The Gut Health Cookbook
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The Gut-Health Top Ten.

Ten of the gut bacteria researchers talk about most, what each one is known for, and the foods linked with them.

By Michael Vestri, author of The Gut Health Cookbook. General information, not medical advice.

Before you start: food can't target one species precisely, and everyone's gut is different. The best-supported approach is the general one: plenty of fibre, a wide variety of plants and some fermented foods. The list below shows why that works, microbe by microbe.

  1. Bifidobacterium

    One of the first groups to colonise the gut in infancy. Bifidobacteria ferment fibres such as those in oats, bananas, onions and garlic, and some strains are among the most studied probiotics.1

    Linked foods: live yoghurt, kefir, and prebiotic fibre from oats, bananas, onions, leeks and garlic.

  2. Lactobacillus

    A group of lactic acid bacteria (now split into several genera) found in many fermented foods. They turn sugars into lactic acid, which is what gives yoghurt and sauerkraut their tang.2

    Linked foods: live yoghurt, kefir, sauerkraut, kimchi, and unpasteurised fermented pickles.

  3. Akkermansia muciniphila

    Lives in the mucus layer that lines the gut. Higher levels have been associated with better metabolic health, and a small trial of an Akkermansia supplement in people with insulin resistance showed promising early results.3

    Linked foods: polyphenol-rich foods such as cranberries, pomegranate, green tea and dark chocolate, alongside fibre.

  4. Faecalibacterium prausnitzii

    One of the most abundant bacteria in a healthy adult gut and one of the main producers of butyrate, the fuel for the cells lining the colon. Lower levels have been found in people with Crohn's disease, which first drew researchers' attention to it.4, 5

    Linked foods: fibre from oats, beans, lentils, leeks, asparagus and wholegrains.

  5. Roseburia

    Another major butyrate producer. In studies, cutting fibre and carbohydrate tends to reduce Roseburia and its relatives.5

    Linked foods: wholegrains, nuts, seeds, lentils, and resistant starch from cooked and cooled potatoes or rice.

  6. Ruminococcus

    Ruminococcus bromii has been described as a keystone species for resistant starch: it starts the breakdown that other bacteria then build on.6

    Linked foods: cooked and cooled potatoes and rice, slightly green bananas, beans, lentils and wholegrains.

  7. Prevotella

    Often more common in people who eat a fibre-rich, plant-based diet. A well-known study found it in children eating a traditional rural diet in Burkina Faso but not in children in Italy.7

    Linked foods: high-fibre plant foods, beans, lentils and wholegrains.

  8. Streptococcus thermophilus

    One of the two classic starter cultures used to make yoghurt. Live cultures in yoghurt help people who have trouble digesting lactose to digest it better.2

    Linked foods: live yoghurt and kefir.

  9. Bacillus coagulans

    A spore-forming bacterium, which helps it survive stomach acid. It is studied mainly as a supplement, for example for bloating and other digestive symptoms, and is found in a few fermented foods.8

    Linked foods: some fermented foods and specific probiotic products.

  10. Clostridium butyricum

    A butyrate producer used as a probiotic in parts of Asia. Not to be confused with its harmful relatives: this species is studied for its role in supporting the gut lining.9

    Linked foods: fermented vegetables and resistant starch foods.

The common thread

Look at the foods again and the pattern is clear: fibre, variety, polyphenols and live fermented foods. That is exactly how the recipes in the book are built.

Sources

  1. Hill C et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology, 2014. doi.org/10.1038/nrgastro.2014.66
  2. Marco ML et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology, 2021. doi.org/10.1038/s41575-020-00390-5
  3. Depommier C et al. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nature Medicine, 2019. doi.org/10.1038/s41591-019-0495-2
  4. Sokol H et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. PNAS, 2008. doi.org/10.1073/pnas.0804812105
  5. Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiology Letters, 2009. doi.org/10.1111/j.1574-6968.2009.01514.x
  6. Ze X, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. The ISME Journal, 2012. doi.org/10.1038/ismej.2012.4
  7. De Filippo C et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. PNAS, 2010. doi.org/10.1073/pnas.1005963107
  8. Majeed M et al. The effects of Bacillus coagulans MTCC 5856 on functional gas and bloating in adults: a randomized, double-blind, placebo-controlled study. Medicine, 2023. doi.org/10.1097/MD.0000000000033109
  9. Stoeva MK et al. Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease. Gut Microbes, 2021. doi.org/10.1080/19490976.2021.1907272
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