Gut Microbiome and Myositis-Associated Interstitial Lung Disease: Could Dysbiosis Be Linked to Rapidly Progressive ILD?

Could the Gut Microbiome Be Linked to Severe Lung Disease in Myositis?

Idiopathic inflammatory myopathies, or IIMs, are a heterogeneous group of autoimmune diseases that can affect skeletal muscle, skin, joints and internal organs.

Among their most important complications is interstitial lung disease, or ILD.

In some patients, ILD develops gradually.

In others, particularly certain autoimmune phenotypes, lung disease may progress over weeks or months and become life-threatening.

This aggressive phenotype is known as:

rapidly progressive interstitial lung disease, or RP-ILD.

The causes of this marked variation remain incompletely understood.

Autoantibodies, genetics and immune pathways clearly matter.

But researchers have begun asking another question:

Could the intestinal microbiome help influence which patients develop chronic ILD and which develop rapidly progressive disease?

Human evidence remains very limited.

However, an important metagenomic study has provided preliminary evidence that patients with myositis-associated RP-ILD may have intestinal microbial patterns that differ from those with chronic ILD. (PubMed⁠)

This is scientifically interesting because it moves the discussion beyond simply asking whether myositis is associated with dysbiosis.

The more clinically important question becomes:

Could the microbiome relate to the pulmonary phenotype and severity of autoimmune ILD?

At present, the answer is possible—but far from proven.

What Is Myositis-Associated ILD?

Idiopathic inflammatory myopathies include several autoimmune disorders, including:

• dermatomyositis

• polymyositis

• antisynthetase syndrome

• immune-mediated necrotizing myopathy

• clinically amyopathic dermatomyositis

ILD is a major pulmonary manifestation of these disorders and may occasionally appear before obvious muscle symptoms.

The spectrum ranges from relatively indolent disease to rapidly progressive respiratory failure. Current 2026 literature continues to emphasize substantial heterogeneity and the importance of myositis-specific autoantibodies in defining clinical phenotypes. (PubMed⁠)

This heterogeneity is crucial when discussing microbiome research.

There may not be one single “myositis microbiome.”

Different autoimmune phenotypes may potentially have different microbial and metabolic signatures.

Why Is Rapidly Progressive ILD So Important?

RP-ILD can deteriorate over a short period and is associated with substantial morbidity and mortality.

It is particularly recognized in patients with certain dermatomyositis phenotypes.

One of the best-known associations is with:

anti-MDA5 antibody-positive dermatomyositis.

Other myositis-specific and myositis-associated antibodies can also help define pulmonary risk.

Myositis-associated ILD therefore provides an especially interesting model for studying whether biological markers—including the microbiome—could eventually help identify distinct disease phenotypes.

The Current Human Microbiome Evidence

The most directly relevant human study was published in Clinical Immunology in 2023.

Researchers performed a metagenome-wide association study using high-depth whole-genome shotgun sequencing.

The study included:

• 30 patients with myositis

• 31 healthy controls

Among the 30 myositis patients:

• 11 had rapidly progressive ILD

• 10 had chronic ILD

This is a small study.

But it is important because it directly compared microbial characteristics between patients with different ILD trajectories. (PubMed⁠)

What Was Different in Myositis Overall?

Compared with healthy controls, patients with myositis had increased abundance of organisms including:

• Alistipes onderdonkii

• Parabacteroides distasonis

• Escherichia coli

They had decreased abundance of organisms including:

• Roseburia intestinalis

• Akkermansia muciniphila

• a Lachnospiraceae bacterium

The investigators also identified differences in microbial metabolic pathways. (PubMed⁠)

These findings suggest that myositis is associated with altered intestinal microbial ecology.

However, they do not tell us whether the dysbiosis:

• preceded autoimmunity

• resulted from autoimmune disease

• reflected medications

• reflected diet

• resulted from reduced physical activity or disease severity

Causality cannot be determined from this design.

What Was Different in Rapidly Progressive ILD?

