Coordinated change at the colony level in fruit bat fur microbiomes through time


The host-associated microbiome affects individual health and behaviour, and may be influenced by local environmental conditions. However, little is known about microbiomes’ temporal dynamics in free-living species compared with their dynamics in humans and model organisms, especially in body sites other than the gut. Here, we investigate longitudinal changes in the fur microbiome of captive and free-living Egyptian fruit bats. We find that, in contrast to patterns described in humans and other mammals, the prominent dynamics is of change over time at the level of the colony as a whole. On average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats’ ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats’ fur, but differs from the more individualized pattern found in the bats’ gut microbiome.

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Fig. 1: Microbial composition of fur and gut samples.
Fig. 2: The prominent pattern in the fur microbiome is that of colony-level change over time.
Fig. 3: Similarity of pairs of samples in the captive colony, from the same individual or from the same date.
Fig. 4: In the gut, sex and individual identity are the primary factors that determine microbiome composition.
Fig. 5: Colony and individual-level patterns in profiles of volatile compounds.

Data availability

All data used in this study has been uploaded to SRA at NCBI, and can be found under Bioproject PRJNA494618 (biosample accession numbers: SAMN10226814SAMN10227267 and SAMN10174956SAMN10175066).


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We thank A. Letten, P.-J. Ke, M. Donald, N. Dudek, W. Van Treuen, L. Costello, M. Maor, T. Simon and E. Ebel for technical help and insightful comments. O.K. is supported by the John Templeton Foundation and Stanford Center for Computational, Evolutionary, and Human Genomics. This research was partially supported by the European Research Council (ERC–GPSBAT).

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O.K., M.W., L.R. and Y.Y. planned the study, analysed the data and wrote the manuscript. M.W., L.R. and L.H. collected and processed the samples. All co-authors commented on the study design, data analysis and manuscript.

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Correspondence to Oren Kolodny or Maya Weinberg or Yossi Yovel.

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Kolodny, O., Weinberg, M., Reshef, L. et al. Coordinated change at the colony level in fruit bat fur microbiomes through time. Nat Ecol Evol 3, 116–124 (2019).

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