Your Gut Can Change Rapidly in Response to Diet

Most of us have probably dieted at one time or another- usually to lose weight, but sometimes for other reasons as well. You might have even tried one version or another of an “extreme diet”, maybe because you wanted to lose weight fast because nothing else seemed to work, or because of dietary restrictions or choices, or certainly you may have patients that have tried them. So what are extreme diets? Extreme diets are any type of diet that is unbalanced when viewed through the lens of human nutritional needs. They can be either very high or very low in fat, carbohydrates or protein. They might be diets that severely restrict calories. Vegan and raw diets can be classified as extreme diets. Even more extreme diets, like all juice diets, binging on one particular food, like celery, are at the far side of the spectrum. It’s not that extreme diets are intrinsically bad, they can be potentially healthy for the right person or the right situation, but they can also be easily mishandled, or wrong for many people. 

One thing that is becoming increasingly clear is that what you eat determines the composition of flora in your microbiome which in turn greatly influences your gut health. Many studies have documented how dietary changes can alter your microbiome, including extreme dieting. What’s maybe more surprising is how quickly an extreme diet can change your microbiome. In one study reported in Nature, one group of volunteers ate a diet consisting only of meat, dairy and eggs; while another group ate only grains and vegetables. Within a few days, the subject’s microbiomes had altered somewhat substantially. Another recent study reported in 2022 surveyed wild and urban-dwelling animals of the same species and found that urban-dwelling animals’ microbiomes shared more in common with urban humans’ microbiomes than they did with individuals of the same species living in the wild. The study’s conclusion was that these animals essentially shared the human diet, so their microbiomes had been shaped to be like humans. You are what you eat. Let’s take a look at some various versions of extreme diets and see what they do to the body, and the microbiome specifically.

Severely Restricted Calorie Diet

Severely restricted calorie diets typically allow only 800 calories a day. These diets have been touted for quick weight loss- sometimes medically necessary, and for life extension. A 1935 study in rats found that severely restricting their calories resulted in as long as a 50% increase in their lifespans. This study is controversial, primarily because we don’t know for sure if it can be translated to humans. Other studies have found, however, that severely restricted caloric diets alter the microbiome, which does indeed lead to weight loss. Unfortunately, the alteration of the microbiome in this case also allows the proliferation in the gut of “Clostridioides difficile, a pathogenic bacterium that can lead to severe diarrhea and colitis”. The study appears in the June 23, 2021, issue of Nature. “Our results underscore that the role of calories in weight management is much more complex than simply how much energy a person is taking in,” said Peter Turnbaugh, PhD, an associate professor of microbiology and immunology and a senior author on the study. “We found that this very-low-calorie diet profoundly altered the gut microbiome, including an overall decrease in gut bacteria.” In addition, the study found that the cause of the weight loss was the result of C. difficile. They also found some inflammation, which you’d expect with that microbe, but not as much as might be expected. They cautioned that a longer-term use of the diet could lead to unknown consequences, but that they wouldn’t recommend C. difficil for weight loss. Aside from the lack of calories, it’s very difficult to get enough fiber in an all-liquid diet (and many severely restricted calorie diets are all liquid), and fiber is well known to be a gut regulator. Unless this diet is medically required, it’s probably not a diet to choose.

Juice Diets

Juice diets, also sometimes called cleansing diets, should only be employed for short periods of time. These diets usually require drinking just the juices of fruits and vegetables for a minimum of three days. These diets are not nutritionally balanced, missing out on energy from proteins and fats, and minerals like calcium. Juices also contain very little fiber compared with whole fruits and vegetables. They can also be dangerous for diabetics since they can cause glucose spikes. They also may be very low in calories, and that coupled with low fiber means they could pose risks similar to severe calorie-restricted diets. If continued for too long, they may result in malnutrition and dehydration, since they can increase diarrhea and an imbalance of electrolytes. Those are mostly dangers of staying on juice diets for too long. A study by Henning, et al in 2017 concluded: “In summary, the 3-day vegetable/fruit juice-based diet induced significant changes in the intestinal microbiota which were associated with weight loss. Further mechanistic studies are required to confirm that changes in the microbiota are directly linked to weight loss. The juice-based diet also significantly increased serum and urine NO and decreased a marker of lipid oxidation.” The change in the microbiome that was observed was an increase in Bacteroides, which has been linked to weight loss, and a decrease in Firmicutes, which has been associated with weight gain when found in larger proportional numbers. The study also found that although the diet was only three days long, the effects were still demonstrable in study participants two weeks later. This makes sense given the Nature study that demonstrated how quickly the microbiome can be altered.  The lesson here? Don’t embark on long juice cleanses, keep it shorter, well balanced, and preferably engage under the supervision of an expert.

