III. Phase 2 – Engraftment and lifestyle (days 25–60)

III. 8 Sleep and circadian rhythm

Sleep is not wasted time but active healing. Your gut flora has a daily rhythm of its own, and when you sleep well, the engrafting bacteria find better conditions too. This chapter shows you how to set your own body clock.

Summary

It is easy to think of sleep as simply "switching off", but the reality is the exact opposite: during sleep your body is at its most active when it comes to repair and recovery. Your gut flora^[G] – including the freshly transplanted bacteria now engrafting – also lives by a daily rhythm: it behaves differently by day than by night. If your own daily rhythm is predictable and restful, you create the background conditions for the new flora to feel at home and take root. This chapter is not about sleeping pills but about simple, adjustable habits: light, dark, consistent timing and a few evening routines that set your body's internal clock alongside your healing.

The internal clock – and why your gut flora cares about the circadian rhythm

Almost every organ in your body works to a shared, roughly 24-hour rhythm – this is what we call the circadian rhythm^[G]. It governs when you are alert and when you are sleepy, when your body temperature rises and falls, and even the pace of your digestion. The internal clock is set chiefly by light: morning brightness tells your body "it's daytime", and evening darkness tells it "it's time to rest".

The surprising part is that your gut bacteria have a daily rhythm of their own too. By day, when you eat and move, they behave differently than by night, when your gut is at rest. When your own rhythm is steady – going to bed and getting up at roughly the same time – you keep your flora's rhythm in order as well. Irregular sleep, late-night eating or a reversed day-night cycle disturb exactly this delicate harmony.

During the engraftment phase, sleep therefore has a dual purpose. On the one hand, you yourself recover better, are less tired and less irritable, which you also need in order to see the course through. On the other, a predictable rhythm creates a favourable, stable environment for the engrafting flora too.

The building blocks of good sleep

Good sleep is not a matter of luck but the result of a few habits. The most important is consistency: try to go to bed at roughly the same time and – more importantly – to get up at the same time, even at the weekend. Your wake-up time anchors your internal clock; if it is steady, falling asleep becomes easier too.

Light is your most powerful tool. In the morning, as soon as possible after waking, let in natural light – draw the curtains, or step outside for a few minutes. In the evening, by contrast, dim the lights, and in the final hour avoid the strong blue light of phones and screens, because this holds back the production of melatonin^[G] – the "falling-asleep hormone". Keep the bedroom dark, quiet and rather cool.

A few practical tricks help a great deal: it is worth giving up caffeine after two in the afternoon, because it lingers in your body for hours; avoid heavy, late-evening meals, because a full stomach worsens sleep quality; and alcohol – although it makes you drowsy – fragments night-time sleep and makes it shallow, and is in any case to be avoided during the course. A calm evening routine – a warm shower, reading, a few minutes of slow breathing – signals to your body that rest is approaching.

Light as the strongest lever of your body clock

Light is worth highlighting separately, because it is the lever with which you can do the most for your internal clock – and most people use it the wrong way round. The circadian rhythm is held together by the alternation of light and dark: your eyes are not only for seeing, but as light sensors they also signal to your body that it is "daytime" or "night-time".

Morning light is the most important dose. As soon as possible after waking, get into strong, natural light – draw the curtains, stand by the window, or step outside for a few minutes, even in overcast weather (outdoors, even an overcast sky is many times brighter than indoor lighting). This morning light dose sets the daily clock, sharpens alertness, and, through a steadier rhythm, makes falling asleep easier in the evening. If you can, pair it with a morning walk or with your coffee beside an open window.

In the evening the goal is the reverse: less light and warmer light. After sunset, dim the lamps, and in the final hour or two avoid the strong, blue-toned light of phones, tablets and television, because this type of light brakes melatonin production and "simulates daytime" to your body. If you do use a screen, switch on the evening/warm colour mode and turn the brightness down. Morning brightness and evening darkness together – not separately – produce a stable rhythm.

When sleep just won't come

It is entirely normal for sleep to stutter at times during illness and treatment – the symptoms, the worry, or getting up for the toilet at night can all disrupt it. Do not make more of it than it is: the more anxious you are about sleep, the harder it becomes to fall asleep.

If you toss and turn for more than twenty minutes, do not stay in bed. Get up, go into another, dimly lit room, do something dull and soothing (read a few pages), and only lie back down when you feel sleepy again. This way you preserve the link between bed and sleep. Avoid short daytime naps – especially in the late afternoon – because they take away your evening sleepiness.

