Improving your gut flora: what fibre, plant variety and fermented food really change, and what a gut scan measures

In this article you read what has really been measured about improving your gut flora: what shapes the composition, what fibre and plant variety change, what fermented food and probiotic supplements do, and how long it takes before the picture comes back after a course of antibiotics. That matters, because almost everything written about improving your gut flora promises more than the measurements carry, and the few things that are well measured are things you can do something with this week. The gut scan from BioProfile measures how much you notice of your gut complaints, and gives you an indication of where you stand today in this area, as the first of the 11 health areas the full scan assesses. This is not a diagnosis. It is insight, to see where you stand today, and to help you make better choices in your food and your way of living. What this scan does not do: point to a cause. Only a doctor can say what is going on.

Improving your gut flora: what shapes the composition

An estimated 1,000 different species of micro-organisms live in a single person.⁠⁴ One of the largest Dutch studies of what shapes the gut flora set the gut microbiomes of 8,208 people from a 3-generation cohort of 2,756 families against 241 host and environmental factors. This produced 7,519 associations with diet, socio-economic factors, the early-life exposome and the current exposome.⁠¹ Only about 6.6 percent of the taxa turned out to be heritable, while living together significantly explained the variance of about 48.6 percent of the taxa.⁠¹

In plain words: what you have inherited counts for much less than what you eat and who shares your kitchen. That is the useful part of those numbers, because a routine at home and a shopping list are things you can change.

Fibre, the best measured factor

Adult women need at least 24 grams of fibre a day and adult men at least 30 grams, a guideline built on the energy requirement at 3.0 to 3.5 grams of fibre per megajoule per day, and many people in the Netherlands do not get enough.⁠⁵ A series of systematic reviews and meta-analyses covering 135 million person-years from 185 prospective studies and 58 clinical trials with 4,635 adult participants compared the highest with the lowest intakes of dietary fibre: the observational data show a 15 to 30 per cent lower all-cause mortality, and the risk reduction across a range of critical outcomes was greatest at a daily intake between 25 and 29 grams.⁠²

What that means for you: the Dutch guideline and the intake with the greatest measured benefit lie close together, so the goal is a single number you can count instead of a whole diet.

What fibre does to the bacteria themselves has been pooled from 64 randomised controlled trials with 2,099 adult participants in good health. Fibre significantly increased the amount of Bifidobacterium spp. and Lactobacillus spp. in the stool compared with the control group, with fructans and galacto-oligosaccharides giving the largest amount of both, and the butyrate concentration in the stool rose, while no significant effect on bacterial diversity was seen.⁠³ A fibre-rich pattern with enough vegetables, fruit, wholegrain products, nuts and pulses encourages the presence of bacteria that ferment fibre.⁠⁴

So more fibre shifts which bacteria are abundant and what those bacteria make. The number of different species stayed the same in those studies. A bloated stomach is a symptom in its own right with its own causes, and those causes are set out in the causes of a bloated stomach and what a gut scan measures.

Plant variety and fermented food

In a citizen science dataset of 15,096 samples from 11,336 participants, with a reference date of May 2017 and mostly from the United States, the United Kingdom and Australia, eating more than 30 types of plants a week was associated with likely fermenters of short chain fatty acids, including sOTUs that probably belong to the species Faecalibacterium prausnitzii and to the genus Oscillospira. Compared with people who ate 10 or fewer types of plants a week, that same group had a significantly lower amount of antibiotic resistance genes for aminoglycosides, chloramphenicol and major facilitator superfamily transporters.⁠⁶

Read that as a second dimension next to grams: this measure counts types of plants, and a herb, a handful of nuts and a spoon of lentils each count as one.

Fermented food has been tested directly against fibre. In a randomised 17 week study in adults in good health, with 18 people per arm, a diet rich in fermented products was set against a diet rich in plant fibre, with immune status as the subject. The arm with fermented food showed a steady increase in the diversity of the gut microbiota over the 17 weeks, while the arm with a lot of fibre showed a stable diversity of the microbial community over the same period and an increase in microbiome encoded glycan degrading carbohydrate active enzymes.⁠⁷

The two arms moved in different ways: fermented food widened the community, fibre changed what the community can break down. Each arm counted 18 people, so read this as a direction rather than as a fixed effect size.

What probiotic supplements do, and what the supplements do not do

A review of 45 studies in adults in good health, published between 1990 and August 2017, found that taking probiotics can lead to a temporary improvement in the concentration of supplement specific bacteria in the gut microbiota. That same review fell short of supporting that probiotics cause lasting changes in the gut microbiota in adults in good health.⁠⁸

In plain words: as long as you take a supplement, the bacteria from the capsule show up in your gut. Once you stop, nothing in this review shows that the change lasts.

After a course of antibiotics

In total, 12 men in good health were followed for 6 months after a 4 day course of 3 antibiotics: meropenem, gentamicin and vancomycin. The gut microbiota came back to close to its baseline composition within 1.5 months, and 9 common species that were present in all subjects at the start were still undetectable in most subjects after 180 days.⁠⁹

For a reader that is two answers in one: most of the community is back after about six weeks, and part of what was there is still missing half a year later. It also shows why a reset button for the gut has never been measured.

What a gut scan measures, and what a gut scan does not measure

The gut scan asks about your gut complaints over the past two weeks. Every answer is given points, the points are added up into a gut score with the reading band the score falls in, and higher is better. What you get is a picture of how much you notice of these complaints, plus a starting value you can repeat and compare in two weeks.

What a series of questions cannot do is name the composition of your gut flora, and even a laboratory number would say less than it seems: because it is not yet clear enough what the relationship is between the precise composition of the microbiome and health, it is too early to conclude that certain foods can influence health through the microbiome.⁠⁴ A score is therefore a reading of your own complaints over two weeks. It is not a diagnosis. Naming a cause is work for a doctor.

Some signals belong with a doctor rather than with a score. Call the same day if you have stomach pain with a fever of 38 degrees or higher, or pain in the lower right of your stomach. Call on a working day if the stomach pain does not go away or slowly gets worse, if you poo differently from usual, or if your weight goes down without you knowing why.⁠¹⁰ Those rules come from Thuisarts, made by doctors and writers according to the guidelines of the Nederlands Huisartsen Genootschap (NHG).⁠¹⁰

In summary

Your gut flora is shaped far more by what you eat and who you live with than by what you have inherited. Fibre is the best measured factor, and the Dutch guideline and the intake with the largest measured benefit lie close together. Counting types of plants adds a second dimension next to grams, fermented food broadened the community in a small randomised trial of 17 weeks, and probiotic supplements showed up in the gut for as long as the supplements were taken. After a short course of antibiotics most of the community came back within weeks, while part of it was still missing half a year later. A gut scan gives you a reading of your symptoms and a baseline to compare against. It is not a diagnosis, and the signals above belong with a doctor.