The core microbiome concept rests on a simple intuition. Within any habitat type, whether a host species, a soil ecosystem, or an ocean region, some members of the microbial community appear again and again across samples, while others come and go. The recurring members are presumed to matter most: they may perform essential functions for the host, stabilize community dynamics, or define the characteristic identity of that environment. In practice, researchers have typically identified the core by counting how often particular taxa occur across samples and keeping those that pass a predefined threshold of presence or abundance. Over the past decade, a rich toolbox of occurrence-based and abundance-based measures has grown around this idea, allowing scientists to quantify which microbes constitute the stable backbone of everything from human guts to coral reefs.

What has been missing, the Clemson authors argue, is evolution. Most existing core microbiome measures treat taxa as isolated labels, blind to the branching history that connects them. That blindness creates two well-known problems. The first is inconsistency across taxonomic rank: a microbe that appears in ninety percent of samples at the species level may be split into several lineages that each fail the threshold, or lumped into a genus that trivially passes it, so conclusions flip depending on whether the analyst works with operational taxonomic units, species, genera, or families. The second is sensitivity to strain variation: closely related strains within a single species can differ enormously in their presence across samples, causing non-phylogenetic measures to register dramatic turnover where, evolutionarily speaking, almost nothing has changed.

Bewick and Camper’s solution begins with a new object they call the core community phylogeny. Rather than selecting individual taxa that pass an occurrence threshold, the approach works directly on the evolutionary tree that describes the relationships among all microbes detected across a set of samples from a single habitat type. Branches of that tree are retained if they are present in multiple samples, in effect asking not whether a particular named species is shared, but whether a particular slice of evolutionary history is shared. The result is a pruned phylogeny whose branches represent the conserved evolutionary fabric of the community, the portion of the microbial tree of life that reliably shows up in that habitat, regardless of how individual strains or species shuffle beneath it.

From this core community phylogeny, the authors derive a family of phylogenetic metrics that mirror the classic questions microbiome ecologists already ask, but answer them in evolutionary currency. The first describes the phylogenetic diversity of a core microbiome within a single habitat type, capturing how much of the tree of life the conserved branches span. The second quantifies phylogenetic turnover between core microbiomes drawn from two different habitat types, measuring how much of the conserved evolutionary history is replaced when moving from one environment to another. The third measures shared phylogenetic diversity across core microbiomes from two or more habitat types, identifying the deep, evolutionarily conserved component that persists across otherwise distinct communities. Together, these measures extend the familiar logic of phylogenetic beta diversity into the specific context of core microbiome analysis.

The technical payoff is consistency. Because the metrics are computed on branches of a phylogeny rather than on labels at a chosen rank, their values remain stable whether the underlying community data are summarized at fine or coarse taxonomic resolution. When the same microbial community is described at the level of strains, species, or higher taxa, the core community phylogeny and its associated measures converge on the same answer, because the evolutionary information is preserved at every level. Likewise, strain-level variation, which can dominate and distort occurrence-based core definitions, is absorbed naturally into the tree: closely related strains contribute overlapping branches, so their idiosyncratic patterns of presence and absence no longer masquerade as wholesale community change. The authors report that, compared with non-phylogenetic metrics, their framework shows greater consistency across taxonomic rank and phylogenetic level, along with reduced sensitivity to strain variation.

That robustness matters far beyond statistical tidiness. Meta-analyses in microbiome science are frequently hampered by the fact that different studies process their sequencing data at different resolutions, making it hazardous to compare core microbiome findings across papers, hosts, or ecosystems. A framework that integrates seamlessly across taxonomic rank and phylogenetic level allows researchers to pool and compare results without first forcing every dataset into an identical labeling scheme. It also opens the door to genuinely novel biological questions. Instead of asking which named taxa form the core of a habitat, scientists can ask which lineages, and which evolutionary functions embedded in the tree, are conserved across hosts or environments, and how deep in the tree that conservation runs. A core defined by deep branches suggests ancient, possibly co-evolved associations; a core confined to shallow branches suggests recent ecological filtering of whatever lineages happen to be available locally.

The study did not emerge from simulations alone. The acknowledgements and supplementary materials reveal an empirical foundation built from fieldwork in New Mexico, where the authors, with support from National Science Foundation awards and Clemson University programs, assembled gut and skin microbiome samples from lizards, along with the read counts, taxonomy assignments, microbial phylogenies, and metadata that accompany them. Lizards, with their partitioned gut and skin habitats on the same individual animals, provide a natural test bed for contrasting core microbiomes across habitat types and for demonstrating how phylogenetic turnover and shared diversity behave when the same host carries distinct microbial communities in different body regions. A simplified worked example accompanying the paper walks readers through the construction of core community phylogenies and the calculation of the associated metrics step by step, lowering the barrier for laboratories that want to adopt the approach.

The implications ripple outward across applied microbiome research. In human health, core microbiome analyses inform debates about which microbes are essential partners rather than transient passengers, and inconsistent rank-dependent results have complicated efforts to define a healthy reference core. In agriculture, core definitions guide the design of synthetic microbial communities and probiotic formulations for crops and livestock, where strain-level variability among commercial inoculants has been a persistent headache. In conservation and ecosystem management, comparing cores across disturbed and intact habitats depends on measures that do not change their verdict when taxonomic pipelines change. A phylogenetically grounded core concept offers each of these fields a common, evolution-aware yardstick, one in which the currency is conserved branch length rather than mutable species lists.

None of this means the era of taxon-based core microbiome analysis is over; named taxa remain indispensable for communication, culturing, and mechanistic follow-up, and phylogenetic measures complement rather than replace occurrence and abundance metrics. But the study marks a conceptual maturation for the field, aligning the core microbiome with the tree-thinking that already underpins much of ecology and evolutionary biology. As microbiome datasets continue to explode in size and diversity, tools that deliver stable answers across resolutions, and that translate the question of what is shared into the question of what evolutionary history is shared, are likely to spread quickly through the community. The core microbiome, long a moving target, may finally have a measure that holds still.

Subject of Research: Phylogenetic methods for measuring and comparing the core microbiome across habitat types

Article Title: Phylogenetic measures of the core microbiome

Article References: Bewick, S. A., & Camper, B. T. (2026). Phylogenetic measures of the core microbiome. Microbiome. https://doi.org/10.1186/s40168-026-02520-8

Image Credits: AI Generated

DOI: 10.1186/s40168-026-02520-8

Keywords: core microbiome, microbial ecology, phylogenetics, community phylogeny, phylogenetic diversity, beta diversity, taxonomic rank, strain variation, microbiome metrics, lizard microbiome, evolutionary conservation, Microbiome journal