Real Culprit Behind Insomnia May Not Be the Brain, but the Small Intestine — A New Scientific Explanation

Have you ever experienced this — the more exhausted you feel, the harder it is to fall asleep? The moment you lie down your gut starts churning, you wake up multiple times during the night, and somehow feel even more tired in the morning? Most of us blame this on an “overactive brain” or “too much stress.” But a newly published study in Cell Metabolism, Intestinal clock shapes sleep-wake cycle via sustaining glutamine homeostasis , offers a completely different explanation: your sleep may actually start falling apart in the small intestine — not the brain.

Once you stay up late, snack at night, live with irregular hours, or stay under chronic stress, the small intestine’s rhythm becomes disrupted — and the brain receives “wake-up signals” at the wrong time. That’s when everything you’re familiar with starts happening: feeling wired when you want to sleep, your gut becoming active the moment you lie down, waking up at night, and feeling even more drained the next day. These scattered symptoms actually point to one hidden pathway you’ve probably never noticed: the “Small Intestine → Brain” axis.

In the following sections, we’ll break down this newly discovered “Small Intestine–Glutamine–Brain” sleep axis in the simplest way: how the intestinal clock sets your wake–sleep rhythm, why modern lifestyles easily throw it off, and most importantly — what you can do to reset this “gut clock” and bring your sleep back into balance.

1 | The Small Intestine Has Its Own “Schedule”: Your Sleep Rhythm Starts Here

When we talk about a “body clock,” most people immediately think of the brain — the command center that tells us to stay alert during the day and wind down at night. But new research shows something surprising: many organs have their own mini clocks, and the small intestine is one of the most important yet most overlooked timekeepers.

For the small intestine, daytime and nighttime are completely different. During the day, its main job is to absorb nutrients and process food; at night, it needs to slow down, rest, and allow the body to enter repair mode.

You can think of the small intestine as an employee with a carefully arranged work schedule: day shift — busy absorbing; night shift — staying quiet so the body can smoothly switch into sleep mode.

Ideally, these two timing systems should run in sync: daytime → both are active; nighttime → both are resting. But modern lifestyles make it hard for the small intestine to follow its schedule.

Staying up late, eating late dinners, grabbing midnight snacks, irregular routines, chronic stress… From the small intestine’s perspective, all of these are like someone constantly rewriting its schedule:

This is why you may feel: low energy during the day, unable to calm down at night, shallow sleep, unstable sleep, or waking up tired. It looks like a brain problem, but very often, it’s the small intestine that loses rhythm first — and the brain simply follows.

So how does the small intestine actually “tell” the brain what time it is? What is the key signal it uses to indicate daytime versus nighttime? In the next section, we start with a common but powerful molecule that influences sleep — glutamine.

2 | Glutamine: The Signal the Small Intestine Uses to Tell the Brain “What Time It Is”

For the brain to know whether it’s time to feel alert or time to wind down, the small intestine needs a way to send a clear signal. According to new research, that signal is a very common nutrient — glutamine.

Glutamine may sound scientific, but you can imagine it as a “time light”:

The small intestine absorbs glutamine at different rates depending on the time of day: More absorption during the day → helps keep you awake; Less absorption at night → helps the body prepare for sleep.

So the small intestine is continuously “reporting the time” to the brain — sending “wake signals” during the day and “rest signals” at night.

But once the small intestine’s rhythm is disrupted, the glutamine “light pattern” becomes chaotic: not bright enough during the day → you feel tired, unfocused; too bright at night → you feel awake even when exhausted, sleep lightly, or struggle to fall asleep.

You think it’s your brain that can’t sleep — but it may actually be the small intestine sending the wrong brightness at the wrong time. And glutamine is the “light” that’s out of sync.

If glutamine is the signal light, then who controls how bright or dim it is? That job belongs to two “intestinal clock genes” — BMAL1 (daytime ON) and REV-ERBα (nighttime OFF). We’ll explore them in detail in Section 3.

3 | BMAL1 × REV-ERBα: The “Dual Clock Switches” That Decide When You Feel Awake or Sleepy

In the previous section, we talked about how the small intestine uses glutamine to tell the brain “what time it is.” What actually decides how bright this “time light” shines, and when it should turn up or down, are two key players inside the intestinal cells: BMAL1 and REV-ERBα.

Although their names sound very technical, you can think of them in a much simpler way: BMAL1 is the daytime ON button, and REV-ERBα is the nighttime OFF button.

Under normal conditions, these two switches take turns like a relay: during the day, BMAL1 turns on → the small intestine is active, glutamine signaling ↑ → the brain receives “stay awake” messages; at night, REV-ERBα turns on → the small intestine slows down, glutamine signaling ↓ → the brain receives “prepare for sleep” messages.

This rhythm sounds simple, but it has a huge impact on sleep. The problem is: modern lifestyles often make these switches fire at the wrong time.

📌 Why is this especially common in office workers, midlife women, and older adults?

● Office workers (stress + low daylight exposure)

Sitting indoors most of the day, staring at screens, and living under chronic stress can disrupt both BMAL1 and REV-ERBα. The pattern becomes: sleepy during the day, wired at night — a completely inverted rhythm.

● Midlife women (hormones × intestinal rhythm)

Hormonal fluctuations can affect gut activity and indirectly weaken REV-ERBα’s “night shutdown” function. That’s why midlife women often report: waking up in the middle of the night, lighter sleep, or difficulty falling asleep.

● Older adults (weaker rhythms by default)

As we age, the activity of BMAL1 and REV-ERBα tends to decline. The small intestine becomes less efficient at switching cleanly between “on” and “off” modes, making daytime drowsiness and nighttime awakenings more common.

4 | When the Small Intestine Rhythm Is Off: Signals from Your Body & What You Can Do Right Away

When the small intestine’s “day mode” and “night mode” don’t switch smoothly, the brain receives conflicting time signals. This isn’t just “having trouble falling asleep” — it’s a whole set of rhythm errors that affect falling asleep, staying asleep, deep sleep, and daytime alertness.

The good news: these states follow clear patterns, and they can often be improved with simple, specific lifestyle adjustments. The table below summarizes the most common “rhythm warning signals” and their matching “repair strategies.”