III. 2 Fibre: the food of the good bacteria
The freshly engrafted flora needs food day after day, and its favourite food is fibre. In the next three days you learn what kinds of fibre exist, why they matter, and how to bring them into your diet gradually and gently.
If your new gut flora is a freshly planted garden, then fibre is the water that keeps it alive. Fibre is the plant component that we ourselves cannot digest – but our bacteria can, and they live on it too. Over these three days we raise the fibre intake step by step, gently, so that you can feed the engrafting flora without overloading your currently still sensitive digestion. The goal is not the perfect diet in a single day, but for every meal of yours to have a little plant-based base.
What is fibre, and why is this exactly what your flora eats?
Fibre[G] is that part of plant foods – the fibrous structure of vegetables, fruit, whole grains, pulses – that our digestive system does not break down. We used to think this was "useless ballast" that simply passes through us. Today we know that this is precisely the most important food of the beneficial bacteria[G] living in the colon. What we cannot digest, they regard as a feast.
When these bacteria digest the fibre, they produce valuable substances from it that feed and strengthen the gut wall. Fibre of this kind, which deliberately feeds the good bacteria, we call a prebiotic[G] – the concept was introduced by Gibson and Roberfroid in 1995 [113]. It is important that this is not the same as a probiotic: a probiotic contains bacteria themselves, while a prebiotic provides the food of the bacteria. During your course we avoid shop-bought probiotics, but we build in prebiotic fibre gradually and consciously – because this feeds the flora you received with the FMT.
There are two kinds of fibre, and you need both (Eswaran, Muir & Chey 2013 [022]). Soluble fibre (for example in oats, apple, pulses) swells in water, becomes a soft gel, and is a particularly favoured food for the bacteria. Insoluble fibre (in whole grains, vegetable skins) helps the bowel movement more. The point is that, from colourful, varied plant foods, both naturally end up on your table.
There is a special kind of fibre that deserves attention in its own right: resistant starch. This is a starch that "resists" our digestion – it is not absorbed in the small intestine, but reaches the colon intact, where the good bacteria feast on it. This is exactly what makes it valuable: it is an excellent source of butyrate, that is, the basis of the substance that feeds and strengthens your gut wall. The good news is that it comes from simple household sources: if you cool cooked rice or potato (even if you reheat it afterwards), part of the starch in it turns resistant; the firmer, green banana is also rich in it. A small portion of cooled rice or a slice of cooled cooked potato is therefore not just a side dish – it is targeted food for your engrafting flora.
How to raise the fibre so that it does not hurt?
Fibre is a wonder substance, but it has a pitfall: if you eat too much of it too quickly, it can temporarily cause bloating and gas formation – especially now, while your gut is still healing. This is why the golden rule is graduality. A little more every day, and always with enough water, so that the fibre passes easily through your system.
Start with the easily tolerated sources: cooked oats, peeled apple or pear, steamed carrot, well-cooked pulses in a small portion. Most healing guts tolerate these well. Leave the raw, coarse fibres – raw cabbage, a lot of onion, a large portion of bran – for later for now. Cooking, steaming and peeling all "pre-digest" the fibre a little, making it gentler this way.
Watch your body's signals, and write them down too. If you feel strong bloating after a particular fibre source, it does not mean that the fibre is bad – only that you need a smaller portion of it for now. The bloating eases over time, as your flora grows stronger and "gets used to" the new food. Your diary is worth its weight in gold here: you see which food affects you how.
Fermentable dietary fibre is the primary energy source of the colonic microbiota; during its bacterial fermentation, short-chain fatty acids[G] (SCFA) – acetate, propionate, butyrate[G] – are produced. Butyrate is the main energy substrate of the colonocytes, strengthens gut barrier integrity and has an anti-inflammatory effect (Koh et al., 2016 [111]). In a fibre-poor environment microbial diversity[G] declines: in mice, the diversity loss on a low-fibre diet compounded across generations and, after four generations, led to taxon extinctions that dietary fibre restoration could no longer reverse (Sonnenburg et al., 2016 [080]).
Among the prebiotic fibres, inulin[G] (from chicory) selectively stimulates the bifidobacteria (Kolida et al., 2007 [090]); it is noteworthy that inulin and potato starch (a resistant-starch source) are also among the excipients of the DiffBiome formulation, which provides a prebiotic substrate for the inoculated community even within the capsule. A gradual increase in fibre is warranted: the link between the quantity of fermentable fibre (FODMAP[G]) and abdominal symptoms was demonstrated in a crossover RCT in IBS patients – a low-FODMAP diet significantly reduced symptoms (Halmos et al., 2014 [070]). That trial did not measure the time course of an adapted fermenting community developing, and was not conducted in a post-FMT population; gradualness here is practical caution.
