Time Restricted Eating: Nutrition, Timing and Microbes

1. Time Restricted Feeding (TRF): Why would the time of day you eat effect your weight and reduce inflammation ?

Recent research has found that when animals eat during the day could be a key factor in weight loss (or gain).

Twelve studies of time restricted eating were identified with daily fasting intervals ranging from 12 to 20 hours, with variability in coordination with light/dark phases and composition of food.   In mice, time-restricted feeding was associated with reductions in body weight, total cholesterol,triacylglycerol, glucose, insulin, interleukin 6, and TNF-α as well as improvements in insulin sensitivity. It is notable that these health outcomes occurred despite variable effects of intermittent fasting on weight loss.  Patterson et al 2015.

Research in animals highlights the potential importance of synchronizing intermittent fasting regimens with daily circadian rhythms. Animals given unlimited access to a high-fat diet eat frequently throughout the night and the day, disrupting their normal nocturnal feeding cycle. These mice fed an unrestricted high-fat diet develop obesity, diabetes, and metabolic syndrome. However, it was unclear whether these diseases result from the high-fat diets, disruption of circadian rhythms, or both.  Mice whose feeding was restricted to normal nocturnal eating times consumed equivalent energy but were protected from obesity, hyperinsulinemia, hepatic steatosis, and inflammation.  Patterson et al 2015 , M Hatori et al 2012 and Chaix, 2014S Gill 2015.

The Effects of Time Restricted Eating on Human Beings.   

Crossover studies found significant reductions in weight (although these studies did not prescribed or measured physical activity). In a study among 29 normal-weight men, a prescribed night-time fasting interval of more than 11 hours resulted in a 1.3% weight loss. Another crossover study compared the effect of consuming one afternoon meal per day for 8 weeks and reported 4.1% weight loss in comparison to an isocaloric (similar calorie values) diet consumed as three meals per day.  One meal per day was also associated with reductions in fasting glucose and improvements in  cholesterol levels. Whereas self-reported hunger was higher in the morning for those consuming one meal per day, this fasting regimen was considered acceptable because there were no mean changes in tension, depression, anger, vigor, fatigue, or confusion.

Although clearly limited, results from these studies of time-restricted feeding are consistent with research in animals indicating that incorporation of regular fasting intervals and eating in accordance with normal daily circadian rhythms (ie, daytime hours in human beings) may be important for maintaining optimal metabolic function. It is well known that in human beings, even a single fasting interval (eg, overnight) can reduce basal concentrations of metabolic biomarkers (such as insulin and glucose) associated with chronic disease.  Patients are required to fast for 8 to 12 hours before blood draws to achieve steady-state fasting levels for many metabolic substrates.

Prolonged nightly fasting may be a simple, feasible, and potentially effective disease prevention strategy at the population level. Overall evidence suggests that intermittent fasting regimens may be a promising approach to lose weight and improve metabolic health for people who can tolerate intervals of not eating, or eating very little, for certain hours of the day or days of the week.  Patterson et al 2015

C R Marinac has also carried out a number of studies on the impact of time restricted dieting on women and found that frequency and circadian timing of eating may influence biomarkers of inflammation and insulin resistance associated with breast cancer risk (C R. Marinac 2015).

There have been positive early findings on the effects of intermittent fasting regimens on inflammation and the immune system (including relieving symptoms of MS) which scientists are currently attempting to explain. In mice, fasting and feeding has been found to elevate the number of stem cells and their regenerative capacity.  Early results suggest this could reboot the immune system. Y Choi et al 2016.  In older mice, this strategy promotes the development of new neuronal cells, i.e. it may have neurorestorative capacity.

One theory is that fasting diets starve the body of sugars and change the metabolism by switching off, or lowering, circulating levels of insulin….these diets cause people to become ketotic. Ketones may have several benefits to health, including brain health.

