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The Gut-Muscle Connection: How Gut Health Affects Muscle and Bone Health

Sep 01, 2026
A fit woman strength training with a barbell, representing the connection between gut health, muscle strength, and bone healt
Gut health plays a key role in muscle and bone health. Learn how the gut-muscle and gut-bone axes affect protein digestion, muscle growth, and bone density—and why supporting digestion is especially important in midlife.

By Suzanne Fenske, MD, FACOG, ABOIM, MSCP

Midlife may be the first time you’re thinking about musculoskeletal health. With age and estrogen loss, muscle mass declines and bone loss accelerates, which has consequences for metabolic health and disease risk. Diabetes, heart disease, and osteoporosis are all linked to muscle loss.

For women taking GLP-1 medications for weight loss, rapid weight loss can often mean losing muscle along with fat. Lower muscle mass can impact bone density and mass as well. GLP-1 microdoses, along with nutrition and exercise interventions, can help preserve muscle and bone.

The number one strategy you’ve likely heard, and even heard from us at TārāMD, is to eat more protein. It’s great that protein is getting the attention it deserves, and you absolutely need to eat enough protein to meet your body composition goals.

However, what about the women who don’t feel good when they increase protein in their diet? Or have digestion side effects from GLP-1s? Or have increased bloating and GI symptoms with perimenopause?

Today’s article will explore the connection between musculoskeletal health and gut health.

In some cases, the “eat more protein” advice isn’t the whole story because we need to look at gut health and digestion first so you can digest, absorb, and utilize the protein your body needs.

Continue reading as we discuss:

  • The gut-muscle axis
  • The gut-bone axis
  • Integrative care for digestive health, protein digestion, and musculoskeletal health

Gut-Muscle Axis

You may already be familiar with the gut-brain axis, the communication pathways between the gut and the brain. The gut communicates with other body systems too, and muscle is no exception.

The gut-muscle axis explains this bidirectional signaling network between the gut microbiome and the muscles. It turns out that muscle growth isn’t only from protein and exercise; the gut plays a role as well.

Exercise directly stimulates muscles, but exercise also modulates the entire gut-muscle axis. Exercise shifts the microbiome to produce more metabolites that favor muscle growth. Here are a couple of examples:

  • The microbiome produces short-chain fatty acids (SCFA), which influence immune cells in the gut that migrate to the muscles to support tissue repair
  • The gut microbiome can synthesize specific amino acids and B vitamins required for muscle protein synthesis.

Different exercise prescriptions can have different effects on the microbiome. While we are still learning more, here are a couple of examples:

  • Endurance training can increase overall microbial diversity, while specifically increasing Akkermansia, a beneficial bacteria that promotes GLP-1 release, metabolic health, and favorable body composition.
  • Moderate-intensity training in those with type 2 diabetes increases probiotic species that produce butyrate, an SCFA.

Understanding the gut-muscle axis may lead to more tools and treatments for muscle loss due to age, disease, menopause, and more.

The Gut-Muscle Axis and Protein Digestion

The science is clear that you need protein for muscle growth. Eating a decent 25-30 gram serving of protein, with enough essential amino acids including leucine, sends your muscles into building mode.

However, you need to be able to digest and absorb that protein!

Undigested protein is not necessarily good for the microbiome. It can promote proteolytic bacteria (bacteria that eat protein) and undesirable metabolites that promote inflammation, muscle wasting, and anabolic resistance.

For protein digestion and absorption, you need:

  • Stomach acid (HCl), which can decrease in perimenopause and with age
  • Digestive enzymes made in the stomach, pancreas, and small intestine
  • A healthy gut barrier
  • Healthy movement through the digestive tract

Infections like H. pylori, dysbiosis (gut microbiome imbalances), low enzymes and HCl, stress, and constipation can impair protein digestion. GLP-1s and other medications can have digestive side effects, slowing transit time and allowing more protein fermentation. In these cases, it may be helpful to optimize digestion before increasing protein for muscle mass.

Gut-Bone Axis

As you maintain or build muscle, you also maintain or build bone. So, it makes sense that microbiome support that favors muscle health also supports bone. But the gut also directly influences bone via the gut-bone axis.

The microbiome is involved in:

  • Nutrient absorption – including the nutrients needed for bone formation (amino acids from protein, calcium, magnesium, vitamin D, boron, etc.)
  • Immunity – butyrate from the gut diffuses into bone marrow and supports T regulatory cells
  • Hormones – the microbiome impacts growth factors and other hormone signals involved in bone density regulation
  • Exercise – promotes microbiome changes that increase calcium absorption (as well as direct mechanical load on the bones)

An Integrative Perspective

It does not make sense to look at any one part of the body in isolation; everything is connected, and intricately so. In integrative medicine, we look at the big picture and work to understand the connections for each patient.

Strong muscles and bones require more than just protein and exercise; we need to be thinking about the health of the gut microbiome for long-term musculoskeletal health.

For women in perimenopause, ovarian hormone changes alter the gut microbiome. It’s not uncommon for bloating, reflux, food sensitivities, and other digestive symptoms to arise during this time. For those taking GLP-1 medications, slower digestive movement is common; it’s one  reason you feel fuller when taking these medications, but we want to support the microbiome and ensure you maintain muscle mass.

So, the advice to just eat more protein is not enough; we want to ensure that your digestive system can handle the protein load optimally, without symptoms, side effects, or poor absorption. This means taking a closer look at digestive health and the microbiome, and the factors that influence them (like perimenopause, stress, toxins, etc.) If you have low stomach acid, GERD, SIBO, dysbiosis, or another gut imbalance, it makes sense to address this first, before increasing protein.