The most interesting comparison involved RP-ILD versus chronic ILD.

Patients with rapidly progressive disease demonstrated increased abundance of organisms including:

• Bacteroides thetaiotaomicron

• Parabacteroides distasonis

• Escherichia coli

and lower abundance of:

• Bacteroides A1C1

• Bacteroides xylanisolvens

compared with patients who had chronic ILD. (PubMed⁠)

These differences raise the possibility that severe pulmonary phenotypes are associated with different intestinal microbial ecosystems.

But the sample sizes—11 RP-ILD and 10 chronic ILD—are extremely small.

The findings should therefore be considered hypothesis-generating, not diagnostic.

Roseburia intestinalis: An Interesting Finding

One organism deserves particular attention:

Roseburia intestinalis.

Roseburia species are generally known for their capacity to participate in production of short-chain fatty acids, especially butyrate.

In the study, R. intestinalis was reduced in myositis and showed potential discriminatory value when comparing RP-ILD with chronic ILD. (PubMed⁠)

This is biologically intriguing because butyrate influences:

• intestinal-barrier integrity

• regulatory T cells

• inflammatory signaling

• immune tolerance

However, several important steps are missing.

Reduced Roseburia does not automatically prove:

• reduced systemic butyrate activity

• increased pulmonary inflammation

• causation of RP-ILD

• benefit from butyrate supplementation

The finding provides a mechanistic clue—not a treatment protocol.

Escherichia coli: Why Did It Attract Attention?

The investigators found increased Escherichia coli in myositis and in the RP-ILD subgroup.

They also found that E. coli contributed importantly to altered microbial metabolic pathways identified in both myositis and RP-ILD. (PubMed⁠)

This may be biologically relevant because Gram-negative bacteria contain lipopolysaccharide, or LPS, in their outer membrane.

LPS can activate innate immune pathways such as:

TLR4 → NF-κB

leading to inflammatory cytokine signaling.

This generates a plausible hypothesis:

dysbiosis with greater pro-inflammatory microbial activity → altered systemic immune signaling → more severe autoimmune pulmonary inflammation

But this remains speculative.

The study did not demonstrate that intestinal E. coli or circulating LPS caused RP-ILD.

Microbial Metabolic Pathways May Matter More Than Individual Bacteria

One of the most valuable aspects of shotgun metagenomic sequencing is that it can investigate microbial functional pathways, not just bacterial abundance.

The 2023 study found multiple metabolic pathways that differed between:

• myositis and healthy controls

• RP-ILD and chronic ILD

and identified E. coli as an important contributor to several pathway differences. (PubMed⁠)

This supports an emerging principle in microbiome science:

What the microbiome does may ultimately matter more than which organisms are present.

Future research is therefore likely to focus on:

• microbial metabolites

• amino-acid metabolism

• SCFAs

• bile acids

• immune-active bacterial products

• metabolomic signatures

  About Dr. Samar Shadly

  Dr. Samar Shadly is a Consultant Pulmonologist and Certified Functional Medicine Practitioner, with advanced subspecialty training in interstitial lung disease, pulmonary fibrosis, pulmonary hypertension, and lung transplantation, together with expertise in functional and integrative medicine.

  Her approach combines evidence-based pulmonary medicine with a broader assessment of factors that may influence a patient’s overall health, including nutrition, gastrointestinal health, the gut microbiome, metabolic health, lifestyle, and relevant environmental exposures.

  A particular focus of her work is the emerging field of Integrative and Functional Pulmonology, especially in pulmonary fibrosis and autoimmune-associated interstitial lung disease. Her goal is to bridge conventional respiratory medicine with scientifically grounded integrative strategies, while clearly distinguishing established clinical evidence from promising but still experimental research.

  Living with Pulmonary Fibrosis or Interstitial Lung Disease?

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  Integrative care is intended to complement—not replace—evidence-based pulmonary treatment and should always be individualized according to the diagnosis and clinical situation.