Other explanations for the effects of time restricted diets focus on alignment with the body’s circadian rhythms. Eating happens at times when the body is more efficient at breaking down foods. The metabolic system evolved to allocate energy resources at different times of day.  Exhaustive research over the past few decades has begun to elucidate the full range of human physiology that is regulated in synchrony with the solar day. With regard to neuronal function, this includes not only the control of sleep and wakefulness, but also modulation of mood, cognition, sensory acuity, breathing rate and body temperature (Schmidt et al., 2007).

Nearly all aspects of digestion and detoxication – from gastric emptying time to fat processing and xenobiotic degradation by the liver – are under circadian control (Dallmann et al., 2014).   Yu Tahara and Shigenobu Shibata have explored nutrition and diet as potent regulators of the liver clock, and circadian rhythms can also influence metabolism.

Many aspects of the circulatory and immune systems, including heartbeat and blood pressure, vascular leakage and even plasma composition, are also regulated daily (Dallmann et al., 2012; Scheiermann et al., 2013). S A Brown 2014. 

2.  The influence of microbiota

Another possible explanation could be the gut microbiota’s influence on biomarkers of inflammation due to the microbiota’s intervention in the relationship between circadian rhythms and redox.

Circadian rhythms are increasing being found to be key to body-brain development and health. Other postings on this site looks at how circadian-redox rhythms are implicated in cell recycling and regeneration (all proliferating cell populations exhibit their own circadian rhythm) and neurogenesis. 

Lowered intake of particular nutrients rather than overall calories is also being researched, as is the nutritional modulation of the microbiome.  Altered food intake, especially protein and insoluble fiber have a profound effect on the gut microbiota structure, function, and secretion of factors that modulate multiple inflammatory and metabolic pathways.  L Fontana 2015.

In a 2014 study, mice were fed a high fat diet. One group ate around the clock, the other group only had access to food in an 8-hour window. Both consumed the same amount of calories overall. But the microbiome of the Time Restricted (TRF) animals looked different to the other group and had more bacterial diversity. The researchers also measured the stool samples of both groups and the mice had more sugar in their stools meaning they had extracted less calories from the food they had eaten than the other group.  The authors concluded that: “TRF for 12 hours or shorter offers metabolic benefits irrespective of diet type.” The researchers also measured the stool samples of both groups and the TRF mice had more sugar in their stools meaning they had extracted less calories from the food they had eaten than the other group.

“Studies show that the gut microbiome is highly dynamic, exhibiting daily cyclical fluctuations in composition. Diet-induced obesity dampens the daily feeding/fasting rhythm and diminishes many of these cyclical fluctuations. TRF, in which feeding is consolidated to the nocturnal phase, partially restores these cyclical fluctuations. Furthermore, TRF, which protects against obesity and metabolic diseases, affects bacteria shown to influence host metabolism. Cyclical changes in the gut microbiome from feeding/fasting rhythms contribute to the diversity of gut microflora and likely represent a mechanism by which the gut microbiome affects host metabolism. Thus, feeding pattern and time of harvest, in addition to diet, are important parameters when assessing the microbiome’s contribution to host metabolism”.A Zarrinpar 2014.

A critical role in the clock-nutrition interplay appears to be played by the microbiota.  The circadian clock appears to operate as a critical interface between nutrition and homeostasis, calling for more attention on the beneficial effects of chrono-nutrition.  G Asher 2015. 

3. The Circadian – Redox Link –  and how Microbiotia could be Influencing this.

Regulation of metabolism by the circadian clock and its components is reciprocal. Specifically, components of the circadian clock sense alterations in the cell’s metabolism.  There is strong evidence of:  the link between the circadian clock and the metabolism ( K Eckel-Mann 2013  , C B Peek 2012), and of circadian redox in mammals.  J S O’ Neill  2014, M U Gillette 2014.

Circadian rhythms are present in all living organisms. They organise processes such as gene transcription, mitosis, feeding, and rest at different times of day and night. These rhythms are orchestrated by a network of core ‘clock genes’ that are organised into transcription–translation feedback loops (TTFLs), producing oscillations with a period of approximately 24 hours. The modern understanding of circadian timekeeping has revolved around the TTFL paradigm.

