Feeding the keystone bacteria

Which foods promote Faecalibacterium, Ruminococcus bromii, Lachnospira and Akkermansia, how well this is shown in humans and why it does not work the same for everyone.

How solid is the research? Promising

Small randomised studies in humans show that certain fibres increase certain keystone species, for example inulin and Faecalibacterium, or resistant starch and Ruminococcus bromii. Whether this alone relieves symptoms or protects against disease has barely been studied. For pectin, the findings on the gut flora so far come from lab experiments and one animal study.

Healthy state

The chapter on Anaerobes Bacteria that live without oxygen. For strict anaerobes oxygen is even toxic; they make up the large majority of the gut flora. More in the chapter “Anaerobic gut bacteria: why the good ones do not fit in a capsule” gut bacteria explains who the oxygen-shy keystone species are and why they can hardly be swallowed as a capsule. This chapter covers the other side: what they eat. Each species has its own toolbox of enzymes and can only break down certain sugar chains. The work is shared out as in a kitchen: specialists crack the tough fibres, others use the fragments, and at the end Butyrate A short-chain fatty acid and the main energy source for the cells of the colon wall. It strengthens the barrier and dampens inflammation. More in the chapter “Butyrate and other short-chain fatty acids” producers turn intermediate products such as acetate and lactate into butyrate. If you want to promote a particular species, you need to know where it sits in this chain.

Faecalibacterium prausnitzii is the flagship among butyrate producers. In the lab, almost all strains tested grew well on apple pectin and held their own against other pectin users. It also uses acetate, which bifidobacteria make from fructans. In humans this is best shown with inulin: 10 g of inulin a day increased Faecalibacterium in a small study of 12 people, and 16 g of a mix of inulin and oligofructose over three months did so in 30 women with overweight, together with bifidobacteria. Mildly acidic conditions, as created by fermentation, suit it: in lab experiments it outcompeted Bacteroides at a pH of 5.5. Bile acids Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea”, on the other hand, it tolerates poorly.

Pectin is the clearest example of targeted feeding. In fermentors with the stool flora of three people, apple pectin mainly promoted Lachnospira eligens, a bacterium that responds almost only to pectin, while inulin stimulated several other species. Diversity stayed higher with pectin. The researchers stress that such effects only show at the level of individual species and strains and are hard to predict. In rats, apple pectin sped up the recovery of the Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity” after a strong course of antibiotics: oxygen-shy Lachnospiraceae returned faster and enterobacteria declined faster. In humans, the effect of pectin on the gut flora has not yet been tested in studies. Which pectins exist and how fast they are fermented is covered in the chapter on Prebiotics Food components, usually certain fibres, that specifically feed beneficial gut bacteria, such as inulin or GOS. More in the chapter “Prebiotics that build up gently” beyond inulin.

Resistant starch has its own door-opener: Ruminococcus bromii. In the lab, of four important starch users it was mainly this one that could break open the tough starch granules, and only with it did the others get at the food. Stool from a person without R. bromii barely fermented cooked and cooled starch until it was added. Experts call this a keystone species. In a controlled diet study of 14 men, the share of its relatives rose to 17 percent on average on a starch-rich diet, compared with just under 4 percent on other fibres. Eubacterium rectale (now Agathobacter rectalis), a butyrate producer, also increased. Even small differences in the structure of the starch matter: natural resistant starch promoted R. bromii and E. rectale, chemically modified starch rather bifidobacteria and Parabacteroides. In another study such details decided whether more butyrate or more propionate was made; more than about 35 g a day brought no additional effect there.

Two groups work in the background. Anaerobutyricum hallii (formerly Eubacterium hallii) and Anaerostipes use lactate released by bifidobacteria and lactic acid bacteria and turn it into butyrate. Faecalibacterium, Roseburia and Eubacterium rectale can hardly do this. The lactate users are therefore an important link so that lactate does not pile up. Akkermansia A gut bacterium that lives on the mucus of the gut wall and stimulates its renewal. In studies, high levels often go along with good metabolic health. More in the chapter “The mucus layer and additives”, in turn, lives mainly on the mucus of the gut wall, not on fibre. It is promoted rather indirectly: in half of the studies in a Meta-analysis An analysis that combines the results of several studies. It is only as good as the studies it includes. on polyphenols from berries, cocoa, tea and coffee, Akkermansia increased. The diabetes drug metformin is also linked to more Akkermansia.

Each keystone species has its own food: starch for Ruminococcus bromii, pectin for Lachnospira, inulin for bifidobacteria. Faecalibacterium feeds off pectin and off the bifidobacteria, and in the end butyrate is made.

Disrupted state: causes and effects

The same diet does not work the same for everyone. In the diet study of 14 men, samples differed more by person than by diet, even though individual groups bloomed quickly after a change of diet. In 174 adults, resistant potato starch raised butyrate mainly in those who already had suitable butyrate producers. If a keystone species such as Ruminococcus bromii is missing, its food largely goes unused. So if you do not respond to a prebiotic, you have not necessarily done anything wrong; you may simply lack the right bacteria.

