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Animals living in highly seasonal environments adapt their diets accordingly to changes in food availability. The gut microbiome as an active participant in the metabolization of the host’s diet should adapt and change with temporal diet fluctuations, but dietary shifts can be short-term and, hence, difficult to detect in cross-sectional studies. Therefore, we performed a longitudinal study combining repeated sampling of fecal samples with observations of feeding behavior in wild redfronted lemurs. We amplified taxonomical marker genes for assessing the bacteria, archaea, protozoa, helminths, and fungi, as well as the active bacterial community inhabiting their gut. We found that the most abundant protozoans were  Trichostomatia  and  Trichomonadida , and the most abundant helminths were  Chromadorea . We detected known members of the gut mycobiome from humans but in low abundances. The archaeal community is composed only of members of  Methanomethylophilaceae . The predominant phyla in the entire bacterial community were  Bacteroidota  and  Firmicutes  while the most abundant genera harbor so far unknown bacteria. Temporal fluctuations at the entire community level were driven by consumption of fruits and flowers, and affiliative interactions. Changes in alpha diversity correlated only with the consumption of flowers and leaves. The composition of the entire and active bacterial community was not significantly different, but the most abundant taxa differed. Our study revealed that monthly changes in the bacterial community composition were linked to fruit and flower consumption and affiliative interactions. Thus, portraying the importance of longitudinal studies for understanding the adaptations and alterations of the gut microbiome to temporal fluctuations.

Dietary shifts and social interactions drive temporal fluctuations of the gut microbiome from wild redfronted lemurs