Light · 14 min read

How Light Controls the Microbiome: A Quantum Perspective

Your gut lives in the dark, yet its bacteria keep time with the sun. Researchers have shown that the light-dark cycle, meal timing and even skin exposure to UVB reshape the microbiome. Dr. Jack Kruse goes further: he describes the gut as a light-driven, quantum system wired to your mitochondria. Here are both stories, told by the people who hold them.

Trillions of microbes live in a sealed, sunless tube. On the surface that sounds like the last place light could matter. Kruse puts the puzzle in a single line: "Your gut is also sunless and holds more cells than you do, so how does it handle light in its dark tube?" (Kruse, Tensegrity #14).

Two very different groups have tried to answer that question. Chronobiologists and microbiologists answer it with clocks, hormones and feeding cycles. Quantum-biology voices answer it with photons, electrons, water and spin. This piece walks through each answer in the words and findings of the people who hold it, labeled with the site's three tiers.

Part 1: The Centralized View: a microbiome that keeps time

Gut bacteria oscillate across the day

In 2014, Christoph Thaiss, Eran Elinav and colleagues at the Weizmann Institute reported that the gut microbiota of mice swings through daily cycles in both composition and function. A sizable share of bacterial groups rose and fell over 24 hours. When the team disrupted the host's clock, by knocking out clock genes or by simulating jet lag, the rhythms were lost and the animals tended toward weight gain and glucose intolerance. Jet-lagged humans showed similar shifts, and stool from jet-lagged people promoted obesity when transferred into germ-free mice (Thaiss et al. 2014). Centralized View

The same year, Amir Zarrinpar, Satchidananda Panda and colleagues at the Salk Institute showed that when mice eat drives much of that rhythm. Mice fed a high-fat diet around the clock lost much of their microbial cycling; restricting the same food to the active phase partly restored it (Zarrinpar et al. 2014). Centralized View

Xue Liang, Frederic Bushman and Garret FitzGerald at the University of Pennsylvania then showed that the host's own clock gene, Bmal1, is needed for these rhythms, and that the patterns differ between males and females (Liang et al. 2015). Centralized View

Light disruption and dysbiosis

Robin Voigt, Ali Keshavarzian and colleagues at Rush University exposed mice to repeated light-dark phase shifts, a model of shift work. The animals' gut microbiota changed, and the changes were stronger when the shifts were combined with a high-fat, high-sugar diet (Voigt et al. 2014). Jennifer Deaver and colleagues at the University of Miami found that constant-light and shifted schedules altered both taxa and the functional genes of the mouse microbiome (Deaver et al. 2018). Centralized View

Bacteria have clocks and eyes of their own

Microbes don't only follow their host. Many keep time and sense light directly:

  • Cyanobacteria run a true circadian clock. Takao Kondo's group identified the kaiABC gene cluster as the clock in Synechococcus (Ishiura et al. 1998). In 2005, the same group rebuilt a 24-hour oscillation in a test tube using only the three Kai proteins and ATP (Nakajima et al. 2005). Centralized View
  • Non-photosynthetic bacteria carry photoreceptors. Seth Davis, Alexander Vener and Richard Vierstra described bacteriophytochromes, red/far-red light sensors related to plant phytochromes, in bacteria such as Deinococcus radiodurans (Davis et al. 1999). Centralized View
  • A gut bacterium responds to melatonin. Jiffin Paulose, Vincent Cassone and colleagues reported that Enterobacter aerogenes, a human gut bacterium, swarms in a rhythmic, circadian-like pattern, and that melatonin, the hormone of darkness, makes that swarming stronger (Paulose et al. 2016). Centralized View

Melatonin: the gut's night signal

The pineal gland is the famous source of melatonin, but George Bubenik's review of gastrointestinal melatonin reports that the gut holds at least 400 times more melatonin than the pineal gland (Bubenik 2002). Russel Reiter and colleagues describe mitochondria as a site of melatonin production and call melatonin a mitochondria-targeted antioxidant, "one of evolution's best ideas" in the words of their paper's title (Reiter et al. 2017; Suofu et al. 2017). Centralized View on gut melatonin levels; Middle Ground on mitochondrial melatonin in human tissue

Sunlight on the skin changes the gut

Else Bosman, Bruce Vallance and colleagues at the University of British Columbia gave healthy women three sessions of narrow-band UVB to the skin over one week in winter. Women who were not taking vitamin D supplements showed a rise in serum vitamin D and an increase in gut microbial alpha- and beta-diversity, along with higher levels of several bacterial families (Bosman et al. 2019). Centralized View for the finding; Middle Ground for how it generalizes

The microbiota-gut-brain axis

John Cryan, Ted Dinan and colleagues at University College Cork have mapped two-way traffic between gut microbes and the brain: the vagus nerve, immune signals, short-chain fatty acids and neurotransmitter precursors such as tryptophan, which is also the starting point for serotonin and melatonin (Cryan et al. 2019). Centralized View

Part 2: The Middle Ground: can light reach the gut directly?

