Microbial Diversity: sometimes you have it, sometimes you don’t
This past January I wanted to see what would happen to my gut flora if I adopted a hunter-gatherer diet for a week – eating the plants, animals and drinking the same water as the Hadza hunter-gatherers of east Africa that I was working with. Among other hypothesis I wanted to test, would immersing myself in this microbial-rich lifestyle increase the diversity of microbes in my tattered western gut? Below is a PCoA plot of what happened.
Think of a PCoA plot as one of those Christmas snow globes you shake up and watch the snow sink to the bottom of the globe. Since you can turn the globe and watch the snow sink from different angles, it’s 3D – and so is the PCoA plot below though flattened (2D) and view from one angle. In short, the closer the dots are together there more similar the bacteria are in those two or more samples.
The plot below is an animated GIF showing the timeline of my little experiment. The first three red dots represent my gut bacteria while I was in Arusha, Tanzania in late January of this year. Arusha is a large town just west of Mount Kilimanjaro where the project rents a little house for storing equipment and serves as our base when we are not in the field. While in Arusha I ate some meals at the house – drank the local tap water – and eat the occasional meal at a restaurant. Food consists of eggs, bacon, misc vegetables, chicken etc – and usually a nightcap of whiskey or wine.
Since I just had arrived from the US, the microbial community represented by the three red dots is a mash up of my US bugs I brought with me and the impact of the food I ate before boarding the plane, the funky in flight food, and the food and microbes I acquired while on the ground in Arusha eating and moving about this new environment. Either way, over those first three days my gut microbial community remained more or less stable (dots are close together suggesting no major shift in the composition of my gut microbiota).
The green dot represents my first day in the field with the Hadza (for this field session). At this point, I dropped the salads and booze and moved onto a Hadza diet. Since it was late January, we were in the wet season and wild honey and berries were plentiful. I also ate lots of tubers. During this particular field session, the Hadza camps we were working in had very little meat, save the occasional bird. In short, they were basically vegetarians! (As a side note, it’s important to remember that depending on what time of year a particular anthropologists or ethnographer visits a group around the world [now or in the past], seasonality will have a significant impact on the observed foods being eaten at that point in time [this is affect is more pronounced in lower latitudes]. That said, someone visiting the Hadza, say 70 years ago during the same time I was during this field session, would note that their diet was 95% plants. On the flipside, visit the Hadza during November, you would see lots of meat and a different picture of the plant:animal ratio would emerge. I’m just saying).
Drinking some of that flavorful baboon shit laden water.
As the green dot suggests, my gut microbial community looks pretty much like my US-Arusha gut – but that was about to change. As the animated GIF shows my microbial community started to shift – or more specifically, reorganize. With each passing day of eating my new hunter-gatherer vegetarian diet and drinking some pretty suspect water (with the occasional baboon turd floating in it) – and cohabitating/mingling with the Hadza on a daily basis (and covered in Hadza Land soil), I started to look less western.
What’s important to note here is that my gut microbes didn’t start to reorganize during the first few days into a nice little cluster – like we see with my Arusha samples. Instead, I’m all over the place from day to day as my gut lapped up and sampled what was no doubt a mob of new microbes – some sticking around, some didn’t. Since the time points only cover a week or so its not known if 1) I would ever settle down – microbially speaking – or 2) how long that would take. I have no doubt, however, that it would – but not sure if I would ever fall into a Hadza cluster which at this point is still a long way from my moving dots. In addition to my chaotic gut flora during that week, something else and unexpected was happening.
Below is another plot showing how the diversity of my gut microbiota was shifting as well. The dots are organized left to right and represent the day they were taken. Here again you see my three red dots representing Arusha, then the green dot representing my first day in Hadza land on a Hadza diet. While in Arusha and my first day in Hadza land, the diversity of bacteria in my gut were more or less the same. But then it began to decrease. Around days four and five on the Hadza diet it bottomed out before starting to tick slowly upwards. This was totally unexpected.
I originally thought that being in this new, microbially-rich environment, I would quickly acquire a greater diversity of gut bacteria. It’s also important to note that I did not participate in the butchering of any animals during this period, as none were killed. But I have no idea if the messiness of butchering would have contributed to my overall gut microbe diversity. In general it seems the diversity of bacteria I brought with me to the field suffered some losses – possibly some combination of flat out disappearance or at least lowered to levels not detectable by 16s methods. This could also be a function of diet – ie, new substrates for the gut microbes to munch on – or being nudged out by new members acquired from this new lifestyle. In either case, the chaotic reorganizing seen in the first graph above suggests that at least in the first few days my losses – for whatever reason – out paced my acquisition of new members. We know from looking at 100s of Hadza poo samples, that the average Hadza harbors nearly twice the microbial diversity as my US-Arusha gut. That said, even though my diversity was on the upswing by the end of the week, I had a long way to go before acquiring the diversity we see in the average Hadza.
