Frontiers for Young Minds

Frontiers for Young Minds
New Discovery Biodiversity Published: May 12, 2023

What Can Tapir Poop Teach Us About Healthy Forests?


The Baird’s tapir is the largest land mammal living in the Mexican Selva Maya, which is the largest tropical forest in America after the Amazon. Tapirs are herbivores that play a key role in maintaining the health of tropical forests by dispersing seeds in their feces (poop). Tapirs are mysterious, silent, and nocturnal characteristics that make them difficult to study. In our research, we analyzed the microbes in tapirs’ feces to understand the health of tapir populations in the Mexican Selva Maya. We found that a large amount of variety in tapirs’ fecal microbes is associated with a healthy tropical forest ecosystem. Maybe the analysis of the fecal microbes of wildlife can be used as a gentle technique to help us understand the health status of animals and the environments in which they live.

The Tapir—Gardener of the Mexican Selva Maya

Hidden in the middle of the deep tropical forest in southeast Mexico known as the Selva Maya, the Mayan city of Calakmul remained undiscovered for hundreds of years. Yet, during that time, a mysterious and silent gardener kept the Selva Maya healthy. This peculiar gardener travels long distances and feeds on many species of trees—but has an interesting way of planting them! The gardener leaves its feces (poop), which contains a mixture of seeds from the fruits it ate and other digested materials that serve as fertilizer, in the forest around Calakmul. When archeologists started exploring the ancient ruins of Calakmul, they were wary of the mighty jaguar, laughed at the sight of the spider monkeys, and enjoyed the bats emerging from the caves at dusk—but they neither heard nor saw the secret gardener: the tapir. In addition to being a protected archaeological site, Calakmul is also home to an important population of tapirs (Figure 1). However, the Selva Maya constantly experiences deforestation events, fires (natural and human-caused) and the increasing effects of climate change, including frequent and intense droughts [1].

Figure 1 - (A) We performed our study in the forest around Calakmul, in the Selva Maya in Mexico.
  • Figure 1 - (A) We performed our study in the forest around Calakmul, in the Selva Maya in Mexico.
  • Sampling sites are shown by colored dots on the map: dry season (red circles) and rainy season (blue squares). (B) A tapir in the dry season. (C) A tapir during the rainy season (Photographs: Jonathan Pérez-Flores).

The tapir species that lives around Calakmul called the Baird’s tapir. It is the biggest mammal in the Selva Maya, which is the largest tropical forest in America after the Amazon. Sadly, tapir populations have declined due to illegal hunting, fires, droughts, and habitat destruction. Baird’s tapir is considered an endangered species by the International Union for Conservation of Nature [2].

Tapirs are shy, nocturnal animals that prefer to live in well-preserved forests, far away from noise and people. Tapirs travel several kilometers each night, visiting the same sites looking for food and water. Their travels create trails through the forest, which other animals can use. Tapirs are herbivores—their diets mainly consist of fruits, leaves, stems, roots, bark, and flowers, from up to 70 plant species. They are not picky eaters and will eat the seeds and the skins of fruits. When they relieve themselves, the seeds return to the ground, along with the best fertilizer in the forest—their feces (Figure 2A). In just 1 year, an adult tapir will disperse over 9,000 seeds in one hectare of tropical forest. This is why they are called the silent gardeners of the tropical forests [3]. Tapir calves have stripes and spots on their bodies that help them hide from predators, such as jaguars. The calves find their own food and water.

Figure 2 - (A) Tapirs are herbivores.
  • Figure 2 - (A) Tapirs are herbivores.
  • Their feces contain seeds from the fruits they eat and provides good fertilizers for the seeds to grow in. Since tapirs walk throughout the tropical forest in search of food, they disperse seeds as they go. (B) We collected samples of tapir fresh feces in both the dry and rainy seasons. In the lab, we analyzed samples to determine the tapirs’ diets and to study the diversity of their fecal microbiomes.

Tapir Feces: A Stinky Investigation?

When we hear the words “bacteria” or “microbes,” we generally think of something dirty or associated with a disease. However, the vast majority of microbes are harmless. In fact, microbes live in and on every single organism, and thousands of microbial communities actually help the animals they live in or on, which are called the hosts. Many recent studies have revealed the strong connection that exists between animals and their microbes. The types of microbes that live on and inside animals vary according to factors such as lifestyle, diet, age, gender, and host health. This tells us that a healthy community of microbes very likely means a healthy animal—which in turn tells us that the ecosystem the animal lives in is probably healthy, too [4].

In the wild, trained teams of scientists and veterinarians can trap animals briefly and release them after they have taken measurements and samples, which can tell them about the animals’ health status. Working with tapirs presents a big problem because they are difficult animals to capture. Further, wild animals get really stressed when people trap them, and the shy tapir is no exception. Recently, a new approach has been developed that allows scientists to study animal health by analyzing the collection of microbes in their feces, called the fecal microbiome. We decided to study the diversity of the fecal microbiomes of Baird’s tapirs from the Selva Maya, to learn about their health status during both the rainy and dry seasons.