Keystone species can be lost. Fewer carbohydrates lowered butyrate and butyrate producers in the stool in a study of 19 people. In mice with human gut flora, a low-fibre diet made species disappear over generations, and reintroducing fibre did not bring them back. After antibiotics it is similar; more in the chapter on microbial diversity. A fibre can only feed bacteria that are still there.

More fibre does not automatically mean more diversity. In a randomised study of 36 healthy adults, a high-fibre diet gave the gut flora more fibre-degrading enzymes, but diversity did not rise, and how the immune system responded depended on diversity at the start. In the same study, fermented foods increased diversity. If you want to promote your keystone species, you probably need both: the right food and enough different species to use it.

More of one species is an intermediate result, not yet a benefit. In a Belgian population study, people with a lot of Faecalibacterium and Coprococcus rated their quality of life higher, and Coprococcus was less common in depression. People with a lot of Akkermansia had healthier metabolic values before a calorie reduction and benefited more from it. These are associations, not proof that the bacteria are the cause. Whether it helps to increase these species on purpose has barely been tested. A kiwifruit product raised Faecalibacterium in nine people with constipation from 3.4 to 7 percent; it was a commercial product tested in a very small group.

And targeted feeding can cause symptoms. Inulin and oligofructose count as FODMAP Short for fermentable sugars and sugar alcohols that are poorly absorbed in the small intestine, such as fructans, lactose, fructose and sorbitol. More in the chapter “Doing low-FODMAP right” and often cause bloating in a sensitive gut; pectin and resistant starch are usually fermented more slowly. How to introduce fibres gradually is covered in the chapter on gentle prebiotics. In Crohn's disease with narrowed sections of the gut, coarse fibres can become a problem.

If the keystone species is missing, its food goes unused: without Ruminococcus bromii, resistant starch hardly becomes butyrate.

What often helps

Lifestyle

Diet, exercise, sleep, social contact and dealing with stress.

A food for each keystone species Cooled potatoes, rice and pulses provide resistant starch for Ruminococcus bromii. Apples, carrots and citrus fruit provide pectin for Lachnospira and Faecalibacterium. Onions, leeks, chicory and Jerusalem artichoke provide inulin for bifidobacteria, which Faecalibacterium feeds off. Berries, cocoa and tea provide polyphenols, which are linked to more Akkermansia. Rotating over the week is easier than eating everything every day. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [1][2][3][4]
Low-fibre diets not for the long term Low-carb, keto or strict elimination diets take food away from the keystone species. Fewer carbohydrates lowered butyrate and butyrate producers in one study, and in mice species were even lost permanently over generations. If you eat this way for other reasons, plan in fixed sources of fibre, such as vegetables, nuts, seeds and berries. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [5][6]
After antibiotics: food first, then capsules After a course of antibiotics, the oxygen-shy species have to come back. In rats, apple pectin sped up this recovery, while a probiotic delayed it in a study in humans. A varied, fibre-rich diet in the weeks afterwards is therefore a sensible approach, even though human studies on this are lacking. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [7][8]

Natural supplements

Supplements do not replace a medical check-up. Discuss dosage and interactions with your doctor or pharmacist.

Inulin or oligofructose, in small doses The best evidence in humans for increasing bifidobacteria and Faecalibacterium: in two small studies, 10 g of inulin or 16 g of a mix a day worked. Both count as FODMAPs and often cause bloating in a sensitive gut. Start with 2 to 3 g and increase slowly; with IBS, choose more slowly fermented fibres instead. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [2][9]
Pectin as targeted food In the lab and in rats, apple pectin specifically promoted oxygen-shy butyrate producers such as Lachnospira and Faecalibacterium. Whether the same happens in humans has not yet been tested in studies. For IBS with diarrhoea there is a first randomised study with 24 g a day. If you try it, start small and drink enough with it. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [3][10][7][11]
Resistant potato starch needs its door-opener Raw potato starch, stirred into cold food, provides resistant starch for Ruminococcus bromii and raised butyrate the most in a large study. Heating makes the starch digestible again. If you lack the right bacteria, you will notice little; then a different fibre is a better bet. Start small, or it will cause bloating. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [12][1][13]

Medical treatments

Information, not a treatment recommendation. Decide together with a doctor. Approval and availability differ from country to country.

Metformin is not for the gut flora Metformin is linked to more Akkermansia, but it is a diabetes drug. It can cause diarrhoea and nausea and, in the long term, vitamin B12 deficiency. Without diabetes or a prescription, it is not a way to grow gut bacteria. If you take it, have your vitamin B12 checked regularly. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [14][15]
Crohn's disease with strictures: discuss fibre Where the gut is narrowed, coarse, fibrous foods can cause symptoms or get stuck. The European nutrition guideline then advises a soft, adapted diet rather than cutting out fibre across the board. If you have Crohn's disease, discuss new fibres and powders with your care team first. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [16]

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How we rate the evidence

Trust score 5 of 5:Established: Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies.
Trust score 4 of 5:Well supported: Several randomised studies in humans with largely consistent results.
Trust score 3 of 5:Promising: Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies.
Trust score 2 of 5:Plausible: Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms.
Trust score 1 of 5:Experimental: Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.

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