Recently, however, this has been challenged by new findings that redox reactions persist in the absence of gene transcription, and that cycles of oxidation and reduction are conserved across all domain of life. These results suggest that non-transcriptional processes such as metabolic state may interact and work in parallel with the canonical genetic mechanisms of keeping circadian time.

Mechanistic links between the redox state and the TTFL framework of circadian rhythms have begun to appear in a variety of organisms – from bacteria to flies to mammals. Although a single model has yet to emerge, studies strongly suggest that redox state may be an oscillation that feeds back upon the TTFL, whereby a cell’s redox state may alter clock gene expression and the clock genes, in turn, regulate redox state. Perturbation of the transcription–translation feedback loop clockwork or the redox system results in a perturbation of the other, indicating that they have a reciprocal relationship. Lisa Wulund 2015,  A Stangherlin – ‎2013.  K Nishio 2015.    N B Milev 2015.  However, the debate on how this works continues.  M Putker 2016.

The redox balance is key for molecules utilised in the context of anti-oxidation protection. A critical event of oxidative stress resets the circadian clock in other mammalian cell lines, resulting in a concurrent activation of a network of circadian genes that then continued onward to modulate an antioxidant, cell survival response. These results strongly suggest that the circadian clockwork is involved in complex cellular programmes that regulate endogenous ReactiveOxygen Species (high ROS levels result in significant damage to cell structures and this is know as oxidative stress). Current evidence seems to support the conclusion that the responses to ROS are mediated both through the regular function of the molecular clockwork and the involvement of the TTFL genes in extra-circadian pathways. Lisa Wulund 2015

Fasting dramatically alters cysteine-residue redox status in D. melanogaster. K E Menger 2015.  Cysteines are among the most reactive residues in proteins, and their side chain thiols undergo various reversible and irreversible redox modifications.  Kim et al and Sun et al have recently proposed a model for redox based signalling, in which such cysteine modifications are generated by diverse physiological signals, proteins can discriminate among redox related signalling molecules and different thiol modifications can have unique functional/structural effects.  L Zhukova 2004.

The circadian rhythms of microbes and hosts maybe interacting in a way which produces the most efficient outcome from such circadian – redox-antioxidants interaction, or in some cases competing and so creating dysfunction.

Microbes may be seeking to entrain the circadian/redox pathways for a number of reasons:

A. To avoid alerting the host’s immune system to their presence, quorum sensing bacteria delay virulence factor production until cell number is high enough that secretion of virulence factors will result in a productive infection.   It would, therefore, be unsurprising to find a link between immunity, quorum sensing, circadian rhythms.

Throughout biology, the circadian clock has been utilised to assist in resistance to infection e.g.

  • A regulatory mechanism links the circadian clock and glucocorticoid hormones to control both time of day variation and the magnitude of pulmonary inflammation and response to bacterial infection.  Gibbs – ‎2014
  • The master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant’s redox state and regulates transcription of core circadian clock genes. M Zhou 2015.

Perhaps due to evolving in response to changing levels of pathogen challenge during the day, most immune cells express circadian clock genes and present a wide array of genes expressed with a 24-h rhythm. This has profound impacts on cellular functions, including a daily rhythm in the synthesis and release of cytokines, chemokines and cytolytic factors, the daily gating of the response occurring through pattern recognition receptors, circadian rhythms of cellular functions such as phagocytosis, migration to inflamed or infected tissue, cytolytic activity, and proliferative response to antigens. Consequently, alterations of circadian rhythms (e.g., clock gene mutation in mice or environmental disruption similar to shift work) lead to disturbed immune responses. N Labrecque 2015.A M Curtis 2014,  C Scheiermann – ‎2013,  A Nakao – ‎2014.

There have been a number of studies on the interactions between gut microbes and the immune system e.g Y Belkaid 2011and 2014C L Maynard 2012,Hsin-Jung Wu 2012F Purchiaroni 2013, Macfarlane et al., 2011Clemente et al., 2012,Ridaura et al., 2013, Everard and Cani, 2013, SM Vieira – 2014,   Zhang 2014, K Aagaard 2014,  A Ardeshir – ‎2014C M da Costa Maranduba 2015, Claire Chevalier 2015,  D K. Podolsky 2015B Sánchez 2015, Adil Mardinoglu 2015,    Q Mu 2015,  , D Pagliari 2015,  C Benakis 2015. D Ruane 2016.    The interaction of the host’s immune system and the microbe has also been explored in depth within microbial endocrinology.  M Lyte 2016.