Red and near-infrared light, and the "photobiomics" idea

Tiina Karu's work in the 1990s identified cytochrome c oxidase, the last enzyme of the mitochondrial electron transport chain, as a main absorber of red and near-infrared light in cells (Karu 1999). Michael Hamblin of Harvard's Wellman Center summarizes photobiomodulation as light being absorbed by mitochondria, raising ATP and nitric oxide release and shifting reactive oxygen and inflammatory signaling (Hamblin 2017). Centralized View that cells absorb these wavelengths; Middle Ground on the size of the clinical effects

Australian researchers Brian Bicknell, Ann Liebert and Hosen Kiat took the next step. In mice, they reported that near-infrared light applied to the abdomen shifted gut microbial diversity, including a rise in Allobaculum, a genus associated with a healthy microbiome (Bicknell et al. 2019). In a 2019 review they coined the term "photobiomics" for the idea that light, both directly and through the host, can shape the microbiome (Liebert et al. 2019). Middle Ground

How deep does light go?

Near-infrared wavelengths travel farther through skin and tissue than visible light, which is why they are used in tissue imaging and photobiomodulation. How much reaches the gut lumen, and whether the effects in Bicknell's work came from light hitting bacteria or from signals in the host's own tissues, is still being worked out by the researchers in this field. Middle Ground

Water near membranes

Gerald Pollack's lab at the University of Washington reports that water next to hydrophilic surfaces forms an ordered "exclusion zone" (EZ) that pushes out solutes and holds a charge, and that infrared light makes this zone grow (Zheng et al. 2006). Pollack argues that light is the energy input that keeps this water structured. The gut lining, coated in mucus and lined with membranes, is one of the body's largest water-membrane surfaces. Middle Ground

Part 3: The Decentralized View: the gut as a quantum light network

This is where Jack Kruse's framework takes over. His view starts from one claim: light, not food, is the master signal, and food is light stored in electrons.

Food is stored sunlight, broken into electrons

Kruse writes that mitochondria have "no carb, fat, or protein transporters," only an electron transport chain, and that "all foods are broken down into electrons." He adds that electrons carry the energy of the photons that built the food, set by the season in which it grows (Kruse, Tensegrity #14). In his model, eating out of season or under artificial light sends the gut mismatched information. Decentralized View

Bacteria talk in light

Kruse's most distinctive claim is that gut bacteria communicate with light. He writes that bacteria "are able to release large amounts of light frequencies in the form of biophotons," and that "Bacteria release 5000 times more light than our cells do. They release this light when we eat" (Kruse, Time #6). He argues that quorum sensing, the way bacterial populations coordinate, will only be fully understood once researchers look at light frequencies, and that the gut microbiome sculpts the host epigenome "with light through its interaction with our eukaryotic cell membranes of enterocytes" (Tensegrity #14). Decentralized View

He leans on a real body of research. Every living cell gives off ultra-weak photon emission, a faint glow from excited molecules created during oxidative metabolism. Michal Cifra and Pavel Pospíšil define and review this "biophoton" emission and how it is measured (Cifra & Pospíšil 2014). German biophysicist Fritz-Albert Popp spent decades arguing that this light is coherent and carries information between cells. Russian microbiologist M. V. Trushin reported experiments in which bacterial cultures separated by glass, but not by light-blocking barriers, influenced each other's growth and light emission (Trushin 2003). Centralized View that cells emit ultra-weak light; Decentralized View that it carries information between cells and microbes

DHA and melanin as the receivers

In Kruse's model, the receiving end is the DHA in the cell membranes of gut cells. As laid out in Cardiolipin and DHA, DHA's six double bonds create a continuous cloud of delocalized pi electrons, which in this framework makes it a quantum semiconductor able to turn light into a direct-current electrical signal and back again. In his gut writing, he describes enterocytes using DHA to convert bacterial light into electrical signals carried to the brain along the vagus nerve. Melanin, which he calls a natural light-to-electron converter, plays the same role in his model wherever it is found. Decentralized View

Mitochondria are domesticated bacteria

Kruse ties the two kingdoms together through the mitochondrion. "What links both kingdoms is our mitochondria," he writes, pointing out that mitochondria evolved from bacteria and still carry their own 37 genes (Tensegrity #14). In his framework, gut bacteria and mitochondria share one photoelectric language, so the microbiome works as an extension of your own mitochondrial network. When one is out of rhythm, the other follows. Centralized View on the bacterial origin of mitochondria; Decentralized View on a shared light-electron network

