As a vital organ in the human body, the liver plays a crucial role in various biological processes, including metabolism and immunity (Trefts et al., 2017). Liver disease refers to pathological changes caused by various internal and external factors, which significantly impair normal liver function. Factors such as alcohol (Bajaj, 2019), viruses (Liang, 2009), and malnutrition (Mandato et al., 2017) can all lead to liver diseases. Liver disease is one of the ten leading causes of death worldwide (World Health Organization, 2018), resulting in up to 2 million deaths annually due to liver-related complications (Asrani et al., 2019). Research indicates that systemic mucosal immune damage in liver disease patients is closely related to changes in the composition and function of the GM (Bajaj and Khoruts, 2020), This association may be mediated through multiple mechanisms, including impaired intestinal barrier function, dysbiosis of the GM, and increased intestinal permeability, these conditions can lead to the entry of bacterial toxins (such as lipopolysaccharides) into the bloodstream, activating the liver’s immune response, triggering inflammation, exacerbating fibrosis and immune dysregulation, and ultimately driving the progression of liver diseases (Tripathi et al., 2018; Wang et al., 2021). Moreover, certain GM can alter the intestinal barrier to intervene in the progression of liver disease (Plaza-Díaz et al., 2020).

GM is defined as the microbial community that inhabits the human gastrointestinal tract and is a critical factor in regulating host wellbeing. The GM is intricately diverse, including beneficial bacteria that assist in digestion, enhance nutrient uptake, and provide protection from pathogens, along with bacteria that could potentially cause disease. In recent years, research on the GM has grown exponentially (Marchesi et al., 2016), progressively uncovering its regulatory role in various liver diseases. AS research delves deeper, researchers have discovered that disturbances in the gut microbial ecosystem may lead to the exacerbation of multiple liver diseases (Albhaisi et al., 2020). The mutual interaction between the gut and the liver is commonly termed the ‘gut-liver axis’, and it is considered a promising therapeutic approach for managing liver diseases (Wang et al., 2021). Existing research has shown that specific probiotics, such as Bifidobacterium and Lactobacillus, can significantly improve the clinical outcomes of various liver diseases, such as alcoholic liver disease (ALD) and non-alcoholic liver disease (NAFLD), by modulating the composition of the GM, enhancing intestinal barrier functions, and reducing inflammatory responses (Hizo and Rampelotto, 2023; Wang et al., 2020).

Currently, an increasing number of studies have identified the GM as a potential target for the treatment of liver diseases (Bajaj et al., 2022). For instance, fecal microbiota transplantation (FMT) has been used to treat alcoholic liver disease and cirrhosis, primarily by restoring the balance of the GM to improve liver function (Boicean et al., 2023). The use of probiotics has also been proven effective for various liver diseases, including ALD (Bajaj, 2019),NAFLD (Vallianou et al., 2021), cirrhosis (Hatton and Shawcross, 2019), and hepatic encephalopathy (Bajaj et al., 2017). These effects are similarly linked to the restoration of GM balance. Thus, Selecting beneficial gut microbes and optimizing the protocols for FMT and probiotics could significantly improve clinical outcomes. However, due to the complexity of GM and its varying roles in different liver diseases, careful selection of gut microbial members and protocol optimization are necessary to maximize clinical benefits. However, it presents a new challenge: what constitutes a “healthy” microbiome that is advantageous for liver diseases? In light of this, establishing a causal relationship between the gut and liver diseases is crucial. This not only aids in revealing the pathogenic mechanisms by which dysbiosis of the GM leads to liver diseases but also provides a basis for precise GM-targeted interventions. However, research in this area is still lacking, and there is an urgent need to explore the causal links between GM and liver diseases. This would enable the identification of ‘liver-beneficial’ microbial communities, thus offering more effective guidance for clinical treatments.

While randomized controlled trials (RCTs) are the gold standard for establishing causality, the complexity of the GM and the influence of host genetics make such trials challenging in this field (Goodrich et al., 2016). The emergence of Mendelian randomization (MR) has made the regulatory role of the GM in diseases more visual. MR, as a statistical method, utilizes genetic variants associated with the exposure as instrumental variables (IVs) and then assesses the association between IVs and outcomes, elucidating causal relationships between exposure and outcomes (Emdin et al., 2017). MR is immune to the influence of confounding factors or reverse causality, ensuring the accuracy and reliability of experimental results (Neeland and Kozlitina, 2017). Consequently, it has garnered significant attention from the scientific community. At present, MR has found extensive application in liver diseases such as non-alcoholic fatty liver disease (Li et al., 2023), autoimmune liver diseases (Fu et al., 2023), and cirrhosis (Xiao et al., 2023). However, there are still research gaps when it comes to diseases like ALD, liver failure, and liver cancer. Furthermore, researchers have not conducted a systematic exploration of the potential relationship between the GM and a variety of liver diseases.