B. To entrain feeding and defecating behaviours through influencing circadian rhythms.  Timing (both from the perspective of the host and microbiota) of foraging related activities as eating, defecating, mating, and nesting, etc, will be important. K Eckel-Mann 2013.   It has been suggested that quorum sensing may be one route that microbes can use to coordinate behavior in order to manipulate host eating behavior and enhance resource delivery.

The circadian clock within intestinal epithelial cells (IECs) is responsible for cyclic glucocorticoid production and is under endocrine control from the pituitary-adrenal axis. The IECs clock is disrupted by depletion of the microbiota, leading to altered corticosteroids levels and consequent metabolic disorders. Thus the microbiota determines the appropriate function of the gut clock, most likely contributing to additional, system wide cyclic homeostasis. This control operates through the innate immune receptors TLRs and NOD2, who expression in IECs is cyclic and under clock regulation.  Thus, changes in the microbiota levels and composition induced by different types of nutritional regimens could differentially regulate gut clock and thereby influence the organism’s homeostasis….another key component in the equation is food, whose intake is also cyclic. Different nutritional challenges alter the composition of microbiota and specific members of the intestinal microbiota have been linked with metabolic disease.   Yet how does time-specific and diet-specific food intake alter in parallel the gut clock and the microbiota. High-throughput genomic and metabolomics analyses have revealed that specific signatures exist for dietary condition, as well as for time-restricted feeding. G Asher 2015.

Examples of evidenced relationships between microbes, circadian rhythms, and gut microbiota:

  • Microbiotia influencing host clock genes EAC Heath-Heckman – ‎2013.
  • Mouse gut microbiota produce metabolites in diurnal patterns, and these can influence the expression of circadian clock genes in the liver. V. Leone et al 2015
  • Circadian rhythms in gene expression occur in both the gut epithelia (PG Falk 1998) and mucosal immune systems (O Froy 2007)  of mammals.
  • A C Thais 2015 explores a number of examples the antimicrobial pathway and innate immune response regulation involving the circadian clock.
  • In mice, indigenous bacteria from the gut microbiota have been found to regulate host serotonin biosynthesis.  Research has demonstrates that microbes normally present in the gut stimulate host intestinal cells to produce serotonin.  Although this study was limited to serotonin in the gut, the research team are now investigating how this mechanism might also be important for the developing brain. J M Yano 2014.   Serotonin, together with histamine, dopamine, acetylcholine, noradrenaline and adrenaline are neurotransmitters that are found across biology including in plants, animals and microbiota.  GABA is also a common factors. M Lyte 2016.
  • In mice it has been observed that gut microbial colonization influences rhythmic signalling events in the ileal epithelium downstream of toll-like receptors (TLRs). This, in turn, regulates the organization of molecular clock activity and glucocorticoid production in the intestine. The microbiota also impacts clock gene expression beyond the gastrointestinal track. Germ-free mice, which are born and raised under strictly sterile conditions in the absence of microorganisms, feature alterations in clock gene expression in the liver and the hypothalamus. A Mukherji 2013.
  • Circadian rhythms are essential for the MAMPs-mediated homeostasis of the gut.

The circadian interactions between host and microbiota are not solely restricted to microbial attempts to control of host clock function but rather constitute a bidirectional cross talk.

