Sorry low carbers, your microbiome is just not that into you-term life


I recently posted a scatter plot (below) on Facebook/Twitter of preliminary metadata that we are accumulating as part of the American Gut project – which includes, among other things, a questionnaire of 50 + questions and a 7 day food journal. Plotting participants self-reported height, weight, and 7 days of dietary info (recorded using an online calorie counter), we can plot low carbpercentage of daily calories from fat (all sources) against body mass index (BMI) – which we calculate from the height and weight of the participant. While the data is of the dreaded self-reported kind, the lack of any significant correlation between % of daily calories from fat and BMI, is still very interesting (note even if you remove the various obvious outliers, the correlation – or lack of – is the same). In other words, as fat goes up in the diet, BMI does not per se. (Note we just started sequencing poo samples. Will be able to see how the metadata correlates with the microbial data in a few months – stay tuned).

As I look at the preliminary generic metadata (below) and follow the conversation around the benefits of a low carb diet, I continue to be concerned about the low-carbers gut microbiota (note I eat meat daily, so my diet is high in fat, animal protein – but also dietary fiber – as I eat a large diversity and qty of plants. Though I don’t consume many grains in any form). While there is no denying the wonderful results many people enjoy on a low (and even lower) carb diet – specifically weight loss, which is well-documented now in the peer-review research – the impact on the gut microbiota is not well understood. As we can see from our accumulating metadata (ultimate goal is 20,000 participants – we are at 6,000 now – with complete metadata on ~1,000 so far), we are likely to have a decent sample of low carb dieters (hopefully). This data will allow us to compare the gut microbial communities of this population against other dietary strategies. (But again, please note we have not completed sequencing of low, low carb eaters and so are not presenting any of that data [the plot is just metadata on fat and BMI – which tells us nothing about gut health of the various dots in the plot]. The following discussion is based on some general observations based on the existing literature about fermentation, pH, and its impact on the gut microbiome).

Screen Shot 2013-06-27 at 6.34.28 AMPlease note the data in the plot above is self-reported and preliminary. As with all self-reported data, its not ideal. As data points are added over the coming months, will be interesting to see if the (lack) correlation holds. The average age of the persons in the plot is 46 – the youngest is 2, the oldest is 90. 55% are female, 45% male. ~99% are from the U.S. The point of showing this particular plot is that “these particular data” do not show any correlation with fat intake as a % of calories and BMI. Again, this has NOTHING to do with gut bacteria – at the moment – just an interesting “lack” of correlation (and should be interesting/useful for those following a HF diet).

Depending on whom you talk with, a low carb diet is many different things to many people. I think most misinterpret a Paleo or Primal lifestyle as somehow low carb. It can be, but most folks eat a diversity and quantity of whole plants that exceed that of the average American – often by a long shot. It can sometimes be a little low carb-like due the absence of high caloric foods made from grains. But I often find people who skip grains, sugar and the like as really paying attention to whole plants in their diet – which is, of course, a good thing. But a bona fide low, low carb eater is another animal all together. Whether you draw that line at 25, 50, or 75g a day of carbs, its low I’m afraid from the perspective of your gut bugs. Especially if those carbs contain a limited amount of resistant starch and other dietary fibers – food for gut bacteria.

That said, even though someone who eats as much as 200-500g of carbs a day can still be starving their guts bugs if those foods contain little to now indigestible substrates (fiber), a generic rule of thumb (albeit an ugly measure) is less overall carbohydrates – especially when you start dropping below 75-100g a day – translates into a dramatic drop in the amount of food reaching your colon where the vast majority of your intestinal microbial community resides. (There are exceptions to every rule, but follow my logic for a moment).

When it comes to the health and well being of your gut microbes, nothing matters more than fermentable substrates (You can read about here,– you get the idea). As the rules/tenants of basic microbial ecology go, a reduction in fermentable substrates derived from carbohydrates means less energy sources for the microbes – who depend on host-derived substrates as well, as in the case of mucin-degraders like Akkermansia. As fermentation drops, so to does the byproducts of fermentation which include short chain fatty acids (primarily acetate, butyrate, propionate), organic acids, and gases like hydrogen. All of this can and will dramatically shift the pH of the colonic environment. As it stands in a healthy or normal gut, the pH of the colon changes from proximal to distal end, being more acidic in the proximal (front) end than the tail end – mainly as a function of more rapid fermentation as food items empty from the small intestine. As the pH shifts to being more alkaline from less fermentation, a number of shoes begin to drop (or can).

A less acidic environment means acid sensitive groups of bacteria, like those in the Phylum Proteobacteria, which includes a who’s who of bad guys like strains of E. Coli, Salmonella, Vibrio, Helicobacter, might bloom – not a good thing. You see the same blooms following antibiotic treatment

In addition, as pH shifts away from acidic, the genus Bacteroides can also bloom as well, gaining an ecological niche in this less acidic environment courtesy of a low carb diet. For those of you keeping score, many talk about the American gut in general being dominated by Bacteroides as a function of our high fat, high sugar diet. The reality is, it might have to do with what we are not eating – dietary fiber (of all kinds). The all-important butyrate producers Roseburia spp. and Eubacterium also drop in abundance as pH shifts away from acidic as well. A drop in fecal butyrate and butyrate producing bacteria was demonstrated in an elegant study comparing diets of varying amounts of carbs. Given the importance of butyrate in colonic health, any dietary strategy that potentially shifts pH away from acidity as a function of reduced fermentation, might contribute to various forms of IBD.

So, low carb equals a less acidic colonic environment due to the drop in fermentation (and I presume harder, and less frequent stools as a function of reduced biomass from bacteria – or maybe not). As pH shifts, prospects for opportunistic pathogens increase, as does opportunities for gram-negative bacteria like Bacteroides and Enterobacter. When you add this up – and a lot of more shifts in the microbial ecology of the low carb gut – you most certainly have a classic case of microbial dysbiosis – as the name implies, an imbalance. This dysbiosis can lead to issues associated with IBD, autoimmune disease, metabolic disorders and so on. But again, a large cohort of low, low carb dieters has never been looked at using 16S rRNA methods. So the jury is still out – but will be fascinating to see.

A bit of a paradox in all of this is the increased likelihood that a low carb microbial community will most certainly lead to increased gut permeability – a well-known phenomenon whereby microbial parts (lipopolysaccharides, which leads to metabolic endotoxemia) and whole microbes themselves (bacteremia) leak from the intestinal track into the blood, leading to low-grade inflammation that is at the root of metabolic diseases such as type 2 diabetes, obesity and heart disease. So it is a paradox that a leaky gut that can be triggered from a low carb (high fat) diet – and a possible increase in gram-negative bacteria and a reduction in healthy bacteria like Bifidobacterium – doesn’t result in weight gain as demonstrated in study after study in mice and humans. Weird.

I hope people do not take this as some kind of attack on low carb diets – couldn’t be farther from the truth. There is NO AGENDA. Again, NO AGENDA. (It’s worth noting I consume a high fat, high protein,

high fiber diet). Just wanted to point out some obvious concerns (maybe unfounded) and that if we get a large enough sample of low carb folks in American Gut, we might be able to provide some interesting insight – or not. Who knows, maybe low carb folks have super healthy gut microbiota (whatever that is).

So to my low carb brothers and sisters out there, try and eat a little more fibrous material if you can – diversity matters –  and help your gut bugs help you. It’s what evolution intended.


**If you follow a low (or low, low) carb diet, would be great if you joined American Gut. The more people we have for each dietary group, the more we will hopefully learn.


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