The gut microbiota refers to the collection of various microbial communities that parasitize the host’s gastrointestinal tract, comprised of bacteria, fungi, viruses, archaea, and protozoa (Lynch and Pedersen, 2016). Typically, these microorganisms exist in a symbiotic relationship with the human host and play a crucial role in maintaining immune function and balance through interactions with the host’s immune system (La Barbera et al., 2022). The Lung-Gut axis is the concept of the mutual connection and interaction between the lungs and the gut, as these two organs are the largest surface organs with highly vascularized and immunologically active tissues. With their exposure to various external environmental challenges, including pathogenic microorganisms, harmful gases, and particulate matter, there is growing attention on the importance of the Lung-Gut Axis in impacting disease states in various ways, such as immune system communication (McAleer and Kolls, 2018), lung inflammation, and gut mucosal barrier. Changes in the gut microbiota have been linked to respiratory conditions like asthma (Barcik et al., 2020), chronic obstructive pulmonary disease (Bowerman et al., 2020), connective tissue-associated interstitial lung diseases (Salisbury et al., 2017), and acute lung injury (Kapur et al., 2018). Therefore, some gut microbial communities can serve as biomarkers for lung diseases.

Idiopathic pulmonary fibrosis (IPF) is a rare and severe chronic respiratory disease characterized by progressive interstitial lung damage and declining lung function. Symptoms of IPF include fatigue, shortness of breath during physical activity, and a persistent dry cough. This condition ultimately leads to organ failure and death. The exact cause of IPF is not fully understood, but various risk factors are thought to contribute to its development, including intrinsic factors such as genetics, aging, gender, and lung microbiota, as well as extrinsic factors such as smoking, environmental exposures, and air pollution. The incidence of IPF has been steadily increasing, likely due to factors such as aging populations and deteriorating air quality (Harari et al., 2020). IPF has an insidious onset and is often diagnosed at an advanced stage, resulting in a median survival of only 3.8 years (Neumark et al., 2020). Unfortunately, there is currently a lack of reliable diagnostic approaches in the early phase of the disease and effective treatments. Recent research suggests that dysbiosis of the gut microbiota might be associated with the progression of IPF (Ntolios et al., 2021; Quan et al., 2022). During acute exacerbation of the disease, patients often exhibit a higher microbial burden in their lungs. While there is a known correlation between the lung microbiome and disease severity, as well as the risk of disease progression and mortality, a causal relationship has yet to be established (Ntolios et al., 2021).

The link between the microbial community and IPF can be connected through related metabolites, such as fatty acids. Regarding bacterial metabolites, fatty acids may closely associate with pathophysiological processes such as mitochondrial dysfunction, functional impairment, oxidative stress, and affecting the progression of IPF (Wu et al., 2022).

Mendelian randomization (MR) analysis is a powerful tool that can leverage pre-existing aggregated data from genome-wide association studies (GWAS) to investigate the associations between complex traits and millions of molecular marker single nucleotide polymorphisms (SNPs). By using genetic variants as instrumental variables (IVs), MR can infer causality between exposure and its effect while mitigating the influence of unobserved confounding factors. Moreover, the accurate measurement of genetic variation in MR is not susceptible to measurement errors. Importantly, genetic variants are randomly allocated before birth (Birney, 2022), which aligns with the chronological order of causal timing and minimizes issues of reverse causality. As a result, MR has become an increasingly important technique in epidemiological research focusing on causal inference (de Leeuw et al., 2022). Through comparative analyses of genetic variants, MR can identify those that influence complex traits (Swerdlow et al., 2016). It offers an advantage over traditional observational studies, as it provides a robust framework for inferring causality while minimizing the risk of bias from confounding variables.