Important: use sleep aids or supplements (including melatonin) only in consultation with your treating physician during the course. If the sleep disturbance is persistent and seriously affects your daily life, that too is a subject for a medical conversation – you do not have to struggle with it alone.

🩺 Clinical block

The central clock of the circadian rhythm sits in the suprachiasmatic nucleus (SCN) of the hypothalamus, set by light sensing in the retina; the peripheral clocks – including the gut epithelium's and the microbiota's own oscillators – synchronise to it (Liang et al., 2017 [071]). The gut microbiota shows daily compositional and functional fluctuation (diurnal oscillation); circadian disruption of the host is accompanied by a shift in the microbiota's rhythm and by dysbiosis: this was shown by the jet-lag model (Thaiss et al., 2014 [021]), while in shift workers reduced α-diversity^[G] and a rise in pro-inflammatory genera have been described (Grasa-Ciria et al., 2025 [145]). Melatonin, a product of the pineal gland, is darkness-dependent, and strong evening blue light suppresses its production (Chang et al., 2015 [081]); it is also present in the GI tract, where it modulates mucosal regeneration and barrier function, and its release is tied to the rhythm of food intake rather than to light (Bubenik 2002 [138]).

Sleep deprivation can be accompanied by a pro-inflammatory state, and sleep disturbance stands in a reciprocal relationship with inflammation (Irwin and Opp, 2017 [074]) – the involvement of the stress-hormone axis (cortisol^[G]) was not examined in this source; after short, partial sleep restriction, a small study of nine healthy men measured a subtle shift in gut microbiota composition and reduced insulin sensitivity – according to the authors the two changes arose independently of one another (Benedict et al., 2016 [061]). During the engraftment phase, a stable sleep-wake cycle is therefore not merely symptomatic comfort but a reasonable supporting factor for flora stabilisation. From a clinical standpoint, melatonin or sedative supplementation during the course is to be avoided without individual medical judgement; recurrent CDI in itself meaningfully worsens anxiety-related quality of life (Hengel et al., 2022 [103]), which is why supporting good sleep and balanced mood is an integral part of the lifestyle pillar of the Patient Recommendation.

The empirical basis of the sleep-hygiene recommendations: morning bright light – 1.5 hours of electric bright light (1,000 lx) per day in a small, 12-participant field study – improved actigraphy-measured sleep efficiency, reduced sleep fragmentation and lessened morning sleepiness within a single workweek (He et al., 2023 [139]); the study measured neither melatonin levels nor circadian phase, and the ±20-minute window around the fixed wake time is a practical allowance, not a study finding. Stimulus control based on getting out of bed ("if you are not asleep within 20 minutes, get up"), and multicomponent cognitive behavioural therapy (CBT-I), are evidence-based recommendations in the AASM guideline for chronic insomnia (Edinger et al., 2021 [140]). 400 mg of caffeine disrupted sleep meaningfully even 6 hours before bedtime (Drake et al., 2013 [141]) – the "no caffeine after 2 p.m." rule is a safety margin relative to this; alcohol shortens sleep onset but fragments and delays REM sleep in the second half of the night (Ebrahim et al., 2013 [142]). The relevance of oral hygiene is that oral bacteria reach the gut by swallowing and can colonise it: this is common even in healthy people (Schmidt et al., 2019 [143]), and in a dysbiotic gut swallowed oral pathobionts can also aggravate inflammation (Kitamoto et al., 2020 [144]).

Note on the level of evidence: that sleep deprivation directly impairs gut barrier function or makes engraftment of the new flora harder is not supported by human data; the results pointing that way come from animal studies. The handbook therefore claims only that ordered sleep is a favourable background condition for recovery.

Day 46 – Anchoring your wake-up

Today you fix your wake-up time and let in light in the morning – these two steps are the foundation of your internal clock. A consistent wake-up is worth more than a perfect bedtime.

Set a fixed wake-up time and keep it at the weekend too (±20 minutes);
Within 10–15 minutes of waking, let in natural light or step outside for a few minutes;
Light reminder: strong, natural morning light is your most powerful lever – even in overcast weather, outdoors your eyes receive the most light;
Drink your morning coffee, but give up caffeine after 2 p.m;
Diary: bedtime and wake-up time, hours of sleep, how you feel.

Day 47 – Winding down in the evening

Today you focus on the evening hours: dimmed light, a screen-free final hour and a soothing routine. This helps the natural rise of melatonin.

In the final hour, dim the lights and put down the phone/screen;
Have dinner at least 2–3 hours before bed; avoid heavy, late eating;
Introduce a short evening routine: a warm shower, a few pages of reading or slow breathing;
Diary: hours of sleep, ease of falling asleep, night-time awakenings.

