We just had our paper on temporal dynamics of meerkat gut microbiomes out in Nat Comms and I'm just super stoked about this one! Three years work, including finding the samples (they were spread across the world), getting them Germany, and then figuring out how to incorporate an internal standard so that we could estimate ratios of bacterial load. This bit took a lot of trial runs to get the concentrations right and was massively facilitated by our very competent lab manager, Kerstin Wilhelm. Read the paper here: https://www.nature.com/articles/s41467-021-26298-5. We have a big project that is aiming to understand how variation in the gut microbiome contributes to fitness (and in particular TB survival, which is the single biggest driver of mortality in this system). But the first goal was to just understand gut microbiome variation, because as any ent would tell you, you shouldn't be so hasty... Plus, there are still so few longitudinal datasets out there that we still don't have a very good understanding of how gut microbiomes change over time, and how repeatable they are within individuals. So, the first step after generating the data was to look at what factors we should be controlling for down the line.
In the end we were surprised to find that the gut microbiome is undergoing these large diurnal changes across the day. There is a huge spike in Clostridium at dawn, probably due to food intake, but also potentially controlled by the meerkats' own circadian rhythm in immune function. They live in arid environments, so later in the day it often gets to hot to forage, and they just chill out, and you can see that the gut bacterial load drops rather dramatically in the middle of the day. Actually it's not really clear what they do in the middle of day, since in general no one is watching them (it's too hot for humans too!), so I emailed Pritish Chakravarty, who has accelerometer data on some individuals, and he kindly checked them and told me that in summer they are generally not moving at all during the middle of the day, suggesting they are seeking shade and certainly not foraging. They start foraging again in the early evening, and we see an increase in bacterial load again at this time (but no where near as large as in the morning). Time of day was by far the strongest predictor of gut microbiome composition. Seasonal effects were super weak, which is surprising since the Kalahari is actually pretty seasonal, with a distinct wet and dry season. Whilst we know what meerkats eat (arthopods, grubs, and small reptiles, mostly), details on how meerkat diet changes over the year is somewhat of a mystery. There is paper by Doolan and Macdonald from 1997, which was very useful, but nothing since. It seems though that their diet doesn't change that dramatically over the year though, which would explain the lack of seasonal effects. The last thing we were particularly interested in looking at was the development and senescence of the gut microbiome over life, which is another process that isn't well understood (apart from perhaps in humans, and even then the senescence side is still elusive). Unfortunately meerkat pups are rather unsociable until about two months of age, after which they emerge from their natal burrows, so we don't have data from when they are super young. As such, at the point we start collecting samples from them they are mostly in their weaning/transitional phase, and eating quite a few tasty grubs and scorpions! Neverthless, we do see an increase in quite a few bacterial genera over age, until about one or two years old. But, we didn't find much evidence of senescence in very old meerkats. Whether this is because our sample size was a bit too low for these old dominants, or because these individuals are just enjoying the fitness advantages of being group leaders and therefore not suffering any chronological age effects, is unclear. But I suspect the microbiome is paired more strongly to biological senescence then chronological senescence. More on that to come once I do more analyses!
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