Can Gut Bacteria Boost Your Metabolism?
This Week’s Research Highlight
Your metabolism never sleeps.
Even when you’re doing absolutely nothing — scrolling through your phone, sitting in traffic, or lying in bed — your body is still burning calories just to keep the lights on. This baseline calorie burn, known as resting energy expenditure (REE), accounts for around 60-75% of the energy you use each day — far more than what you burn through exercise.
Curiously, there is reason to believe that we are burning fewer calories at rest now than our ancestors did.
One large-scale analysis found that total daily energy expenditure has declined significantly over the past few decades. This was not attributable to a reduction in physical activity, like you might assume, but rather due to a drop in our basal energy expenditure — the calories our bodies burn at complete rest.
Similarly, recent research by Harvard scientists estimates that resting metabolic rates in the US have decreased by about 6% since the 19th century, a trend mirrored by a steady drop in average body temperatures.
This trend is particularly notable, of course, in light of the ever-increasing rate of obesity worldwide. Recall that REE accounts for over 60% of daily energy expenditure, so even very small decreases in this foundational metabolic rate could have meaningful long-term implications for energy balance.
But what exactly is driving this?
Well, metabolism isn’t just a fixed number on a chart. It can fluctuate in response to a constellation of factors. For example, when you are exposed to cold, your body activates brown adipose tissue, a special type of fat that has evolved to generate heat. Research shows that exposure to cold temperatures can increase resting energy expenditure by as much as 80–200 calories per day.
But cold exposure isn’t the only factor that might influence metabolism in surprising ways. Emerging research suggests that your gut bacteria could also play a role in how efficiently your body burns energy, even when you're sitting around doing nothing.
A team of Japanese researchers recently tested whether a specific strain of beneficial bacteria — Bifidobacterium animalis subsp. lactis GCL2505 — paired with inulin, a fiber that fuels its growth, could boost resting metabolic rate. Let’s take a look at what they did, and how you can take advantage of the findings.
How They Tested It
To investigate whether probiotics and prebiotics could influence resting metabolism, researchers conducted a double-blind, placebo-controlled clinical trial with 44 Japanese adults, who were slightly overweight but otherwise healthy.
The participants were randomly assigned to one of two groups:
One group received a dairy-based drink containing the probiotic strain Bifidobacterium animalis subsp. lactis GCL2505, paired with 5 grams of inulin fiber — a prebiotic that serves as food for beneficial gut bacteria.
The other group received a look-alike placebo drink without the active ingredients.
To measure how efficiently participants burned calories at rest, researchers used indirect calorimetry, a gold-standard method for assessing metabolism.
Before each test, participants spent the night at the research facility, ensuring a controlled sleep and dietary routine. The next morning, they breathed through a specialized mask connected to a high-precision metabolic analyzer.
Because metabolism isn’t static, tracking these values over time allowed researchers to determine whether probiotics and prebiotics had a measurable impact on energy expenditure.
Over the course of four weeks, researchers collected several key data points, including:
- Resting Energy Expenditure (REE): The primary outcome; measured at baseline, two weeks, and four weeks.
- Stool samples: To analyze gut bacteria composition and see whether probiotic intake altered microbial populations.
- Dietary records: To ensure that any metabolic changes weren’t simply due to differences in food intake.
By carefully controlling sleep, diet, and environmental factors, the researchers aimed to isolate the effects of probiotics and prebiotics on metabolism.
The Power of Probiotics
When the researchers crunched their data, they found shifts in both microbial composition and calorie-burning capacity.
Participants taking the probiotic-fiber combination saw a significant increase in beneficial Bifidobacteria, confirming that the intervention was actively reshaping the gut’s microbial landscape.
But the most striking result was a significant increase in resting energy expenditure. After just four weeks, participants in the probiotic group were burning an extra 84.4 calories per day at rest — without any changes to their diet or physical activity.
Okay, an extra 84 calories burned per day might not sound particularly impressive. But over time, small metabolic shifts like this can add up.
In theory, here’s what it could mean:
- Over a month, this adds up to roughly 2,500 extra calories burned — equivalent to about three-quarters of a pound of fat.
- Over a year, that’s 30,000 extra calories burned, potentially translating to a weight difference of 4–5 pounds, assuming no other changes.
(In reality, homeostatic adjustments — like changes in appetite, energy efficiency, and metabolic adaptation — make this calorie math quite a bit more complicated)
How Gut Bacteria Can Boost Energy Expenditure
When we consume Bifidobacterium alongside inulin fiber, we’re doing more than just feeding our gut bacteria. We’re setting off a metabolic chain reaction.
First, the probiotic bacteria flourish in the gut, thriving on the inulin, their preferred food source. As they break down the fiber, they release short-chain fatty acids (SCFAs) — tiny molecules that serve as metabolic messengers.