Using the summary statistics of gut microbiota from the largest GWAS meta-analysis conducted by the MiBioGen consortium (Kurilshikov et al., 2021) and the latest summary statistics of IPF (Allen et al., 2022), FEV₁, FVC and FEV₁/FVC (Shrine et al., 2023) limited to European ancestry, we performed a bidirectional two-sample MR analysis to evaluate the causal association between gut microbiota and IPF and lung function. Four taxa were found causally associated with the risk of IPF. Order Bifidobacteriales, Family Bifidobacteriaceae, and Genus RuminococcaceaeUCG009 exerted protective effects on IPF, while Genus Coprococcus2 promote the development of IPF. Several taxa were causally associated with lung function. Among them, the most prominent beneficial microbiota comprised by Class Deltaproteobacteria, Order Desulfovibrionales, Family Desulfovibrionaceae, Class Verrucomicrobiae, Order Verrucomicrobiales, and Family Verrucomicrobiaceae. Meanwhile, Family Lachnospiraceae, Genus Oscillospira, and Genus Parasutterella were associated with the impairment of lung function. In the reverse MR analysis, the abundance of Order Bifidobacteriales, Family Bifidobacteriaceae, and Genus Bifidobacterium increased with the improvement of FEV₁ and FVC. The MVMR results suggested that fatty acids (monounsaturated fatty acids, total fatty acids, saturated fatty acids, and ratio of omega-6 fatty acids to total fatty acids) probably played a role in the genetic pathway from the gut microbiota to IPF, especially for Bifidobacteriales.

The lung is the largest human organ in direct contact with the environment. The lung was considered non-sterile partly due to the failure of isolating bacteria in lung specimens with traditional culture techniques. Only in the setting of infections, such as pneumonia or bronchiectasis, as in such disorders microbes could be culture-isolated and considered pathogenic of the disease (Ntolios et al., 2021). The introduction of sequencing of the 16S rRNA gene technique allowed recognition of the fact that bacteria not only exist within the human lung but are altered in lung disease and correlate with alveolar immunity and clinical outcomes (Invernizzi et al., 2020). The normal lung microbiota is primarily composed of gram-negative bacteria and facultative anaerobes. A previous MR analysis has suggested that gut microbiota can impact chronic respiratory diseases (CRDs), including chronic obstructive pulmonary disease (COPD), asthma, interstitial lung disease (ILD), sarcoidosis and occupational lung diseases (Shi et al., 2023). The presence and abundance of specific gut microbiota in various disease conditions imply a potential role in modulating immune responses and contributing to the development or resolution of inflammation-related disorders.

Utilizing 16S rRNA gene sequencing, Wei’s research (Wei et al., 2023) indicates that bleomycin (BLM) induced pulmonary fibrosis (PF) could alter the relative abundance of many microbiotas in mice gut. At the family level, compared to the control group, the abundance of Bifidobacteriaceae, Erysipelotrichaceae, and Lactobacillaceae showed an elevation in PF group, while some beneficial microbiota was significantly decreased, such as Bacilaceae and Lachnospiraceae. At the genus level, the abundance of Akkermansia, Bacillus, and Lactobacillus showed reduction in the PF group while was significantly increased for Clostridium, Erysipelatoclostridium, Faecalibaculum, and Lachnoclostridium compared to the control group. Consistent with Wei’s study, we used MR to validate the genetic beneficial effect of Genus Akkermansia on lung function. Recent investigations have elucidated the significance of Akkermansia muciniphila (A. muciniphila) in modulating the pathophysiology of interstitial lung diseases, notably in cystic fibrosis (CF) and COVID-19 convalescent patients. Pharmacological interventions aimed at augmenting A. muciniphila populations have demonstrated the potential to alleviate intestinal inflammation (Manor et al., 2016), diminish pathogenic bacterial loads, and thereby emerge as a therapeutic target for microbiome-based therapies in CF. According to a study performed on SARS-CoV-2 recovered patients (Yeoh et al., 2021), an elevated presence of A. muciniphila correlates with markers of inflammation, implicating its association with dysbiosis of the gut microbiota and systemic inflammatory responses during disease states. Yoon and colleagues (Yoon et al., 2021) extracted genomic DNA from lung tissues of patients with IPF and found that the relative abundance of Lactobacillus, Paracoccus, and Akkermansia was increased in patients with IPF compared with that in the controls. Based on the findings of our study, which suggest that Akkermansia acts as a protective factor for lung function, it is warranted for further investigation of the specific mechanisms of Akkermansia for the impact on IPF. Wei et.al (Wei et al., 2023) also concluded that Family Bifidobacteriaceae would exacerbate the microbial burden in IPF and promote disease progression, while our findings suggested that an increase in FEV₁ can give rise to the abundance of Family Bifidobacteriaceae. The latter was present as a probiotic to reduce the risk of IPF.A study (Yeoh et al., 2021) conducted on individuals who recovered from SARS-CoV-2 also observed that certain species of Bifidobacteria were present at reduced levels.