Interestingly, there were some notable shifts in major groups (Phyla) of microbes. The graph below shows how – at the phylum level – three groups of microbes shifted. As you can see the Firmicutes (red bar) were up and down – nothing too exciting. However, Bacteroidetes and Proteobacteria were on the move.
As for the drop in the phylum Bacteroidetes, the Genus Bacteroides seems to account for much of it (see graph below). As discussed in a previous post, Bacteroides are the dominant group of bacteria in the western group. I’ve suggested that this is 1) not a function of our high fat-sugar diet in the west, but rather represents 2) our drop in the quantity and diversity of dietary fiber. If dietary fiber intake goes down, so to does the output of short chain fatty acids from fermentation of that fiber. This results in a less acidic colonic environment. Since many strains of Bacteroides don’t like acidity – and grow better in more alkaline environments – then my new diet of copious amounts of fiber from roots and berries would have made my colon more acidic and thus less inviting for Bacteroides. However, I ate virtually no meat during this period so that complicates things a bit – if meat/fat/protein is an important variable. Note our Hadza data reveal that the Hadza harbor virtually no Bacteroides – even during periods of high meat consumption. However, I did eat mountains of yummy wild honey – larvae and all. On some days I suspect my caloric haul from honey alone ranged from 1,000 to 3,000 calories. Some days I felt like I was going to barf from eating so much honey! Add to this daily handfuls of sweet berries, I was literally bouncing around the landscape.
The significant increase in Proteobacteria can be attributed to a jump in the Family of Enterobacteriaceae. This Family of gram-negative microbes include many harmless symbionts, but also includes some well-known and potentially harmful bugs like e. coli, salmonella, shigella, yersinia, and so on. By the last day of sampling, this group of bacteria accounted for an astounding 50% of all the bugs in my gut. Maybe I should have cut back on the baboob shit water – but not sure of the source, yet. At this point we aren’t sure if the increase in my Proeobacteria is harmful or helpful. Stay tuned.
Another interesting shift was also noted in the relative abundance of the genus Akkermansia. Akker has been getting a lot of ink lately in peer-review journals as its been shown to negatively correlate with obesity (ie, more Akk is a good thing) and other measures of metabolic health. As a mucin-degrader, Akker helps turn over the mucus layer lining your large bowel and as such, clings closely with your mucus barrier. My Akker levels went from low to none to being a dominant player (though fluctuating).
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My shifting levels of Akker is interesting when you consider the gut bacteria of fasting/hibernating animals like squirrels and periodic-eating pythons is dominated by Akker – or at least Akker increases during periods of reduced nutrient availability. One of the things you quickly notice when on a Hadza diet is that your hungry – not starving or in want of food all the time – but you always feel a little hungry. Interestingly, the Hadza don’t jump up in the morning and start eating – remember they don’t have refrigeration and limited to no storage. Unlike us westerners who start eating literally the minute we get up – and graze nearly continuously on something throughout the day, the Hadza don’t.
I’m gonna go out on a limb here and suggest that the Hadza – and presumably our ancestors – were periodically fasting. No news here, but… I don’t mean starving (like argued in the Thrifty Genome Hypothesis) and I don’t mean going all day without food – there’s plenty of food in Hadza land. Plenty. But rather they don’t immediately solve hunger pangs by opening a bag of chips as it takes just a little bit of effort to get some food and sometimes you delay your desire to eat because of it. This little bit of extra time between mouthfuls is what I mean by intermittent fasting in the case of the Hadza and what I experienced when I was following the diet. Note that I don’t think my Akker levels had anything to do with caloric intake, as I was awash in sugary calories thanks to berries and wild honey (and fat from the larvae). Which is odd as Akker seems to be associated with how much is coming down the pipe everyday. That is, less substrates in the colon equals greater levels (relative abundance) of Akker.
So, unless my increased levels of Akker are being triggered by something from my new diet and/or somehow I was acquiring them from the environment, then I suspect my presumably beneficial increase in Akker had to do with my new foraging lifestyle. Makes you wonder if there might be something to the idea of intermittent fasting – but maybe more correctly thought about from a foraging perspective, not the starve yourself for a day that many put forward in a dizzying number of diet books. It’s also interesting to consider that my new high fiber diet, which was minimally processed, may have mechanically scrubbed more Akker from my intestinal wall than my previous diet. This scouring effect would have resulted in more Akker in my stool and thus more overall abundance. Just a thought – would be worth testing at some point.
Stay tuned – more experiments to follow.
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