Electrons tunnel, protons cohere

Some of the physics here is mainstream. Harry Gray and Jay Winkler at Caltech have shown that electrons move between redox centers in proteins by quantum tunneling, at rates set by distance (Gray & Winkler 2003). Centralized View Kruse builds on this: he argues that light, cold and DHA tighten the spacing in the respiratory chain so electrons tunnel faster, and that protons moving through ATP synthase behave coherently. At night, he proposes, the gut switches modes: "During daylight we use electrons to live our observable life. During sleep might the gut microbiome use protons and light to conduct our quantum abilities?" (Tensegrity #14). Decentralized View

Real quantum biology lives in bacteria

The strongest published evidence for quantum effects in living energy systems comes from microbes. In 2007, Gregory Engel, Graham Fleming and colleagues reported long-lived quantum coherence, a wavelike sharing of energy, in the Fenna-Matthews-Olson light-harvesting complex of green sulfur bacteria (Engel et al. 2007). Centralized View that coherence was observed; Middle Ground on how much it matters for function at body temperature Quantum-biology voices take this as proof that bacteria evolved to use quantum mechanics for handling light, and Kruse argues the same toolkit is conserved in the bacteria of the gut and in our mitochondria. Decentralized View

Spin and magnetism

The radical-pair mechanism, first modeled by Thorsten Ritz, Klaus Schulten and colleagues to explain how birds sense Earth's magnetic field, relies on light creating pairs of electrons whose spins stay quantum-linked (Ritz et al. 2000; Hore & Mouritsen 2016). It is triggered by blue light in cryptochrome proteins, which are also found in bacteria. Middle Ground Kruse extends this idea to the whole body in his Tensegrity #5: Your Magnetic Sense, arguing that the light and magnetic environment sets the spin state of electrons in the gut and mitochondria. Decentralized View

Deuterium, UV and the "biomass switch"

Kruse writes that ultraviolet light drives the forward flow of electrons in chloroplasts, the retina and mitochondria, and that a shift in the terminal electron acceptor in the gut acts as a "biomass switch" that sets how bacteria grow (Kruse, Ubiquitination 25). He links this to NAD+, ketosis and the seasons. Kruse and deuterium researchers such as László Boros also argue that sunlight-driven mitochondria make deuterium-depleted metabolic water, and that heavy hydrogen jams the ATP synthase rotor (see Cold Is Information for that thread). Decentralized View

Light at night and non-native EMF

In this framework, blue-heavy artificial light after dark suppresses melatonin, so the gut loses its night signal, and the clock-driven rhythms seen in the Thaiss and Voigt mouse studies break down. Kruse goes further and argues that non-native electromagnetic fields from devices scramble the light and spin signals that gut bacteria and mitochondria share. Middle Ground on light at night and melatonin; Decentralized View on non-native EMF and the microbiome

Light and the microbiome in practice

Here is what the featured voices recommend, in their own frameworks. None of it is advice from this site.

  • Morning sun. Kruse tells readers to see the sunrise and get daylight on bare skin and eyes early, which in his model sets the eye clock that the gut "takes its lead from" (Time #6). See the Light pillar.
  • UV on skin. Kruse argues for regular midday UV exposure. Bosman's team used narrow-band UVB in a clinical setting.
  • Dark nights. Kruse recommends cutting artificial blue light after sunset and sleeping in darkness to protect melatonin. Researchers in the shift-work studies describe light-dark disruption as a driver of dysbiosis in their models.
  • Eat with the sun. Panda's group promotes time-restricted eating within a daytime window. Kruse argues for eating local, seasonal food during daylight.
  • Red and near-infrared light. Bicknell, Liebert and colleagues are studying abdominal photobiomodulation. Kruse prefers natural sunrise and sunset light, which are rich in red and infrared.
  • Seafood, DHA and cold. Kruse pairs light with DHA-rich seafood and cold exposure as one system.

Evidence map

Claim Label
Gut microbes oscillate daily; host clock and meal timing drive it Centralized View
Light-dark disruption alters the gut microbiota in mice Centralized View
Cyanobacteria run a KaiABC clock; bacteria carry light sensors Centralized View
The gut holds far more melatonin than the pineal Centralized View
Skin UVB raises gut microbial diversity Centralized View / Middle Ground
Abdominal near-infrared light reshapes the microbiome Middle Ground
EZ water forms at membranes and grows with infrared Middle Ground
Quantum coherence in bacterial light harvesting Centralized View / Middle Ground
Gut bacteria communicate with biophotons Decentralized View
DHA and melanin turn bacterial light into vagal signals Decentralized View
Gut bacteria and mitochondria form one photoelectric network Decentralized View
Non-native EMF scrambles microbial and mitochondrial signals Decentralized View

This article presents viewpoints, attributed to their sources. It is not medical advice.

Sources

Dr. Jack Kruse (viewpoint sources, jackkruse.com):

Research:

Disclaimer. This article is for education only and presents viewpoints, attributed to their sources. It is not medical, legal or financial advice and is not a substitute for a qualified professional. Full disclaimer

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