Day 48 – The bedroom and handling challenges

Today you set up the environment and how to handle difficult nights. The goal is for the bed to remain the place of sleep.

Make the bedroom dark, quiet and cool (blackout, quiet, ~18–20 °C);
If you don't fall asleep within 20 minutes, get up, do something dull in dim light, and only lie back down when sleepy;
Avoid late-afternoon naps;
Use a sleep aid (including melatonin) only in consultation with your doctor;
Oral hygiene: keep twice-daily brushing and interdental cleaning – the mouth is part of the microbiome too, and bacteria can reach the gut from the mouth.

🍽️ Eating during these days

The theme of these three days is sleep and circadian rhythm, and although the three days are primarily about sleep hygiene (fixed wake-up and morning light – day 46; evening winding-down, a screen-free final hour – day 47; bedroom and difficult nights – day 48), eating has a concrete task here too: avoiding a heavy, late dinner and having dinner at least 2–3 hours before bed, as well as giving up caffeine after 2 p.m. – these all support sleep quality and the natural rise of melatonin.

For these days, the Plant Calendar (Appendix F) recommends olives (day 46), extra-virgin olive oil (day 47) and green tea / matcha (day 48) – three polyphenol^[G]-rich sources. These days fall into the calendar's "gradual expansion" (days 31–50) phase, where the aim is to gradually increase plant diversity and polyphenol sources. On reaching the colon, polyphenols become food for the good bacteria, support a diverse flora, and also have an anti-inflammatory effect – so alongside increasing diversity, they also help to calm post-infection inflammation. Green tea additionally counts towards your fluid intake; just take care, because of its theophylline content, not to drink it in the late afternoon or evening, so that it does not disturb your sleep.

📊 Data

During the sleep phase, record daily:

sleep: bedtime and wake-up time, hours of sleep;
ease of falling asleep and number of night-time awakenings;
how you feel (1–5) and mood;
fluid intake (litres);
daily stool count and Bristol scale – core CDI data;
DiffBiome dose (capsules/day) and LOT number;
Movement: type + minutes, step count (target/actual);
Stress level (1–5) and mood (1–5).

Why does this matter?

Sleep is active healing: this is when you recover, and a stable daily rhythm also creates a favourable environment for the engrafting gut flora. You don't need sleeping pills but a few adjustable habits – a fixed wake-up, morning light, evening winding-down – that set your body's internal clock alongside your healing.

References

[021] Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Elinav E et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. 2014. Link

The composition and function of the gut microbiota follow a daily rhythm: bacterial abundance and metabolic activity oscillate across the light-dark cycle, and this oscillation is driven chiefly by the host's feeding rhythm. When the rhythm is disrupted — modelled here in mice and in human samples after intercontinental flight — microbiota oscillation is abolished and dysbiosis develops; transferring the arrhythmic flora into germ-free mice induces metabolic disturbance. Conclusion: a regular daily rhythm is one precondition of microbiota stability — hence the value of a fixed wake time and morning light from the first days of treatment.

[061] Benedict C, Vogel H, Jonas W et al. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol Metab. 2016. Link

Randomized within-subject crossover study in 9 normal-weight men comparing two nights of partial sleep deprivation (PSD; 02:45–07:00) with two nights of normal sleep (22:30–07:00) under standardized in-lab meal and exercise conditions. Faecal samples were collected and oral glucose tolerance was tested. The study assessed whether short-term sleep loss alters gut microbiota composition and metabolic function, providing early human evidence linking sleep restriction to acute microbiota shifts and insulin resistance.

[071] Liang X, FitzGerald GA. Timing the Microbes: The Circadian Rhythm of the Gut Microbiome. J Biol Rhythms. 2017. Link

Review of circadian organisation in the gut microbiome. The mammalian circadian system (master clock and peripheral clocks) coordinates biological processes in response to external cues like the light-dark cycle, but prokaryote chronobiology — outside cyanobacteria — is poorly understood. The review summarises evidence of time-of-day-dependent compositional and functional structure within the gut microbiota, host regulation of these oscillations, and the reciprocal influence of the gut microbiome on host circadian timing.

[074] Irwin MR, Opp MR. Sleep health: reciprocal regulation of sleep and innate immunity. Neuropsychopharmacology. 2017. Link

This review and overview examines reciprocal interactions between sleep disturbances, including insomnia, and the innate immune system. Insomnia complaints, extreme sleep duration and experimental sleep deprivation alter genomic, cellular and systemic markers of inflammation and contribute to inflammaging. Inflammatory mediators in turn reshape homeostatic regulation of sleep continuity and macrostructure. Clinical implications include the link between sleep disturbance and inflammation-related depressive symptoms, and the potential of insomnia-targeted interventions to reverse inflammation. The findings underscore that sleep disturbance is a tractable risk factor for inflammatory disease.

