6.8 Diet Change

After a lifetime of enjoying a banana or two almost every day, a microbiome test from DayTwo suggested that I stop eating them. It also said I stop eating most grains, and if I do, to eat them with fat. Generally the recommendations pointed toward me eating a more fat and fewer carbs. So for three months (Dec - Feb) I switched my diet to more of a low carbohydrate high fat (LCHF), with a goal of getting to under 25% carbs and 50% fat. (Figure 6.34)

Summary of the macro nutrients I ate the year before switching to my Goal diet.Summary of the macro nutrients I ate the year before switching to my Goal diet.

Figure 6.34: Summary of the macro nutrients I ate the year before switching to my Goal diet.

This was harder than it might seem. I think of myself as a typical ominivore on a reasonably-healthy American diet: no sugary drinks or fast food, plenty of vegetables, mostly home-cooked with minimal processing. Sure, I make exceptions now and then, but my generally good health and weight level mean I don’t worry too much about what I eat. I thought skipping bread and rice would be enough, but I learned that carbs are everywhere. To get under 25%, I’m allowed only 65g/day. Just my morning latte is 15g. A single banana is 23g, and if you add one more apple (22g), I’m over my daily limit. You can easily add fat: a tablespoon of olive oil (13g) or a tablespoon of butter (11g) won’t seem like much food, but it adds up quickly. The problem, I found, is that fatty foods also tend to fill me up, so I eat less. And as a percentage of my calories, that means I’m allowed even fewer carbohydrates.

But I persevered. I’m not going to claim I was perfect – I’m doing this experiment for fun, not for serious scientific research – so there were days when I indulged differently. Still, just making a conscious effort was enough to push my eating habits in the general direction of less carbs, more fat. And soon I began to notice some effects.

Three months into the new diet, I noticed my sleep had changed slightly: I seemed to be sleeping longer and feeling better, from an average of 25 minutes extra per night – a 5% improvement. (see Figure 6.35) Could this have a microbiome explanation?

My sleep duration apparently increased by about 5% after switching to the new diet.

Figure 6.35: My sleep duration apparently increased by about 5% after switching to the new diet.

To find out, I compared four gut microbiome samples taken after starting the new diet with four taken before. (Table 6.3)

Genus level differences before and after a change of diet.

Figure 6.36: Genus level differences before and after a change of diet.

Table 6.3: Phylum level abundances before and after a change to a low carb, high fat diet.
Regular Regular Regular Regular LCHF LCHF LCHF LCHF
Firmicutes 43.76 67.37 62.27 64.54 52.70 51.03 51.58 52.78
Bacteroidetes 29.11 25.28 30.58 27.20 23.31 34.56 27.30 31.26
Verrucomicrobia 21.55 1.82 2.26 3.24 17.93 6.94 13.05 7.17
Proteobacteria 4.10 2.76 2.72 2.50 4.15 3.00 4.08 4.77
Euryarchaeota 1.76 2.51 2.14 2.39 1.80 3.35 3.76 3.00

Note the substantial difference in the level of Firmicutes (Table 6.3). All of the LCHF samples seem to have Firmicutes just slightly over 50%, whereas three of the four “Regular” samples are much higher. Is that a coincidence? Is it statistically significant?

To find out, I looked at all my gut samples from the previous six months, when I was on my “regular” diet, a total of 72 samples. The average (mean) abundance of Firmicutes in those samples is shown in Table 6.4, plus the output of a simple T-Test that shows the likelihood that the difference could be due to chance alone.

Table 6.4: Mean Abundance of Regular Samples Compared to Low Carb/High Fat
Regular (Ave) LCHS
60.21 52.02
## 
##  Welch Two Sample t-test
## 
## data:  f$abundance and ff$abundance
## t = 6.4034, df = 65.885, p-value = 0.00000001848
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##   56344.51 107402.49
## sample estimates:
## mean of x mean of y 
##  602076.0  520202.5

The extremely low p-value (0) implies that the difference in sleep is unlikely to be due to chance. P-values have serious problems as a way to measure whether something is statistically significant, but as a sniff-test, in this case the value is so low that it’s worth investigating further.

Incidentally, among those Regular samples there were a few with under 50% Firmicutes abundance, but were easily explained: for example, three of them happened after my Soylent experiment.

Conclusion: A low-carb high fat diet can affect Firmicutes abundance.


What about after my diet. Did things bounce back to normal? Although I’m more conscious of what I eat, and do generally try to eat fewer carbs (e.g. I’ve stopped all banana eating), I wouldn’t say I keep to the diet as rigorously as I did. But here are the results from the tests I took after finishing the experiment:

2018-02-11 2018-02-12 2018-02-16 2018-02-20 2018-02-26 2018-03-15 2018-03-25 2018-03-29 2018-04-02 2018-04-03 2018-04-10 2018-04-17 2018-05-10 2018-09-18 2018-11-14 2018-12-10 2019-02-18 2019-03-24 2019-05-01
Firmicutes 51.58 52.78 55.32 55.66 58.80 58.47 49.91 35.29 43.69 60.06 63.29 42.10 51.72 56.24 54.51 49.66 32.56 50.63 34.79
Bacteroidetes 27.30 31.26 22.50 32.96 33.44 30.31 26.44 26.83 30.79 24.85 25.83 35.76 24.63 25.75 25.03 26.09 34.20 32.70 26.42
Verrucomicrobia 13.05 7.17 14.02 4.41 2.31 2.54 16.18 23.09 19.95 10.56 4.50 18.14 18.38 11.94 13.84 18.03 20.73 8.27 30.23
Proteobacteria 4.08 4.77 3.78 4.74 3.56 5.93 3.67 13.33 2.58 2.64 3.54 1.50 1.13 2.49 2.30 3.33 11.40 3.55 5.03
Euryarchaeota 3.76 3.00 3.77 1.98 0.33 1.76 3.15 2.15 1.30 4.13 5.68 3.10 2.28 3.12 4.02 2.59 1.42 5.64 4.34
Actinobacteria 1.95 1.82 1.43 1.07 1.18 1.96 2.96 0.78 1.92 1.27 1.85 2.02 3.84 2.94 3.46 2.30 0.80 4.23 1.91
Synergistetes 1.10 1.27 1.90 0.33 0.40 0.27 0.67 0.50 0.69 0.31 0.40 0.43 0.22 0.39 0.74 0.53 0.21 0.33 1.49
Lentisphaerae 0.78 0.88 0.92 0.55 0.31 0.40 0.13 0.12 0.36 0.32 0.52 0.05 0.08 0.23 0.11 0.05 0.08 0.26 0.10
Tenericutes 0.15 0.04 0.12 0.25 0.00 0.11 0.03 0.06 0.00 0.00 0.06 0.00 0.00 0.01 0.00 0.00 0.02 0.02 0.01
Fibrobacteres 0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.01 0.00 0.02 0.00 0.00 0.00 0.01 0.00 0.00 0.01 0.00