Raw Diets

Really we’re talking about two or three different diets here: Paleo-raw, meaning that you attempt to recreate a theoretical diet from a primitive era where primarily meats and other proteins are consumed, with barely any carbs, and possibly fewer vegetables. A more extreme version of this diet is to only eat uncooked versions of these foods. The second type of raw diet is a raw vegan or vegetarian diet where meat is eschewed, and only vegetables and grains that can be eaten raw are consumed. The vegetarian version might add in some products from animals that can be consumed raw. The third version would be a raw diet where both animal and vegetable sources are together consumed, but also raw. I’m going to look at these together. Dr. Turnbaugh, who was quoted earlier in this piece when he was discussing his study in Nature, has said that he initially thought there would be no difference in the microbiome between raw and cooked foods. When a colleague questioned that, he decided to test it with a study on mice. What he discovered was that there was indeed a difference- but only for vegetables, not meat: “However, we were surprised to find that there wasn’t a clear distinction in the gut microbiomes of mice fed raw and cooked meat.

In contrast, the microbiomes mice fed raw and cooked tubers were fundamentally different in terms of their structure, transcriptional activity, and metabolic end-products.”

The study team then tried the same experiment with other vegetables and also transplanted the microbiomes into germ-free mice, which surprisingly found that they gained weight and fat. Their most recent project orchestrated and conducted by a team at Harvard was to conduct a similar experiment with humans, which found that “short-term intervention markedly altered the human microbiome and that the changes were distinct between the raw and cooked diets.” Something is going on here for sure, but more research is needed. For now, raw vegetable diets, perhaps combined with animal proteins (or not) look like they could indeed accomplish what they’re attempting to do. Of course, as with all diets, there are risks, and balancing your nutrition is critical.

Ketogenic Diets

Dr. Peter Turnbaugh, who has weighed in on some of the other diets mentioned here, has also investigated ketogenic diets. A UCSF research note on the subject explains that “in ketogenic diets, carbohydrate consumption is dramatically reduced in order to force the body to alter its metabolism to using fat molecules, rather than carbohydrates, as its primary energy source – producing ketone bodies as a byproduct – a shift that proponents claim has numerous health benefits.” Dr Turnbaugh explains why he decided to investigate ketogenic diets: “I got interested in this question because our prior research showed that high-fat diets induce shifts in the gut microbiome that promote metabolic and other diseases in mice, yet ketogenic diets, which are even higher in fat content, have been proposed as a way to prevent or even treat disease,” said Peter Turnbaugh, PhD, a UCSF associate professor of microbiology and immunology, member of the UCSF Benioff Center for Microbiome Medicine and a Chan Zuckerberg Biohub Investigator. “We decided to explore that puzzling dichotomy.” There were several very interesting conclusions: “The researchers observed that as animals’ diets were shifted from a standard diet towards stricter carbohydrate restriction, their microbes also began shifting, correlated with a gradual rise in ketone bodies.” The reason that this is so important is that it shows that even a partial shift to a ketogenic diet could generate ketone bodies- benefits of ketosis might occur gradually. Once the team realized this fact, they next tested whether feeding ketone bodies directly to the mice would alone generate the changes in the microbiome. It did.  “This is a really fascinating finding because it suggests that the effects of ketogenic diets on the microbiome are not just about the diet itself, but how the diet alters the body’s metabolism, which then has downstream effects on the microbiome,” Turnbaugh said. “For many people, maintaining a strict low-carbohydrate or ketogenic diet is extremely challenging, but if future studies find that there are health benefits from the microbial shifts caused by ketone bodies themselves, that could make for a much more palatable therapeutic approach.” Again, more research is necessary, but it appears that even a partially ketogenic diet might shift the microbiome in a positive direction.

Vegan and Vegetarian Diets

Vegetarian diets, where no animals are eaten, and vegan diets, where no animals or any products derived from animals are eaten, may not seem very extreme as far as diets go. As far as the microbiome goes, they are worth taking a look at to see what kind of effect can be seen. In general, it seems as if they have a positive effect on the microbiome: “Additionally, vegans and vegetarians have a significantly greater richness (alpha diversity) compared to omnivores, specifically counts of certain Bacteroidetes-related operational taxonomic units (OTUs) (Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study). It seems likely that many health benefits of vegetarian/vegan diets are, in part, mediated by the gut microbiota—not only through the higher relative abundance of those OTUs that are currently considered to be protective (Bacteroidetes, Prevotella, Roseburia, etc.), but also from postbiotic and epigenetic effects on various risk factors for chronic inflammation and chronic degenerative diseases” (Tomova, et al 2019).