Resistant starch (RS) ferments in the colon and is butyrogenic: a meta-analysis of randomised trials in healthy adults found that it significantly increases faecal butyrate concentration and lowers faecal pH (Shen et al., 2017 [112]). Butyrate is the primary energy source of the colonocytes and a key mediator of barrier integrity and anti-inflammation (Koh et al., 2016 [111]). (There is no head-to-head comparison with other prebiotic substrates, so we do not claim resistant starch to be more butyrogenic than those.) Its dietary sources: the retrograded starch (RS3) of heat-treated then cooled starchy foods (rice, potato), green banana and pulses (RS2). In the mechanism of colonisation resistance, SCFAs – alongside secondary bile acids – directly inhibit C. difficile (Reed & Theriot, 2021 [003]). (This is a mechanistic review: no interventional trial has shown that targeted dietary butyrate supply in the post-FMT period improves outcome.)**
Today there will be a little plant-based base at every meal – gently, from well-tolerated sources. This will be the foundation on which these three days are built.
- For breakfast, a portion of cooked oats (with water or plant-based milk), with a little peeled apple on top;
- For lunch or dinner, a portion of steamed vegetables (carrot, courgette, squash);
- Drink a large glass of water with every fibre-rich meal;
- Diary: stool count, Bristol, bloating, fluids; note down the fibre sources of the day.
Today we put soluble fibre to the fore – this is the flora's favourite, and it is gentle on the gut.
- For breakfast oats again, or a small portion of well-cooked red lentils during the day;
- A peeled pear or ripe banana as an afternoon snack;
- Keep the fluid intake high (30–35 ml per kilogram of body weight; for 70 kg that is 2.1–2.5 litres), so the fibre moves easily;
- Diary: stool count, Bristol, bloating, fluids; which fibre source you tolerated and how.
Today we bring in a new, gentle fibre source not tried before – carefully, in a small portion. The goal is gradual expansion.
- Try a new, well-tolerated fibre in a small portion (e.g. steamed green beans, baked sweet potato without the skin);
- Bring in a small portion of resistant starch as a butyrate source: cooled cooked rice or potato, or perhaps a riper but still firm banana;
- Keep the already proven sources too – the point is variety, not replacement;
- If any new food causes strong bloating, reduce its portion, do not leave it out entirely;
- Diary: stool count, Bristol, bloating, fluids; the tolerability of the new fibre.
🍽️ Eating during these days
In these three days fibre is at the centre – the daily food of the freshly engrafting flora – and you raise the fibre intake gradually and gently. Your tasks: on day 28 have a little plant-based base at every meal (for example oats in the morning, steamed vegetables at lunch), on day 29 put soluble fibre to the fore (oats, well-cooked red lentils, ripe banana), and on day 30 bring in a new, well-tolerated fibre source in a small portion. Drink a large glass of water with every fibre-rich meal; if a food causes strong bloating, reduce its portion, do not leave it out entirely – the secret is graduality.
For these days, the Plant Calendar, still in the firming foundation phase, recommends gentle, digestion-soothing sources: on day 28 ginger (a small amount as a tea, digestion-soothing), on day 29 cinnamon (a blood-sugar-friendly spice), and on day 30 chokeberry (aronia) – in moderation – which contains tannin and polyphenols[G]. Alongside these, it is worth keeping the already proven, gentle fibre sources too, since the goal is gradual expansion, not replacement. Build the plant of the day into at least one meal; if you do not tolerate one of them well, try it in a small portion, or return to it later.
During these days, record daily:
- DiffBiome dose (capsules/day) and LOT number, if the course is still ongoing;
- daily stool count;
- stool Bristol scale (1–7), watch the trend heading towards 3–4;
- bloating (0–5);
- bloody stool (yes/no);
- fluid intake (litres);
- the fibre sources of the day and their tolerability;
- wellbeing (1–5);
- Movement: type + minutes, step count (target/actual);
- Stress level (1–5) and mood (1–5);
- Sleep (hours + quality 1–5).
Why does this matter?
The engrafted flora only stays and grows stronger if it receives food every day – and this food is fibre. In these days you have learned that fibre is the bread of the good bacteria, that there are two kinds of fibre, and that the secret is graduality: a little more every day, always with enough water. If the bloating appears now and then, it is not a fault but a sign of the flora adapting. In the next three days we will build further on the variety of fibre sources.
