Adapting to a seasonal diet

Kyoto, Japan -- Humans everywhere may be able to eat bananas all year round, but wild animals must always eat "in-season". For them, seasonal shifts in food availability present a major challenge, especially in temperate regions like Japan with strong seasonal variation.

Japanese macaques reside further north and in a colder climate than any other non-human primate. They like to eat fruits and seeds, but when unavailable the monkeys must rely on low-quality foods such as leaves and bark. How animals like macaques adapt to such dietary shifts has long been a central question in ecology.

It is well known that the composition of the gut microbiome changes with diet and environment in many animals, so research has increasingly focused on how gut microbes help animals cope with seasonal dietary changes. But scientists still do not fully understand how these microbial changes affect digestive efficiency.

This inspired a team of researchers at Kyoto University to uncover how the gut microbiome of Japanese macaques responds to their dietary changes. The team conducted a year-long study focusing on macaques living on Yakushima Island in southern Japan.

Through behavioral observations, the research team recorded the type and amount of foods macaques eat, linking this information to changes in their gut microbiome. They collected fresh fecal samples from wild macaques to extract gut microbes, using 16S rRNA gene analysis to examine the composition of the microbiome, and an in vitro fermentation assay to directly measure the gut microbiome's fermentative ability against different food items that are part of the monkey's food intake.

"This study was challenging because I often had to wake up in the middle of the night to monitor fermentation and then continue following monkeys the next day," says corresponding author Wanyi Lee. "But it was worth it to see the in vitro fermentation assay reveal the hidden power of gut microbes."

Their findings show that both the composition and fermentative ability of the gut microbiome shift flexibly across seasons, while the latter in particular increased during the harsh winter when macaques relied on leaves. In contrast, foods such as fruits and seeds were easily digestible by all kinds of gut microbes.

The researchers were intrigued to find that mature leaf consumption in particular, rather than fiber intake in general, boosted the fermentative ability of the gut microbiome. This suggests that leaf consumption may be selecting for microbes that can metabolize not only fiber but also the plant secondary metabolites found in leaves, helping the monkeys handle chemically defended foods during harsh seasons.

"By linking both microbial composition and function, our study provides a comprehensive perspective that can be applied not only to other primates but also to a wide range of wild animals," says Lee.

As climate change and deforestation continue to alter the habitats of wild animals, understanding how much microbial flexibility can buffer hosts against food shortage will be critical for predicting resilience and informing strategies for wildlife conservation.

###

The paper "Seasonal Adaptation of the Gut Microbiome in Japanese Macaques: Linking Gut Microbiome Shifts with Fermentative Function" appeared on 1 September 2025 in Ecology and Evolution, with doi: 10.1002/ece3.72076

About Kyoto University

Kyoto University is one of Japan and Asia's premier research institutions, founded in 1897 and responsible for producing numerous Nobel laureates and winners of other prestigious international prizes. A broad curriculum across the arts and sciences at undergraduate and graduate levels complements several research centers, facilities, and offices around Japan and the world. For more information, please see: http://www.kyoto-u.ac.jp/en