Nutrition is so foundational for chronic disease prevention and long-term wellness, but we want to look at the overall dietary pattern in addition to specific nutrients. In addition to eating enough protein, we want to consider nutrition that nourishes the microbiome, which means more plant foods, rich in fiber, resistant starch, and polyphenols, the colorful compounds in whole plant foods. Interestingly, polyphenols can protect against amino acid fermentation in the microbiome!

While eating more protein and exercising, especially strength training, is good advice for building lean body mass and maintaining bone density, it’s time we add gut health to our recommendations.

It can be a lot to think through on your own, and we are here to guide you. We offer comprehensive integrative medical care for women, which includes personalized nutrition, microbiome testing and treatment, bioidentical hormone therapy, and thoughtful peptide strategies. If you’re ready to get started, please reach out today!

Frequently Asked Questions About Gut, Muscle and Bone Health

What Is the Gut-Muscle Axis?

The gut-muscle axis describes the two-way communication between the gut microbiome and skeletal muscle. Gut microbes produce metabolites, including short-chain fatty acids, that can influence inflammation, metabolism, muscle repair, and other processes involved in maintaining healthy muscle.

Exercise also influences this relationship by changing the composition and activity of the gut microbiome, making the gut-muscle axis an emerging area of research in muscle health, aging, and muscle loss.

Can Gut Health Affect Muscle Growth?

Yes. Building and maintaining muscle requires more than strength training and eating enough protein. The digestive system must also be able to properly digest protein, absorb amino acids and other nutrients, and make them available for muscle protein synthesis.

The gut microbiome may also influence muscle health through the production of short-chain fatty acids, amino acids, B vitamins, and other metabolites involved in muscle metabolism and repair.

Can Poor Digestion Make It Harder to Absorb Protein?

Yes. Eating enough protein is important, but the body must first break it down into amino acids that can be absorbed and used.

Stomach acid, digestive enzymes, a healthy intestinal barrier, and normal gastrointestinal motility all contribute to protein digestion and absorption. Factors such as low stomach acid, dysbiosis, H. pylori, stress, constipation, and certain medications may interfere with this process.

Why Does Eating More Protein Sometimes Cause Bloating?

Increasing protein intake may worsen bloating or other gastrointestinal symptoms in some people, particularly when digestion or gastrointestinal motility is already impaired.

When protein isn't adequately digested and absorbed, more may reach the colon, where bacteria can ferment it and produce metabolites. For women experiencing bloating or digestive symptoms, addressing digestive health may therefore be an important part of successfully increasing dietary protein.

How Does Gut Health Affect Bone Health?

The gut and bones communicate through what's known as the gut-bone axis. The gut microbiome influences nutrient absorption, immune activity, hormones, and other processes involved in maintaining healthy bones.

A healthy digestive system also helps the body absorb nutrients needed for bone formation and maintenance, including amino acids, calcium, magnesium, and vitamin D.

Does Perimenopause Affect Gut and Muscle Health?

Perimenopause can affect both. Changing ovarian hormones influence the gut microbiome, while declining estrogen contributes to changes in muscle mass and bone density.

This makes midlife an especially important time to consider gut health, adequate protein intake, strength training, and other strategies that support muscle and bone health together.

Do GLP-1 Medications Affect Muscle and Gut Health?

GLP-1 medications can slow gastrointestinal motility and commonly cause digestive side effects. Weight loss can also include loss of lean mass as well as body fat, making preservation of muscle particularly important.

Adequate protein, resistance exercise, and attention to digestive health can therefore be important considerations for women using GLP-1 medications. Individual recommendations should be personalized with a healthcare professional.

What Foods Support the Gut-Muscle Axis?

A dietary pattern that provides adequate protein while also supporting the gut microbiome can help support overall musculoskeletal health.

In addition to sufficient protein, plant foods rich in fiber, resistant starch, and polyphenols help nourish the gut microbiome while providing nutrients and compounds involved in overall health.

Can Exercise Improve the Gut Microbiome?

Research suggests that exercise can influence the composition and activity of the gut microbiome. Different forms of exercise may have different effects, including changes in microbial diversity and bacteria associated with beneficial metabolites.

Exercise simultaneously provides direct stimulation to muscle and bone, making physical activity particularly relevant to both the gut-muscle and gut-bone connections.

Should You Improve Gut Health Before Increasing Protein Intake?

For someone who tolerates a higher-protein diet well, there may be no need to delay increasing protein. However, if increasing protein causes significant bloating, constipation, reflux, or other digestive symptoms, it may be helpful to investigate digestive health rather than simply continuing to increase protein.

Addressing factors that interfere with digestion and absorption may help the body better tolerate and utilize dietary protein.

References

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  2. Arukha, A. P., Nayak, S., & Swain, D. M. (2025). Effect of Akkermansia muciniphilaon GLP-1 and Insulin SecretionNutrients17(15), 2516.
  3. Li, Z., Wang, Q., Huang, X., Wu, Y., & Shan, D. (2024). Microbiome's role in musculoskeletal health through the gut-bone axis insights.Gut microbes16(1), 2410478.
  4. Indrio, F., & Salatto, A. (2025). Gut Microbiota-Bone Axis.Annals of nutrition & metabolism81(Suppl 1), 47–56.
  5. Wu, J., Zhang, S., Wu, J., Luan, Y., Yao, X., Xu, B., Wang, Y., Sheng, Y., Xue, Y., & Ren, Y. (2026). Targeting the gut‑bone axis through exercise: A novel approach to osteoporosis prevention and treatment (Review).International journal of molecular medicine57(4), 91.
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