References
[003] Reed AD, Theriot CM. Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium**. Microorganisms. 2021. Link
This review examines how commensal *Clostridium* species mediate colonization resistance against C. difficile. Commensal *Clostridia* modify primary bile acids into secondary bile acids that suppress C. difficile spore germination and vegetative outgrowth. They additionally produce antimicrobial peptides and short-chain fatty acids that directly inhibit C. difficile and compete for limiting nutrients such as proline, important for C. difficile growth via Stickland fermentation. Loss of commensal *Clostridia* after broad-spectrum antibiotics is a key mechanistic step toward CDI susceptibility. The authors conclude from this that new therapies against CDI are urgently needed; the clinical validation of defined *Clostridium* consortia comes not from this review but from the VE303 phase 2 trial [56].
[022] Eswaran S, Muir J, Chey WD. Fiber and functional gastrointestinal disorders. American Journal of Gastroenterology. 2013. Link
Review of the role of fibre in functional bowel disorders. The authors organise fibres by solubility and fermentability and stress that these two properties decide which fibre suits a given patient. Fibre ferments partly or completely in the distal small bowel and colon, producing short-chain fatty acids and gas, and thereby affecting gut function and sensation. Where fibre is recommended for functional bowel disease, the evidence best supports a soluble, gel-forming supplement (ispaghula, psyllium). Even when used judiciously, however, fibre can worsen abdominal distension, flatulence, constipation and diarrhoea, so the dose should be built up gradually.
[070] Halmos EP, Power VA, Shepherd SJ, Gibson PR, Muir JG. A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology. 2014. Link
Randomised single-blind cross-over trial in 30 IBS patients and 8 controls compared a low-FODMAP diet (<0.5 g/meal) with a typical Australian diet for 21 days each (>=21-day washout). Almost all food was provided. The low-FODMAP arm produced significantly greater reduction in IBS symptoms measured on 0-100 mm visual analogue scales, supporting the low-FODMAP diet as an effective intervention for symptom control in IBS compared with a standard Western diet.
[080] Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. . 2016. Link
In mice on a low microbiota-accessible carbohydrate (fiber) diet, gut microbiota diversity declined and the effect compounded across generations: over four generations the low-fiber diet led to cumulative taxon extinctions no longer reversible by dietary fiber reintroduction.
[090] Kolida S, Meyer D, Gibson GR. A double-blind placebo-controlled study to establish the bifidogenic dose of inulin in healthy humans. Eur J Clin Nutr. 2007. Link
OBJECTIVE: To evaluate the bifidogenic efficacy of two inulin doses in healthy human adults. DESIGN: A double-blind, placebo-controlled, crossover human study. SETTING: Food Microbial Sciences Unit, The University of Reading, Reading, UK. SUBJECTS: Thirty healthy volunteers, 15 men, 15 women (age range 19-35). INTERVENTIONS: Subjects consumed a chocolate drink containing placebo (maltodextrin, 8 g/day), 5 g/day inulin and 8 g/day inulin for a 2-week treatment period. Each treatment was followed by a 1-week washout at the end of which volunteers progressed to the next treatment.
[111] Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell. 2016. Link
Mechanistic review of short-chain fatty acids (SCFAs), produced by bacterial fermentation of dietary fibre. Fermentable fibre is the primary energy source for the colonic microbiota; the main fermentation products are **acetate, propionate and butyrate**. **Butyrate is the principal energy substrate of colonocytes**; SCFAs also influence barrier integrity, immune function and, once in the circulation, host metabolism, partly via G-protein-coupled receptors (GPR41/43) and histone deacetylase inhibition. This entry is the source for the textbook-level claims of III.2 (S-0302-01, -02). Important: a **review**, not original experimental data.
[112] Shen D, Bai H, Li Z, Yu Y, Zhang H, Chen L. Positive effects of resistant starch supplementation on bowel function in healthy adults: a systematic review and meta-analysis of randomized controlled trials. Int J Food Sci Nutr. 2017. Link
Systematic review and meta-analysis of randomised controlled trials in healthy adults on the effect of resistant starch on large-bowel function. Resistant starch significantly **increased faecal butyrate concentration** (SMD 0.61; 95% CI 0.32-0.89) and faecal wet weight (WMD 35.51 g/d), and significantly **lowered faecal pH** (WMD -0.19); the change in defecation frequency was not significant. Important for the handbook: the meta-analysis establishes that resistant starch is butyrogenic in humans — it does **NOT** examine whether it is more butyrogenic than other prebiotic substrates (no head-to-head comparison), and it was not conducted in an FMT population.
[113] Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr. 1995. Link
This paper introduced the concept of the **prebiotic**: a non-digestible food ingredient that selectively stimulates the growth or activity of one or a limited number of bacteria in the colon, thereby improving host health. The authors distinguish it from the **probiotic** (which delivers live microorganisms) and the **synbiotic** (a combination of the two), and highlight non-digestible oligosaccharides — including inulin and fructo-oligosaccharides — as examples. This entry is the source for the prebiotic definition in III.2 (S-0302-04). Important: a 1995 conceptual paper; the definition has since been refined several times.