  • In vertebrates, the gastrointestinal system expresses circadian patterns of gene expression, motility and secretion in vivo and in vitro, and recent studies suggest that the enteric microbiome is regulated by the host’s circadian clock. In addition, least one species of commensal bacterium from the human gastrointestinal system, Enterobacter aerogenes, is sensitive to the neurohormone melatonin, which is secreted into the gastrointestinal lumen, and expresses circadian patterns of swarming and motility. Melatonin specifically increases the magnitude of swarming in cultures of E. aerogenes, but not in Escherichia coli or Klebsiella pneumoniae. Altogether, these data demonstrate a circadian clock in a non-cyanobacterial prokaryote and suggest the human circadian system may regulate its microbiome through the entrainment of bacterial clocks.  J K Paulose 2016.
  • The host circadian rhythms may  invoke changes in the abundance of mouse gut bacteria, over a 24-hour cycle, particularly in females, is tied to rhythms in the internal clock and clock genes. Disruption of the host circadian clock by deletion of Bmal1, a gene encoding a core molecular clock component, abolished rhythmicity in the fecal microbiota composition in both genders.  Xue Liang et al 2015.
  • It has been demonstrated that the intestinal microbiota undergoes rhythmic fluctuations in taxonomic composition and, consequently, genomic coding capacity. As a result, different times of the day feature distinct microbial community configurations and microbiota functions. Thus, in addition to the intrinsic circadian timing systems identified in cyanobacteria, the intestinal microbiota undergoes community-scale rhythmicity on the level of metagenome composition. These compositional fluctuations are controlled by the circadian clock of the host, since they cease in the absence of a functional host molecular clock. Furthermore, the type of diet and the rhythmicity of food intake are major drivers of the oscillations in the intestinal microbial ecosystem. In addition, recent insights using parenteral feeding raise the possibility that further, still-unidentified host factors are involved in regulating microbial oscillations. Taken together, symbiotic microbial colonization is required for circadian homeostasis of the host. In turn, a functional host circadian clock ensures periodic oscillations of its symbiotic microbial ecosystem. IA C Thais 2015. 

4. Eating To Support a Microbiome That Supports Good Health

This bidirectional cross talk means that in theory the host can influence the microbiota, and perhaps this is what we are doing when we chose what we eat, and when we eat it, with care.

Mark Lyte (2013) has looked at evidence of whether diet can influence bacteria e.g to produce neuroendocrine hormones that interact with the enteric nervous system (ENS) or are absorb into portal circulation.  He suggests the possibility that this could present a new mechanism by which nutrition could impact on the host and ultimately influence various aspects of behaviour, as well as food preferences and appetite.  It is known that the neurochemical composition of food can influence the growth of particular bacteria, and perhaps different species of bacteria will commute a specific need to its host (via neuroendrocrine hormones).   One hypothesis is that there is a feedback loop between the microbia and the brain, in determining food preferences.

Although the number of different neuroendocrine hormones that are secreted into the gut lumen by elements of the ENS  are at least 30, less is known about the ability of the microbiome to produce may of the same chemicals – presenting possible mechanisms for the microbiome to influence the brain.

There are various studies that point to a relationship between microbes, nutrution, learning, anxiety and behaviours.

There may be a limit to how far humans should seek to influence this relationship as it may be key to our evolution.  Bacteria that may have once have been harmful will have become symbiotes.  It may also be the case that they have influenced our genetic makeup, and therefore attempting short “detox like” gut “make overs” are unlikely to have any long term effects.   I have explored the idea of a possible influence on genes in a separate posting. 

However the following are suggestions for how to influence your gut microbia through what you eat. It may also eventually turn out that combining this with when you eat may increase positive effects.  There is evidence that the way the body digests nutrients, carbohydrates, and proteins is partially contingent on the time of day.

However, a warning need to be given here. The following suggestions are mainly focused on preventative action.  If you have an existing condition, particularly a condition that effects your gut (which is likely to be sensitive to a change in diet) or immune system, then you should speak to your doctor before changing your diet.   

A. Timings

Try and leave as long an interval as reasonably possible between your evening meal and breakfast.  Do your best not to eat between meals (and this includes sugary and milky drinks).  There have been various findings (in mice models) on which timings might be most effective e.g  Y Fuse 2012, and  H Kuroda 2012.