Quan and colleagues (Quan et al., 2022) showed that after BLM induced PF in mice, the microecological balance of the gut microbiota was destroyed, and the relative abundance of some intestinal probiotics like Firmicutes, Lactobacillales, Lactobacillaceae, Lactobacillus, and Catenibacterium dramatically lowered while the relative abundance of Verrucomicrobiales and Enterobacteriales remarkably increased. Differently, our study found that Family Lachnospiraceae was associated with impairment of FEV₁. Yoon’s study (Yoon et al., 2021) revealed a relatively increased abundance of Lactobacillus and Bifidobacterium in the lung tissue of IPF patients. Lactobacillus generally resides in the gastrointestinal and reproductive tract, where it maintains a healthy microecology with lactic acid production. However, given the well-known association between IPF and gastroesophageal reflux disease (Cheng et al., 2023), the high prevalence of GERD in IPF might contribute to the increase in the relative abundance of Lactobacillus in IPF. Levels of lactic acid and lactate dehydrogenase-5, which induce the differentiation of fibroblasts into myofibroblasts by activating transforming growth factor (TGF)-ß1, were elevated in lung tissues from patients with IPF compared with healthy persons (Kottmann et al., 2012). Therefore, bacteria that produce lactic acid might also contribute to the progression of IPF. However, a different conclusion drawn by wang and colleagues (Wang et al., 2022) was that Lactobacillus mucosae can regulate immune responses and intestinal micro-ecological balance by reducing the proportions of inflammatory cells, including granulocytes and monocytes in the blood, and increasing interferon (IFN)-β, interleukin (IL)-1β, IL-10, and tumor necrosis factor (TNF)-α levels. The observed discrepancies in the role of lactic acid-producing bacteria, notably Lactobacillus mucosae, concerning IPF progression, may be attributed to multifactorial influences and intricate mechanisms. Firstly, strain-specific variations play a pivotal role, as different strains within the same species exhibit diverse immunomodulatory capacities, thereby influencing their impact on IPF. Secondly, individual host characteristics, encompassing genetic predispositions, immune status, and general health conditions, exert a substantial effect on the host’s response to bacterial interventions. This inherent variability among IPF patients might account for the divergent outcomes following exposure to Lactobacillus mucosae. Lastly, the efficacy of Lactobacillus mucosae seems to be intricately tied to the administered dose and duration of treatment, thereby accentuating the necessity for meticulous attention to these variables in forthcoming research endeavors.

This MR study found that an increase in Genus Parasutterella abundance leads to a decrease in FEV₁ and FVC. Gong and colleagues (Gong et al., 2021) calculated the sequence proportions of microbiome and made comparison between fibrotic animals and control ones, showing that Parasutterella were synchronously up-regulated in PF group and Parasutterella was negatively correlated with thymidine. There are very close correlations between distinctive gut microbiota and metabolites under pulmonary fibrotic pathological conditions (Bai et al., 2019; Fang et al., 2020). In recent scientific explorations centered around the “gut-lung axis,” alterations in gut microbial composition and their metabolic byproducts have been implicated in the development of fibrotic interstitial lung diseases. The gut microbiome participates in lung fibrogenesis through metabolically mediated pathways. TGF-β-driven stimulation of fibroblasts enhances glutamine and glutamate concentrations, necessitating glutaminolysis for myofibroblast differentiation and activation (Bernard et al., 2018). In macrophages, arginine boosts glutathione levels and curbs the secretion of pro-inflammatory cytokines such as TNF-α, IL-1β, and IL-6, with arginine derivatives like iNOS and cNOS exerting bidirectional effects on airway inflammation (Fu et al., 2020; Wu et al., 2021). Arginine also restrains NF-κB activation and suppresses MMP-2 and MMP-9 activities implicated in fibrosis (Hnia et al., 2008). Tryptophan, interacting with aryl hydrocarbon receptors, dampens pro-inflammatory T-cell subsets (Takei et al., 2020), and upon conversion to 5-MTP in fibroblasts, it impedes macrophage activation and inflammatory mediator release by interfering with TGF-β/SMAD3 and PI3K/Akt signaling, concurrently hindering myofibroblast formation (Fang et al., 2020). Furthermore, butyrate inhibits TGF-β and fibroblast expression through HDAC-mediated histone acetylation (Park et al., 2021), whereas bile acids stimulate the TGF-β1/Smad3 pathway, promoting alveolar epithelial and lung fibroblast activation (Chen et al., 2017). Collectively, these findings underscore the complex interplay between gut-derived metabolites and the progression of lung fibrosis, highlighting potential therapeutic avenues.

