource-consumption frameworks. A key obstacle is that the environmental conditions microbes naturally encounter remain poorly identified and characterized. Here, we address this challenge for Escherichia coli. By combining abundance data with intestinal flow measurements, we show that E. coli proliferates primarily in the transition region between the small and large intestine. Linking environmental conditions with growth phenotypes reveals tight adaptation to this niche, shaped by steep gradients of nutrients and oxygen. Together, these findings call for novel ecological models that explicitly couple environmental conditions with the internal allocation of cellular resources.