Consider the common black rat Rattus rattus. Although native to southern India, the black rat, also called a ship rat because of its habit of boarding ships, has been scoring free passage and conquering the world since the Roman era. After centuries of destroying crops, raiding rations and spreading plagues, it has possibly become the most hated species in the genus Rattus.

On the other hand, there is the Sahyadris forest rat Rattus satarae. One would be hard pressed to find too many faults with this wild rat species. Unlike its globetrotting cousin, the Sahyadris forest rat is endemic to the Western Ghats, where it lives on trees and eats insects and fruits.

What makes these two species so different? What makes one rat species a pest that is difficult to eradicate and the other a forgotten endemic species vulnerable to extinction? To answer the question, ecologists from the National Centre for Biological Sciences have been looking inside their gut.

The Sahyadris forest rat, lives on trees and eats only insects and fruits. Their gut microbes seem similar to other wild rat species in the world. Photo Credit: Amruta Varudkar
The Sahyadris forest rat, lives on trees and eats only insects and fruits. Their gut microbes seem similar to other wild rat species in the world. Photo Credit: Amruta Varudkar

Birds, mammals, insects, plants, even humans – most living organisms are reservoirs for other lifeforms. On us, within us, we host millions of microorganisms. While some are benign and some harmful, several are extremely useful for survival.

“We are increasingly recognising the diverse ways in which symbiotic microflora interact with the host organism,” said biologist Amruta Varudkar. Varudkar and her doctoral advisor and conservation geneticist, Uma Ramakrishnan, became particularly interested in symbiotic microflora in the gut.

Biologists see the gut or the digestive tract as a particularly important ecosystem because its microbial inhabitants help break down food the host animal is eating, to release nutrients. Moreover, according to Kevin Kohl, whose lab studies host microbe interactions in the University of Pittsburgh, gut microbes could enhance immune system of the hosts or change their behaviour by producing small molecules that enter their blood stream.

“I think these actions work in a sort of loop, where an animal begins eating a new food, the microbes become adapted to that diet and that benefits the animal, allowing it to survive and continue to eat this new food,” he said. “Overall, we still know very little about all these effects and interactions,” he added.

Could these interactions be key to the differences in the black rat and the forest rat?

Being able to stomach human food

For instance, one reason why black rats survive in every human dominated landscape in the world is that they eat what humans eat, which means they must have the stomach (or rather the gut) for human food. The Sahayadris forest rat on the other hand is never in contact with human beings.

Varudkar and Ramakrishnan reasoned that not only should both rat species have different gut microbes, but also that the microbial species found in their gut should be an indication of the lives they lead. To see if they were right, the duo caught rats of the two species in the Western Ghats across Maharashtra, Tamil Nadu and Karnataka and examined their gut. In these locations, the two rat species overlapped geographically but occupied different habitats. The forest rat of course lives in the forests and the black rat in the towns and villages surrounding the forests.

Although the black rat originated in India, it is now one of the most invasive species across the world. Its success is partly because of its ability to eat human food. Photo Credit: H. Zell/Wikimedia Commons [Licensed under CC BY 3.0]
Although the black rat originated in India, it is now one of the most invasive species across the world. Its success is partly because of its ability to eat human food. Photo Credit: H. Zell/Wikimedia Commons [Licensed under CC BY 3.0]

The researchers found 42,054 microbes in the guts of the two species. Around 53% of these microbes were unique to one or the other rat species.

“I think the differences between these rodent species is interesting, but not all that surprising,” said Kohl, who was not associated with this study.

Kohl pointed out that the genetic history of the host was likely to be linked to the community of microbes in their gut. Basically, rats of one species were likely to have different gut microbes compared to rats of another species.

Ramakrishnan agreed. “For example, the gut microbial community of elephants, whether they were in Myanmar or South India, will be more similar than say a bonnet macaque,” she explained. “But within the elephants also there will be some difference.”

The researchers were looking for such differences within the two rat species. In the forest rats, the microbial composition changed slightly with the location in which they were studied. But black rats showed no such difference. Varudkar pointed out that in a previous study the researchers observed a similar pattern of genetic differentiation in the two species of rats.

The forest rat in the same 10 locations showed slight difference in their genetic relatedness to each other, indicating the forest rats in northern Western Ghats, for instance, were not meeting and breeding with forest rats in the southern part much. The black rats meanwhile were probably piggybacking with human beings across the landscape, mused Varudkar.

Researchers in this study set traps were set in forests of the Western Ghats as well as villages bordering the Western Ghats. Photo Credit: Amruta Varudkar
Researchers in this study set traps were set in forests of the Western Ghats as well as villages bordering the Western Ghats. Photo Credit: Amruta Varudkar

Such a relationship between genetic relatedness and microbial composition could have some interesting applications according to Ramakrishnan. “There are some suggestions about monitoring population health and we are trying to do this with tigers in Ranthambore where we are characterising the pedigree of the entire population,” she said.

As tiger habitats like Ranthambore are increasingly cut off from each other, conservationists fear that tigers may become heavily inbred. Inbreeding and the loss of genetic diversity could reduce the resistance of the population to disasters like a disease epidemic.

“But estimating inbreeding in the wild is really tough,” explained Ramakrishnan. “But if inbred and related animals had similar gut microbiomes and this was a robust correlate of inbreeding, that could be great.”

Researcher Amruta Varudkar in the field extracting tissue samples from the Sahyadri forest rat. Photo Credit: Amruta Varudkar
Researcher Amruta Varudkar in the field extracting tissue samples from the Sahyadri forest rat. Photo Credit: Amruta Varudkar

Rats, humans and dogs similar at the gut level

Not only did the black rat have similar gut microbes throughout the Western Ghats, some of the gut microbes were common to two other extremely successful species on the planet: human beings and domestic dogs. Bacteria called Lactobacilli and Bifidobacteria found in the black rat were also common in dogs and humans.

Lactobacilli are bacteria are believed to help break down lactose sugars found in milk while Bifidobacteria are believed to help enhance digestion in humans and considered a cure for disorders like Irritable Bowel Syndrome. Like dogs, black rats were possibly adapting well to human food.

“Clearly there is some kind of associative sharing of microbiota,” Ramakrishnan pointed out.

While this similarity and proximity might be great for the black rats, the study found that for humans this could be problematic. Varudkar pointed out that several species of bacteria known to cause human diseases such as plague, brucellosis, typhus fever were more abundant in the black rat that lives amongst humans, than in the forest rat.

“This is contradictory to the prevalent, commonly held belief that “wild” rats act as reservoirs of human pathogens,” she said.

Black rats enjoying a communal bowl of milk in a temple in Rajasthan. Gut microbes that can help break down dairy in were found in black rats in the study; a possible adaptation to human diets. Photo Credit: Arian Zwegers/Wikimedia Commons
Black rats enjoying a communal bowl of milk in a temple in Rajasthan. Gut microbes that can help break down dairy in were found in black rats in the study; a possible adaptation to human diets. Photo Credit: Arian Zwegers/Wikimedia Commons

Monitoring pathogenic bacteria in commensal rat faeces would have significant public health implications.

Kohl thinks that gut microbes could help here as well. “It has been shown that animals harbouring certain gut microbes are less likely to harbour potential diseases,” he said, adding that altering the composition of gut bacteria in black rats through antibiotics, diet or faecal transplants from wild rodents lower the abundance of potential human pathogens.

“This idea would certainly require more in depth and manipulative studies and may not be feasible for large scale efforts across many villages, but I do think the idea is intriguing,” said Kohl.

This article first appeared on Mongabay.