Tomova, et al also mention studies that demonstrate the effect of high animal protein consumption on the microbiome: “For instance, individuals consuming a high animal protein diet, from beef which is also high in fat, displayed lower abundances of bacteria, such as Roseburia, Eubacterium rectale, and Ruminococcus bromii, that metabolize dietary plant polysaccharides (Diet rapidly and reproducibly alters the human gut microbiome. Nature. (2014). Populations of bacteria that increase in response to a high animal protein diet when compared to subjects consuming a meatless diet are typically bile-tolerant microorganisms, such as Bacteroides and Clostridia (Effect of a high-beef diet on the fecal bacterial flora of humans. Cancer Res. (1977). Additionally, a high-protein diet typically limits carbohydrate intake, which may lead to a decrease in butyrate-producing bacteria, and thereby to a proinflammatory state and an increased risk of colorectal cancer”

Similar studies have found that conversely, “Individuals consuming pea protein exhibit increases in beneficial Bifidobacterium and Lactobacillus and decreases in pathogenic Bacteroides fragilis and Clostridium perfringens and, consequently increases in intestinal SCFA levels (Influence of diet on the gut microbiome and implications for human health. J Transl Med. (2017). Likewise, plant-derived proteins have been associated with lower mortality than animal-derived proteins” So plant-based proteins may have a healthier effect on the microbiome, and that is indeed their conclusion: “Current research indicates that diet is the essential factor for human gut microbiota composition, what in its turn is crucial for metabolizing nutrients into active for the host postbiotics. Up-to-date knowledge suggests that a plant-based diet may be an effective way to promote a diverse ecosystem of beneficial microbes that support overall health.” They note as well how complex all of this is and that more research is needed.

Take Aways

So what’s our takeaway from all of this? Well, it’s obvious that research is ongoing, but we can draw a few conclusions. 

• First, our diet definitely seems to affect our microbiome. 
• Second, our microbiome is essential not just for gut health, but for overall health. 
• Third, certain “extreme” diets may indeed be justified- particularly for shorter periods of time to try them out. 
• Fourth,  unless medically restricted, get a normal level of calories, exercise, and watch the research- there are a lot of factors here. 

I haven’t attempted to look at all diets- there are certainly many even more extreme diets, like single food diets- those are likely to not provide enough calories or nutrition and may not be tolerated well by the body. Certainly, they couldn’t be for any length of time. Remember that your gut microbiome can change very rapidly- for better or worse. Consider supplementing with a good probiotic as well. Probiotics have been shown to help restore the composition of the gut.

Monitoring your microbiome

It’s a good idea to take a survey of your microbiome occasionally, particularly if you utilize one of the diets mentioned here or other diets that extremely alter standard consumption patterns. Precision Point Diagnostics offers a number of ways to do so:

Advanced Intestinal Barrier Assessment– The Advanced IBA profile stands out for its unique, clinically relevant markers which tell a complex story about gut barrier health. Histamine and diamine oxidase (DAO) give information about histamine balance and gut mucosal health. Plasma Zonulin is a well-documented marker of intestinal tight junctions and is the preferred specimen for assessment. Lipopolysaccharides (LPS) are endotoxins produced by gram-negative bacteria. LPS antibodies give information about inflammation and intestinal permeability.

GI-MAP™– The GI-MAP stool test utilizes cutting edge, Quantitative PCR technology to provide a true DNA/PCR based stool test. This technology has high sensitivity, specificity and a rapid turnaround. The GI Pathogens section includes Bacterial Pathogens, Parasitic Pathogens and Viral Pathogens.

G-DAP – Gut & Detox Assessment Profile– looks at Zonulin, DAO, Histamine, LPS IgG, IgA and IgM, 8-OHdG, % Reduced Glutathione, Total Glutathione, F2 Isoprostane, Oxidized LDL, HgA1c, hsCRP, & Vitamin D. By analyzing markers of the gut that have been implicated in systemic inflammation and autoimmune conditions, this test can be a good fit for a patient with difficult to diagnose symptoms. Similarly, the inclusion of markers of oxidative stress can also assist the physician to target treatment protocols. Combining these markers with vitamin D can be especially effective for certain populations who are known to be prone to having vitamin D deficiencies. Low vitamin D can interact synergistically with oxidative stress, inflammation, cardiac function, and cancer risk.

GI360™ Profile– is an innovative, comprehensive, and clinically-applicable stool profile, utilizing multiplex PCR molecular technology coupled with growth-based culture and ID by MALDI-TOF, sensitive biochemical assays and microscopy to detect and assess the status of pathogens, viruses, parasites and bacteria that may be contributing to acute or chronic gastrointestinal symptoms and disease.

Comprehensive Stool Analysis with Parasitology– All fundamental building blocks for gut health are included in this profile. While traditional stool tests only look for a few gastrointestinal pathogens, this test evaluates hundreds of different species of microbes to assess the impact on intestinal health. By analyzing parasites in three separate specimens, even hard-to-detect parasites will be uncovered.