B.  More Fibre

Adding more fibre to a diet can shift a microbial profile linked to obesity to one correlated with a leaner physique.  It has also been found that when microbes are starved of fibre, then start to feed on the protective mucus lining of the gut, possibly triggering inflammation disease.  Beneficial microbes feast on fermentable fibres, which can come from various vegetables, whole grains and other foods – including high fibre snack bars.  These resist digestion by human made enzymes as they travel down the digestive tract.   Microbes extract the fibres energy, nutrients, vitamins and other compounds for humans.  Short chain fatty acids are of  particular interest as they are linked to improve immune functions, decreased inflammation, and protect against obesity.

However those with Irritable Bowel Syndrome should be aware that in some cases, extra fibre can make symptoms worse.  

C.  Choosing the Best Prebiotics and Probiotic

Recently researchers found “no convincing evidence exists for consistent effect of examined probiotics on faecal microbiota composition in healthy adults” when they reviewed the results of seven randomised trials of probiotic products and supplements.  Work is now being undertaken to find out if they can have a preventative effect. There is some evidence from previous reviews that probiotic interventions may benefit those with disease-associated imbalances of the gut microbiota.

There are various natural prebiotics and probiotics e.g Jerusalem artichokes, asparagus, leeks, onions, bananas, polenta, broccoli and other cruciferous vegetables (kale, cabbage, and cauliflower), blueberries, beans/legumes, fermented plant-based foods (e.g sauerkraut, kimchi, tempeh and soy sauce).

Some of the above prebiotics and probiotics are more effective than others e.g Jerusalem artichokes is one of the most effective prebiotics, and evidence suggests that kimchi and other fermented foods may be a particularly effective probiotic.  Be careful of fruit as fructose is a form of sugar and so may cause damage.

Man made probiotics (e.g liquids, powers and capsules) are not always effective, because not all of them survive the digestive tract.  Scientists at University College London put eight probiotic products through three tests and found only one passed all of them.

It is possible that yogurts labeled as containing “live and active cultures”, do not meet the requirements of the definition of probiotics.  That is, they may not contain sufficient amounts of live microorganisms to bestow a health benefit on the consumer.   The evidence that yogurts provide positive health outcomes is mainly based on animal models, so the jury is still out on this one.

D. Reduced Fat and Sugar

Findings from a new study at Oregon State University found that a diet high in sugar caused changes in the gut bacteria of mice, impairing the mice’s ability to adjust to changing situations, called “cognitive flexibility.” The change in gut bacteria also negatively affected the mice’s long-term and short-term memory.

This could also combined with timing. A model of chronic circadian disruption was used to determine the impact on the intestinal microbiome.  Mice underwent once weekly phase reversals of the light:dark cycle (i.e., circadian rhythm disrupted mice) to determine the impact of circadian rhythm disruption on the intestinal microbiome and were fed either standard chow or a high-fat, high-sugar diet to determine how diet influences circadian disruption-induced effects on the microbiome. Weekly phase reversals of the light:dark (LD) cycle did not alter the microbiome in mice fed standard chow; however, mice fed a high-fat, high-sugar diet in conjunction with phase shifts in the light:dark cycle had significantly altered microbiota.  R M. Voigt 2014.

But be careful of artificial sweetners, as there is evidence in mice models that this may also harm the bacteria that protect against obesity, etc.

For more suggestions on how to promote positive gut microbial health see The Gut Makeover by Jeanette Hyde. However be aware, that your microbiome may be part of your genetic makeup (e.g see hologenomic theory), and so short programmes aimed at changing the microbiome are unlikely to have a long term impact.  In any case very rigid diets are very hard to keep up, so as always a good balanced diet (that takes into account the above findings) would seem like the best idea.

Circadian clocks are influenced by factors other than foods e.g light and temperature.  Ensure you get a sufficient amount of light in daylight hours and sleep during the night.  Another factor to considered is the use of equipment (e.g Iphones and Ipads) that issues artificial light.  Try and avoid such equipment in the hours before sleep, and do not charge your devices in the same room that you sleep in.


Nina Schuller Copyright April 2016  (but only in terms of joining up other peoples work into an overall system.  I have referenced others works so it is clear that others have provided the individual pieces of evidence I have used to shape a specific systems approach


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