These layers respond differently to land-use change and give rise to very different network structures.
Together, they help explain how microbiomes can be both resilient and highly context-dependent at the same time, with potential consequences for host health and function.

9/9

Big picture: the microbiome isn’t one community playing by one set of rules.
It has at least two layers:
🔸 a stable, drift-driven core, and
🔹 a flexible, environmentally filtered non-core.
8/9

Then we asked: does land-use change actually shape these network patterns?
For non-core microbes, the answer is a clear yes.
Module composition appears to relate to vegetation and elevation.
For core microbes, basically no.
Across most thresholds, land-use variables didn’t explain much at all.
7/9

Non-core microbes show strong heterogeneous selection between modules, with environmental filtering creating phylogenetically distinct communities, and more drift within modules.
So non-core modules reflect environmental sorting; core modules reflect stochastic turnover among similar taxa.
6/9

To link structure with process, we quantified the roles of heterogeneous and homogeneous selection, dispersal limitation, and ecological drift.
We found contrasting patterns:
Core microbes are dominated by ecological drift, both within modules and between them.
5/9

One clear pattern: core and non-core microbes form distinct network structures.
Core microbes → few big modules.
Non-core microbes → many small, fragmented ones.
Common taxa spread across many hosts, while rarer ones form localized host–microbe pockets across the landscape.
4/9

We asked how host–microbe networks assemble, and whether various parts of the microbiome follow different rules.
We built individual-rat networks across a land-use gradient in Madagascar, using a moving prevalence threshold to track how structure and assembly shift from rare → common microbes.
3/9

Ecological network structure is key to understanding how communities form and function. But we still know surprisingly little about the processes that build these networks, especially under human-driven environmental change.
2/9