When do human-driven changes to wildlife microbiomes become a One Health concern?

Suppose researchers find a strain of bacteria normally associated with people in the gut of a wild animal living near a city. Has a human microbe crossed the species boundary, or is it simply passing through after exposure to human waste, food or water? If it has crossed, has it become a lasting member of the animal’s microbiome—and, if so, does it cause harm, help the animal adjust to city life, or make no meaningful difference at all?

These questions matter because animals live in close partnership with communities of microbes that support digestion, immune development, and defence against pathogens. Human activities are changing those partnerships, but we are still struggling to interpret what the changes mean.

In our PLOS Biology article, we organise these effects into three interacting pathways. Pollution exposes wildlife and their microbes to antibiotics, pesticides, heavy metals and other contaminants. Habitat transformation changes animals’ diets, stress levels, movements, and opportunities to exchange microbes with members of their own species. Meanwhile, human expansion and the movement of domestic, feral, and invasive animals create new contact between species and new routes for microbes to travel.

Change does not always mean damage

The central mystery is no longer whether wildlife microbiomes are affected by human activity. The more challenging question is when a changed microbiome represents damage, adaptation, or simply a temporary or inconsequential response.

Pollution or habitat disruption may remove microbes that have lived alongside their animal hosts for thousands or even millions of years. Losing these long-standing partners could affect nutrition, immunity, or resistance to infection. Yet some microbial changes may be helpful. Bacteria that tolerate or break down pollutants, for example, might help an animal survive in a contaminated environment. New microbes could also expand the foods an animal can digest or help it cope with warmer temperatures.

This makes simple labels such as “healthy” and “disrupted” difficult to apply to microbial communities in the gut. A decline in microbial diversity is not automatically harmful, and an increase is not inherently beneficial. The outcome depends on which microbes change, what they do, and how the animal is affected.

A similar uncertainty surrounds the increasingly “human-like” microbiomes reported in captive and urban wildlife. These patterns may indicate that human-associated microbes are moving into other species. But they could also arise because people and wildlife are exposed to similar foods, antibiotics, or environments. Detecting a human-associated bacterial species is not enough to prove transmission, persistent colonisation, or a health effect. Not every microbe that crosses between species poses a threat, but understanding which microbes persist and how they change after entering a new host is important for both wildlife and human health.

Moving beyond microbial snapshots

Much of the available evidence comes from samples collected at a single time point. These snapshots might reveal that two microbial communities differ, but not what caused the difference, how long it lasts, or whether it matters to the host.

We therefore argue that the field must continue to move beyond cataloguing microbial change towards studies that pair microbiome sampling with measures of animal health, immunity, behaviour, reproduction, and survival. Researchers might follow the same animals or populations over time and study the combined pressures they actually experience. Pollution, dietary change, habitat fragmentation, stress, and interactions with new species rarely occur in isolation.

We should also look beyond lists of bacterial species by tracking individual strains and microbial functions, while including viruses, fungi, and other often-overlooked members of the microbiome. These approaches can help reveal where microbes came from and what impacts they might be having.

Controlled experiments in wildlife are often constrained by ethical and practical challenges. Accordingly, we encourage researchers to combine approaches rather than accept uncertain conclusions. These might include long-term field monitoring, non-invasive sampling, comparisons across species and environments, carefully designed studies in zoos or rehabilitation centres, and targeted experiments in appropriate model systems.

From hidden change to early warning

Wildlife microbiomes may eventually serve as early warning systems for environmental change. In Swedish brown bears, for example, antimicrobial resistance preserved in decades-old dental calculus (hardened plaque) rose and fell alongside national antibiotic use. Similar microbiome-based monitoring might eventually help detect anthropogenic pressures before more visible signs of ecological stress or declines in wildlife populations become apparent.

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Microbiome research may also inform captive breeding programmes, habitat restoration, and disease surveillance. But these applications depend on learning to distinguish harmless change from beneficial adjustment, harmful disruption, and emerging disease risk.

For One Health, the crucial task is no longer merely to document that human activity is reshaping wildlife–microbe relationships. It is to understand when those hidden changes affect the health of animals, ecosystems and, ultimately, us.

Katherine M. Lagerstrom, PhD, is a Postdoctoral Research Associate in the Moeller Lab, Department of Ecology and Evolutionary Biology, Princeton University, and is a Trustee with Applied Microbiology International and Co-Chair of its One Health Advisory Group.