Kolodny, O.*, Weinberg, M.*, Reshef, L., Harten, L., Hefetz, A., Gophna, U., Feldman, M.W., Yovel, Y., 2018. Coordinated change at the colony level in fruit bat fur microbiomes through time. Nat. Ecol. Evol.

Written by: Maya Weinberg and Oren Kolodny

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Being the only mammals that can perform real active flight, bats are unique mammals.  This characteristic gave the bat order its scientific name – Chiroptera, or hand-wing in Greek. The diversity of bats (often attributed to their ability to fly) is outstanding, with every fifth species of mammal on earth being a bat, and over 1250 different species of bats spread worldwide. Fruit Bats (Pteropodidae) are a family within the Chiroptera. In Israel, fruit bats are represented by a single species: the Egyptian fruit bat, Rousettus aegyptiacus. Bats from this species are renowned for their preference to sleep in big crowded colonies in caves during the day time. They are extremely vocal within these caves, constantly communicating with their neighbors; the colony consists of males and females that live together year around. A special characteristic of the genus is its ability to echolocate, while other fruit bats lost this ability along their evolution. Egyptian fruit bats are found throughout Africa and the Middle East, as far east as Pakistan and northern India and as far north as Turkey and Cyprus. They eat ripe fruit from a large variety of trees such as Ficus, Lilac, Palm, Carob, Mulbery and many others. They are an extremely gentle animal to work with, calm to handle, and covered with a soft fur that is  pleasant to touch and that smells, naturally, of fruit. They have big round ears, big eyes – as their visual sense is highly developed – and a protrusive snout, with a respectively keen sense of smell. They can live up to 30 years and even longer in captivity. Each individual has a complex system of social interactions with individuals in the colony and in other colonies, with which it interacts during its long life.

Despite being so common in Israel and its surroundings, not much is known of this species. Rousettus bats tend to form highly condensed clusters where it is almost impossible to tell who is who. In captivity they typically breed well, but cannot perform the full scope of their natural behaviors. In the zoological garden in Tel Aviv University, we have access to an imprinted colony: a wild colony whose individuals sleep in our facility during daytime, and fly out to forage nightly. During these forays they also meet and interact with bats of neighboring wild colonies. Following two colonies, the imprinted colony and a captive colony, we were able to follow individual bats in a longitudinal study over 13 weeks. We sampled bats for their fur and gut bacteria by a noninvasive method of collecting swabs from their fur in several body sites and rectal discharge that represents the gut bacteria. We followed 14 bats, 10 from the captive colony and 4 from the wild colony (a fifth decided to drop out of the study early on – one of the downsides of a colony in which bats come and go at will). Samples were collected during daytime, when bats are less active and don’t eat. Since undigested food would be an annoying burden during flight, bats’ intestines are pretty empty during the day, so we believe that the anal discharge gave us a pretty good reflection of their actual gut microbiome. We also collected fur samples, which we analyzed for volatile components found on the bats’ fur, using gas chromatography. The results, after deep sequencing using 16S rRNA gene amplification of over 450 samples, were a bit surprising, but make total sense when considering the fruit bats’ particular eating and social behavior.

We found that 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: the fur microbiome changes over time, in a manner that is coordinated across the colony!

The pattern of synchronized changes over time at the colony level is also reflected in the profile of volatile compounds in the bats’ fur; however, it differs from what we see in the bats’ gut microbiomes. There, we find the ‘traditional’ pattern, which has been seen in many studies of other species and particularly of humans: each individual’s gut microbiome is different from others, and two samples from the same individual are nearly always more similar to one another, even if sampled two months apart, than two samples from different individuals collected on the same day. Why does the fur microbiome of the colony change in a coordinated manner? We suggest this is a direct reflection of the bats’ ecology: they spend their days huddling, allowing plenty of opportunities for the microbiome to be homogenized across individuals. Moreover, they spend their time in a closed space, sharing a very particular environment for large parts of the day, and while doing so they groom themselves and one another with their tongues, providing further opportunities for bacteria to spread. Conditions for sharing of bacteria probably can’t get much better than this...

Although aligned with findings in other species, the relative ‘individualization’ that we find of the gut microbiome is also non-trivial. This is because in our setup, what is often thought to be the major contributing factor to inter-individual diversity of gut microbiome, individualized diets, is largely controlled: these bats eat from a shared fruit bowl, and often even grab fruit from one another’s mouth. Perhaps inter-individual differences in the gut microbiomes should thus be attributed to the individuals’ physiology, immune system, or to a transmission limitation on the bacteria, such that once a species colonizes the gut, it remains stable for a long period of time because competitors for their specific ecological niche arrive only rarely.

A final reflection of the bats’ unique ecology may perhaps explain another finding: 86% of the bacterial species were found in both the gut and the fur. This might be the combined result of a few factors:

(1) The fast passage of food from mouth to anus, which minimizes unnecessary weight during flight and perhaps also increases the correlation between the oral and the gut microbiome. This microbiome may be spread over the fur during grooming.

(2) Grooming might also homogenize the bacteria across the fur, including the region near the anus, spreading bacteria that originate in it across the rest of the fur.

(3) Bats defecate during flight. In a cave that’s dense with bats, well... shit happens. In our next microbiome experiment we plan to study the ontogeny of this special gut microbiome, from birth and breast feeding, via a mixed diet of fruit and mother’s milk, to independent foraging for fruit, and compare it to the development of the fur microbiome.

In our next microbiome experiment we plan to study the ontogeny of this special gut microbiome, from birth and breast feeding, via a mixed diet of fruit and mother’s milk, to independent foraging for fruit, and compare it to the development of the fur microbiome.