Importantly, these SCFAs do not remain confined to the gut. They enter the bloodstream and interact with specialized receptors throughout the body. One of these is GPR41, a receptor found in fat and muscle tissue. When SCFAs bind to GPR41, they trigger a series of metabolic responses — including stimulating brown adipose tissue, which burns calories to produce heat, as well as activating the sympathetic nervous system. It's like slightly turning up the thermostat of your cellular machinery
The metabolic influence of gut microbiota isn’t just a modern discovery — it may be part of an ancient biological partnership shaped by millennia of evolution. Hunter-gatherer societies like the Hadza of Tanzania offer a window into this ancestral state, revealing how traditional diets might have primed our metabolism for higher energy expenditure. The Hadza diet, rich in fibrous plant foods, fosters a unique gut microbiota profile, distinct from that of modern industrialized societies. Compared to urban controls, the Hadza exhibit significantly higher gut microbial diversity and richness, and this diverse microbial ecosystem leads to increased production of SCFAs.
In essence, by nourishing our gut microbiota with the right combination of probiotics and prebiotics, we’re tapping into an ancient metabolic pathway — one that holds the potential to counteract some of the metabolic slowdowns observed in modern life.
Putting It Into Practice
While this study focused on a specific probiotic strain and inulin, the broader takeaway is clear: nurturing beneficial gut bacteria may be a low-effort way to support metabolic health.
There are several practical steps you can take right now to help encourage Bifidobacteria growth and SCFA production:
1. Eat more fermentable fiber.
Bifidobacteria thrive on fermentable fibers — including inulin, resistant starch, and beta-glucans.
Some of the best sources include:
- 🥦 Vegetables: Garlic, onions, leeks, asparagus, artichokes, and cruciferous vegetables
- 🍌 Fruits: Bananas, apples, and berries
- 🌾 Whole grains: Oats, barley, and rye
- 🌰 Legumes & nuts: Lentils, peas, chickpeas, almonds, and pistachios
These types of fibers are particularly potent at fueling production of short-chain fatty acids.
2. Incorporate foods rich in Bifidobacteria.
While probiotic supplements are one option, you can also boost Bifidobacteria naturally through food. Consider adding:
- 🥛 Fermented dairy: Yogurt and kefir with “live and active cultures”
- 🥬 Fermented vegetables: Sauerkraut, kimchi, and pickled vegetables (just make sure they’re unpasteurized to retain live bacteria)
- 🧀 Aged cheeses: Certain cheeses like gouda, parmesan, and cheddar contain Bifidobacteria
3. Diversify your diet for a resilient microbiome.
The gut microbiome thrives on diversity. Eating a wide range of plant-based foods and fiber sources encourages microbial richness, which has been linked to better metabolic flexibility, immune function, and overall gut health.
Random Trivia & Weird News
🦠 Our gut microbes might manipulate our eating behavior to serve their own nutritional needs.
It is well established that bacterial species have evolved to thrive on specific nutrients. With that in mind, researchers have proposed that our gut bacteria might send chemical signals to our brain to make us crave their preferred menu items.
Sounds a bit far-fetched, but it is biologically plausible that microbes could exert this kind of control via the gut-brain axis. In support, the scientists point to several intriguing pieces of evidence. For instance, people who intensely crave chocolate have different microbial byproducts in their urine, compared to "chocolate indifferent" individuals, even when they are eating identical diets. Perhaps more tellingly, transferring gut bacteria from one organism to another can actually transfer food preferences along with them!
The good news? Our gut microbiome is at least somewhat malleable. Diet changes, probiotics, and other interventions can shift its composition within days — potentially offering new approaches to managing those seemingly unstoppable food urges.
Podcasts We Loved This Week
- Karl Herrup: The shortcomings of Alzheimer’s research. Via STEM-Talk.
- Sahil Bloom: The five types of wealth. Via Plain English with Derek Thompson.
Products We Like
Bob’s Red Mill Oat Bran
As I mentioned above, β-glucan is a fermentable fiber, which has been proven to boost levels of beneficial Bifidobacteria as well as fuel the generation of short-chain fatty acids.
Oat bran is nature’s richest source of β-glucans, containing more than twice as much as the same volume of whole oats (the bran is where the β-glucan lives).
Oat bran has some other advantages over oatmeal too:
- Higher protein content
- More total fiber
- Lower sugar content
- Quicker cooking time
I eat it almost every day and have actually come to prefer it over regular oatmeal.
humanOS Catalog Feature of the Week
Fiber — From the Mediterranean Diet Course
The Mediterranean diet is probably best known for featuring healthy sources of fats, like olive oil, which are linked to reduced cardiovascular risk. However, another major component of this dietary pattern that is at least as important is fiber, which is why we chose to highlight it specifically in our Mediterranean diet course.
Key insights from this lesson:
- Traditional Mediterranean diets contain more than double the fiber of typical Western diets
- Fiber works through multiple pathways, including nutrient absorption and microbiome support
- Research shows fiber intake is the strongest predictor of "successful aging" — i.e., living a long life free of disease and disability
Wishing you the best,