[081] Chang AM, Aeschbach D, Duffy JF, Czeisler CA. Evening use of light-emitting eReaders negatively affects sleep, circadian timing, and next-morning alertness. Proc Natl Acad Sci USA. 2015. Link

Average sleep duration and quality have declined, and 90% of US adults report electronic device use in the hour before bed. Short-wavelength-enriched light from these devices can suppress melatonin, shift circadian phase and increase alertness. In a controlled comparison, the authors evaluated the biological effects of reading on a light-emitting e-book device versus a printed book before bedtime, examining melatonin, circadian timing, sleep latency and next-morning alertness. The LE-eBook condition delayed circadian timing, suppressed evening melatonin, lengthened sleep onset and reduced next-morning alertness. The findings indicate that pre-bedtime use of light-emitting screens degrades sleep and circadian alignment.

[103] Hengel RichardL, Schroeder ClaudiaP, Jo Jinhee, Ritter TimothyE, Nathan RameshV, Gonzales-Luna AnneJ, Obi EngelsN, Dillon RyanJ, Van Anglen LucindaJ, Garey KevinW. Recurrent Clostridioides difficile infection worsens anxiety-related patient-reported quality of life. Journal of Patient-Reported Outcomes. 2022. Link

This patient-reported study measures how health-related quality of life (HrQOL) changes after treatment of Clostridioides difficile infection (CDI), using the anxiety-focused Cdiff32 instrument. Among 144 adults treated with bezlotoxumab, the mean score improved from 26.4 at baseline to 56.4 at 90-day follow-up (higher scores indicate better quality of life). Patients without recurrence improved significantly more (34.1-point increase) than those with recurrent CDI (6.7-point increase; P < 0.001). Recurrent CDI therefore meaningfully worsens anxiety-related quality of life, and the Cdiff32 instrument is useful for assessing these humanistic outcomes.

[138] Bubenik, G. A. Gastrointestinal melatonin: localization, function, and clinical relevance. Dig Dis Sci. 2002. Link

Review of the gastrointestinal (GI) tract's own, extrapineal melatonin. Melatonin concentration in GI tissues exceeds blood levels 10-100 fold, and the gut contains at least 400 times more melatonin than the pineal gland. GI melatonin release is tied to the **periodicity of food intake** rather than to the photoperiod, and it acts locally (endocrine/paracrine/autocrine) to **foster epithelial regeneration**, enhance gut immune function, reduce smooth-muscle tone and protect the mucosa as an antioxidant. This entry is the source for the III.8 clause that melatonin is also present in the GI tract and modulates the mucosa and motility. **LIMITATION:** a review built largely on animal and cell-level data; it does not concern CDI or FMT and does not address melatonin's role as the sleep hormone.

[139] He M, Ru T, Li S, Li Y, Zhou G. Shine light on sleep: Morning bright light improves nocturnal sleep and next morning alertness among college students. J Sleep Res. 2023. Link

Field intervention study on whether morning bright light improves nocturnal sleep. Twelve university students received 1.5 h of bright electric light (1000 lx, 6500 K) versus regular office light (300 lx, 4000 K) on the mornings of one workweek, in a crossover design, measured by actigraphy and sleep diary. Morning bright light produced **higher sleep efficiency** (83.8% vs. 80.4%), a **smaller fragmentation index**, earlier sleep onset, shorter sleep latency and **lower morning sleepiness**. This entry is the source for the III.8 recommendation that morning light after waking stabilises the daily rhythm and eases evening sleep onset. **LIMITATION:** a very small sample (n=12) of healthy university students over a one-week intervention; not a clinical or CDI population.

[140] Edinger JD, Arnedt JT, Bertisch SM, Carney CE, Harrington JJ, Lichstein KL, Sateia MJ, Troxel WM, Zhou ES, Martin JL. Behavioral and psychological treatments for chronic insomnia disorder in adults: an American Academy of Sleep Medicine clinical practice guideline. J Clin Sleep Med. 2021. Link

American Academy of Sleep Medicine (AASM) clinical practice guideline on behavioural and psychological treatments for chronic insomnia disorder in adults, using GRADE methodology. The guideline recommends **multicomponent cognitive behavioural therapy (CBT-I)** as first-line treatment and separately appraises single-component methods, including **stimulus control** (using the bed only for sleep; if sleepiness does not come, get up), **sleep restriction** and relaxation techniques. This entry is the source for the III.8 practical advice that on persistent difficulty falling asleep one should get out of bed and return only when sleepy again. **LIMITATION:** a chronic-insomnia guideline; not CDI- or FMT-specific, and not developed for the transient sleep disturbance during a course of treatment.