The Search for Baird’s Tapir Feces

Our team took long walks in the interior of the Selva Maya, in search of tapir latrines, as tapir toilets are commonly known. When we found a fresh fecal sample, we carefully stored it and brought it back to the laboratory. First, we used the fecal samples to study the diets of the tapirs, by analyzing the percentages of fruits, leaves, and stems present. Then, a part of the sample was used for genomic analysis, which tells us the numbers and types of microbes present in the tapir feces. During our year of sampling work, it was even possible to include samples from a sick tapir, which provided us with valuable information about the differences between fecal microbiomes from healthy and sick animals.

Fecal Microbes: A Clue to Tapirs’ Health

Our study used feces samples from tapirs as a safe and animal-friendly technique to study their health. We analyzed 47 samples, and the diversity of microbes found in these samples confirmed that tapirs have good health during both dry and rainy seasons, but the sick tapir had fewer bacteria in its feces (Figure 2B). Tapirs (and other animals) that are in poor health often have decreased microbial diversity in their fecal microbiomes; this is known as dysbiosis.

The names of bacteria are often a bit complicated to pronounce, even for scientists, but it is important to know their names and their roles within the host. The most abundant microbes living in tapir feces were Firmicutes, Bacteroidetes, Proteobacteria, and Kiritimatiellaeota, among others. Knowing which microbes are present helps us to understand what they do. Leaves, twigs, and fruits are not easy to digest, but with the help of microbes, they can be broken down into substances animals need to stay healthy, including proteins, vitamins, lipids, and sugars. When an animal feeds on the same food for a long time, such as when it lives in captivity and has a diet with no variety, the diversity in the fecal microbiome is lost, and that animal becomes more susceptible to certain diseases. We were happily surprised by our results! Despite the major weather differences between the rainy and dry seasons in the Selva Maya, tapirs’ fecal microbiomes did not change significantly (Figure 3). For this stability to occur, the environment must also be healthy, because our results showed that tapirs consumed similar amounts and types of food during both the dry season and the rainy season.

Figure 3 - We learned that the tapirs of the Selva Maya around Calakmul are in good health because their microbiomes remained diverse through both the rainy and dry seasons.
  • Figure 3 - We learned that the tapirs of the Selva Maya around Calakmul are in good health because their microbiomes remained diverse through both the rainy and dry seasons.
  • This tells us that the tropical forest is also healthy because it contains a great diversity of plants for tapirs to feed on throughout the year.

Our results suggest that the Selva Maya is a preserved tropical forest, with lots of water available and a great diversity of plants. The diversity of tapirs’ fecal microbiomes helps maintain a healthy tropical forest because a healthy microbiome helps a tapir to digest many kinds of food and to then disperse a variety of seeds through its feces. In the future, we could study fecal samples to assess the health of other animals, too. Imagine what we could discover about other animals in the forests around Calakmul.


Feces: Material that is evacuated during defecation. Stool is made up of undigested food, bacteria, mucus, and cells from the intestines.

Bacteria: Groups of tiny organisms, they are most diverse organisms on the planet.

Microbes: Tiny organisms, most commonly bacteria or fungi, that can only be seen with a microscope.

Host: An organism on or in which another organism (like a bacterium) lives.

Fecal Microbiome: All the various microorganisms that are part of an animal’s feces.

Diversity: Variety and number of species in a community.

Genomic Analysis: Study (identification, measurement, or comparison) of all the genes of an organism (plants, animals, fungi, or microbes). Almost every cell in an organism’s body has a complete copy of the genome.

Dysbiosis: Loss of microbial diversity that can affect the health of the animal.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Funding for this research came from Instituto de Ecologia, UNAM and Soluciones Ambientales ITZENI, AC.

Original Source Article

Yanez-Montalvo, A., Gaona, O., Águila, B., Arias-Domínguez, N., Falcón, L. I., and Pérez-Flores, J. 2021. Tapirus bairdii-associated fecal microbiome from a critical conservation area: Calakmul, México. Curr. Microbiol., 78:2648–59. doi: 10.1007/s00284-021-02531-8


[1] Pérez-Flores, J., Mardero, S., López-Cen, A., and Contreras-Moreno, F. M. 2021. Human-wildlife conflicts and drought in the greater Calakmul Region, Mexico: implications for tapir conservation. Neotrop. Biol. Conserv. 16:539. doi: 10.3897/neotropical.16.e71032

[2] Naranjo, E. J., Amador-Alcalá, S. A., Falconi-Briones, F. A., and Reyna-Hurtado, R. A. 2015. Distribución, abundancia y amenazas a las poblaciones de tapir centroamericano (Tapirus bairdii) y pecarí de labios blancos (Tayassu pecari) en México. Therya 6:227–49. doi: 10.12933/therya-15-246

[3] Paolucci, L. N., Pereira, R. L., Rattis, L., Silverio, D. V., Marques, N. C., Macedo, M. N., et al. 2019. Lowland tapirs facilitate seed dispersal in degraded Amazonian forests. Biotropica 51:245–52. doi: 10.1111/btp.12627

[4] Zolti, A., Green, S. J., Sela, N., Hadar, Y., and Minz, D. 2020. The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts. Microbiome 8:1–18. doi: 10.1186/s40168-020-00850-9