Our study suggested the potential protective roles of specific monounsaturated fatty acids and saturated fatty acids in the genetic association between Bifidobacterium and IPF. Previous research demonstrated that exposure to a high-fat diet rich in palmitic acid, a saturated fatty acid, increased lung fibrosis in wild-type mice after being administered bleomycin. This effect was found to be associated with the activation of the unfolded protein response and apoptosis of lung epithelial cells (Chu et al., 2019), suggesting that high intake of saturated fatty acids may be a contributing factor to the pathogenesis of EMT due to a defect in long-chain fatty acid family member 6 enzyme. Additionally, intratracheal administration of fatty acids has shown potential for therapeutic application in the treatment of PF (Zhao et al., 2014). These findings suggest that a diet rich in essential fatty acids or targeted delivery of fatty acids directly to the lungs may represent a promising approach for the prevention and treatment of lung fibrosis.

To our knowledge, this study is the first comprehensive investigation utilizing large-scale MR analysis to examine the causal relationship between gut microbiota, fatty acids, IPF, and lung function. We utilized the latest and largest GWAS data of individuals with European ancestry. The strength of the study lies in the use of MR analysis, which reduces the impact of measurement errors and addresses potential issues such as reverse causation and confounding factors commonly associated with observational studies. Furthermore, we conducted various sensitivity analyses using multiple complementary MR approaches to assess the robustness of the association and potential bias from pleiotropy. Overall, this study provides valuable insights into the gut-lung axis in IPF and contributes to the understanding of potential preventive and treatment strategies for this condition.

This study has limitations that need to be acknowledged. First, the study population is limited to individuals of European ancestry, thereby rendering the findings not generalizable to populations of other ancestral backgrounds. As IPF prevalence varies across regions and races, further research is warranted to determine regional or racial disparities. Second, heterogeneity among IPF patients may lead to inconsistent results, limiting the conclusions that can be drawn. The underlying mechanism of the lung-gut axis in IPF remains unclear as our research focuses on correlation analysis. Therefore, further investigations are needed to explore specific mechanisms. Comprehensive studies on the lung-gut axis are essential as factors such as seasonality, age, living habits, diet structure, genetic background, and treatment regimens may affect fecal composition in IPF patients. Such studies may provide new directions and strategies for the prevention and treatment of IPF.

In summary, the current study suggested the casual effects of the specific gut microbes on the risk of IPF and lung function. In turn, lung function also exerted a positive role in some gut microbes. Maintaining an appropriate dietary consumption of lipid substances can provide a certain level of protection against the development and progression of IPF. Our findings provided novel insights into the potential role of gut microbiota for IPF and indicated a potential mechanism of gut microbiota-mediated prevention of IPF.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .

YR: Writing – original draft, Software, Methodology, Investigation, Formal Analysis, Data curation, Conceptualization. YZ: Writing – review & editing, Methodology, Investigation, Data curation, Conceptualization. YC: Writing – review & editing, Methodology, Investigation, Data curation, Conceptualization. HQ: Writing – review & editing, Methodology, Investigation, Data curation, Conceptualization. HZ: Writing – review & editing, Supervision, Project administration, Funding acquisition.