[141] Drake C, Roehrs T, Shambroom J, Roth T. Caffeine effects on sleep taken 0, 3, or 6 hours before going to bed. J Clin Sleep Med. 2013. Link

Randomised home-based study of how a fixed caffeine dose given at different times disrupts sleep. The authors gave 400 mg caffeine **0, 3 and 6 hours** before habitual bedtime, versus placebo, with self-reported sleep data and a validated portable sleep monitor. All three timings — even **6 hours before bedtime** — significantly disrupted sleep relative to placebo; based on the reduction in total sleep time, the authors recommend at least 6 caffeine-free hours before bed. This entry is the source for the III.8 caffeine rule. **LIMITATION:** a single fixed dose (400 mg) in healthy sleepers, partly self-reported; the "no caffeine after 2 p.m." rule is a safety margin relative to this, not the paper's direct finding.

[142] Ebrahim IO, Shapiro CM, Williams AJ, Fenwick PB. Alcohol and sleep I: effects on normal sleep. Alcohol Clin Exp Res. 2013. Link

Review of the effect of alcohol on nocturnal sleep based on studies in healthy volunteers. At all doses alcohol **shortens sleep onset latency** and makes the first half of sleep more consolidated, but **increases sleep disruption in the second half of the night**. REM sleep onset is significantly delayed at all doses, and total-night REM proportion falls at moderate and high doses; slow-wave sleep in the first half of the night rises. This entry is the source for the III.8 claim that alcohol — though it makes one drowsy — fragments and shallows nocturnal sleep. **LIMITATION:** a qualitative review in healthy volunteers; not a CDI or FMT population and not about the microbiota.

[143] Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Sunagawa S, Zeller G, Bork P. Extensive transmission of microbes along the gastrointestinal tract. Elife. 2019. Link

Population metagenomic study in 470 individuals from five countries, comparing salivary and faecal strain populations of 310 species. The authors found that **transmission of oral species to, and their colonisation of, the large intestine is common and extensive even in healthy people** — not the rare, disease-marking event previously assumed. A vast majority of oral species are transferable; transmission is higher in colorectal cancer and rheumatoid arthritis and for opportunistic pathogens. This entry is the HUMAN source for the III.8 rationale that the oral cavity is an endogenous reservoir of gut microbial strains, so oral hygiene matters during the course. **LIMITATION:** observational strain tracking; it establishes the reservoir but not that daily toothbrushing changes the CDI or FMT outcome.

[144] Kitamoto S, Nagao-Kitamoto H, Hein R, Schmidt TM, Kamada N. The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis. Cell. 2020. Link

This study describes the intermucosal connection between the mouth and gut in a mouse model: during oral inflammation (periodontitis), oral pathobionts that bloom and are swallowed — including Klebsiella and periodontally primed Th17 cells — translocate to the gut, where they colonise a dysbiotic intestinal environment and aggravate colitis. Two independent axes — microbial (ectopic oral bacteria colonising the gut) and immunological (orally primed T cells migrating to the gut) — jointly link chronic periodontal disease to intestinal inflammation. This entry is the source for the III.8 mechanistic claim that the oral cavity acts as a reservoir of dysbiotic organisms reaching the gut via swallowing. **LIMITATION:** a mouse, mechanistic model; not CDI or FMT and not proof of a human clinical outcome.

[145] Grasa-Ciria D, Couto S, Samatan E, Martinez-Jarreta B, Cenit MDC, Iguacel I. Disrupted Rhythms, Disrupted Microbes: A Systematic Review of Shift Work and Gut Microbiota Alterations. Nutrients. 2025. Link

Systematic review of whether shift work — especially night shift — alters the gut microbiota. The authors searched three databases up to March 2025; five studies were eligible (four small observational and one Mendelian-randomisation). The observational studies reported **reduced alpha-diversity** and increased **pro-inflammatory genera** (Escherichia/Shigella, Blautia, Dialister) in night-shift workers, i.e. shift work is accompanied by dysbiosis. This entry is the source for the III.8 clause that shift work, one form of the host's circadian disruption, is accompanied by disturbance of the microbiota. **LIMITATION:** few, small studies; the compositional difference does not prove causation, and the review is not about a CDI or FMT population.