How Cities Are Changing the Rodent Gut Microbiome

A study conducted by scientists from Swansea University in the UK, working with international collaborators, has explored the gut microbiomes of rodent species living in both urban and rainforest habitats in Borneo. Their findings have important implications for our understanding of how the tiny organisms living in rodents’ guts may help animals adapt to new environments, and what this means for their health and the spread of infectious diseases. Let’s look at the study in detail.

Human-Induced Habitat Alteration

Humans are constantly encroaching on natural habitats previously inhabited only by native species. This leaves the animals that live there with two stark choices: either restrict their range (and possibly suffer population declines due to increased competition for resources) or adapt to the new human-altered environment—a classic case of ‘if you can’t beat them, join them.’ The only other alternative is extinction. This has resulted in the emergence of urban-adapted native species and a natural experiment for scientists to study.

The location chosen for this research was the Kota Kinabalu area of northern Borneo in Sabah, Malaysia. The city has undergone significant urban expansion, particularly since the 1970s, leading to increased encroachment on surrounding tropical rainforest areas. The urban-adapted native species chosen for this study was Muller’s giant Sunda rat (Sundamys muelleri). However, that is only part of the story.

Urban Non-Native Species

Human development does not come alone. With us, we bring non-native species that have, over thousands of years, adapted to become as urban-dwelling as we are. They are referred to as urban-dwelling non-native species, and they are used to thriving in landscapes highly modified by humans. The four species sampled in this research were the native Muller’s giant Sunda rat (Sundamys muelleri), the Asian black rat (Rattus rattus), the Norway rat (Rattus norvegicus), and the Asian house shrew (Suncus murinus).

Within this ‘natural laboratory’, scientists can examine how these two groups of animals affect each other. In particular, this study looked at the gut biomes of the animals.

What Is the Gut Microbiome?

A biome is a distinct ecosystem, so the gut biome is the ecosystem inside the gut. The animals in this study, along with humans and countless other species, have millions of bacteria, viruses, and fungi living in their guts. These microorganisms are not freeloaders; they play a vital role in digesting food, protecting against pathogens, and regulating the nervous and endocrine systems. While each individual has a unique gut biome, there are common patterns shared within a species.

How Was the Research Carried Out?

Traps were set at locations accurately recorded by GPS devices and numerically scored according to the human impact in the area. For example, a forest was given a value of ‘1’, and a housing compound was ‘5’. Fecal (poop) samples from the colons of the 245 rodents were analyzed for microbiome diversity. Researchers recorded both the different types of bacteria and their abundance in each animal (host).. In all, the scientists identified 1864 different amplicon sequence variants (ASVs). These are marker genes for different bacteria. Of these, 64 were found in all four rodent species. The most common bacteria were Lachnospiraceae, Prevotellaceae, and Lactobacillaceae.

Important Findings

The findings of this study revealed some interesting new information about how gut biomes vary within and between species in altered environments. Here are the main findings.

Species Is Not the Only Determinant of Gut Biome

The most important factor in determining the gut biome profile in this study was the rodent species. Importantly, the bacterial community found in the shrew was distinct from that of the rats. This is not surprising given the differences in diet and structural differences of the gastrointestinal tract. More significantly, they found that the black rat (an invasive species) had a gut microbiome more similar to the native rainforest rat than to its close relative, the Norway rat.

This suggests that shared environmental use may influence the gut biome. This may be through a common diet or through the exchange of microbes with the environment, where animals share land and water sources.

Land Use Intensity Influences the Microbiome in the Norway Rat

This research also indicated that land use intensity may change the microbiome composition of rodents within a species. This may be caused by dietary changes where the rats need to rely on more natural sources of food in less urban areas.

Why This Is So Important

The findings of this study suggest that the gut biomes of animals are not just governed by genetics. It has been shown that animals that share an environment can develop a similar gut biome. What’s more, the type of habitat and diet influences gut biomes within a species. Ultimately, this opens up new areas of research into the role of gut biomes in helping animals adapt to new environments.