To address this gap, this research is based on the principles of scientific reliability and replicability, using MR as the primary method to probe the potential causal connections between the GM and five distinct liver diseases. We take the GM as the exposure and select five common and progressively worsening liver diseases, namely ALD, cirrhosis, liver failure, benign liver tumors, and primary liver malignancies, as the outcomes. We have found a significant causal association between the GM and the aforementioned liver diseases. What’s astonishing is that the particular genus Prevotella has exhibited a protective effect in all these liver conditions. Additionally, our single-cell analysis revealed significant differences in the expression of Prevotella-related genes under various liver states. This study employs both MR and single-cell, focusing on the GM perspective, to offer more precise treatment strategies for addressing the socioeconomic burden resulting from liver diseases.

As far as we are aware, this study represents the first MR investigation of the causal relationships between GM and various liver diseases. In order to explore the regularities between these factors, we conducted a comprehensive analysis of the GM associated with the nominally significant taxa in “ALD”, “Cirrhosis”, “Hepatic failure, not elsewhere classified”, “Benign neoplasm: Liver”, and “Malignant neoplasm of liver, primary”. The results indicate that ALD has 10 positive causal directions and 1 negative causal direction; Cirrhosis has 7 positive causal directions and 4 negative causal directions; Hepatic failure, not elsewhere classified has 4 positive causal directions and 3 negative causal directions; Benign neoplasm: Liver has 6 positive causal directions and 1 negative causal direction; Malignant neoplasm of liver, primary has 6 positive causal directions and 3 negative causal directions (Figure 16). Notably, as shown in Figure 16, Prevotella is considered a protective factor in the five liver diseases mentioned. Additionally, our single-cell analysis results indicate that genes related to Prevotella exhibit significant expression differences across different liver conditions. Through further literature research, we found that Prevotella bacteria have been recognized as beneficial microbiota involved in the regulation of various diseases.

Prevotella belongs to the phylum Bacteroidetes, class Bacteroidia, and genus Prevotella. It is a group of Gram-negative bacteria and constitutes a fundamental component of the human GM. It is widely present in human mucosal, respiratory, and intestinal ecosystems. It plays a key role in regulating the host’s metabolic health and maintaining immune balance and is considered a critical participant in the balance between health and disease (Tett et al., 2021). Chang et al. (2019) have already regarded it as a promising candidate for the next-generation probiotic. Prevotella is generally recognized as a bacterium associated with plant-based diets (De Filippis et al., 2016; Ruengsomwong et al., 2016). The intake of dietary fibers facilitates the colonization of Prevotella in the intestines, which not only helps maintain the balance of the GM but also enhances the host’s metabolic functions through various pathways (Shen et al., 2017). Firstly, Prevotella participates in the fermentation of polysaccharides (Fehlner-Peach et al., 2019), effectively breaking down dietary fibers into short-chain fatty acids (SCFAs) such as acetate and butyrate (Kumari et al., 2022) These SCFAs play a crucial role in regulating intestinal homeostasis, adipose tissue, and liver metabolism (Canfora et al., 2015). Acetate, one of the most common SCFAs, enters the circulatory system to influence whole-body energy metabolism and serves as a precursor for lipid synthesis, aiding in fat storage and liver fat metabolism regulation (Frost et al., 2014). Butyrate, as a primary energy source for intestinal epithelial cells, helps maintain the integrity of the gut barrier and reduces the translocation of harmful substances into the bloodstream (Morrison and Preston, 2016). Furthermore, SCFAs inhibit inflammation through multiple mechanisms, thereby reducing liver damage. For instance, they elevate anti-inflammatory Treg cell levels, lower metabolic endotoxemia, and decrease the expression of pro-inflammatory adipocytokines and chemokines (Al-Lahham et al., 2012). Research also indicates that SCFAs regulate gut hormones such as glucagon-like peptide-1, leptin, and peptide YY, which help maintain energy balance and prevent metabolic diseases such as obesity, dysregulated glucose and lipid metabolism, and NAFLD (De Vadder et al., 2014). Secondly, the succinates produced by Prevotella (Kovatcheva-Datchary et al., 2015), as intermediates in the tricarboxylic acid cycle, not only regulate intestinal gluconeogenesis to maintain host glucose homeostasis but also influence the host’s energy metabolism, aiding in the prevention of insulin resistance and associated metabolic diseases (De Vadder et al., 2016). Concurrently, Prevotella coexists with other bacterial phyla such as Actinobacteria, Firmicutes, Proteobacteria, and Archaea, forming a complex gut ecosystem that enhances carbohydrate fermentation (Kovatcheva-Datchary et al., 2015).

However, under certain pathological conditions, some Prevotella species may exhibit pathogenic characteristics. For example, Prevotella can activate Toll-like receptor 2, driving systemic Th-cell-mediated immune responses that may exacerbate inflammation (Larsen, 2017). Research shows that an overgrowth of Prevotella is associated with the progression of liver inflammation and fatty liver disease (Schnabl and Brenner, 2014). Furthermore, specific metabolic products of Prevotella, such as succinate, may exacerbate inflammation under certain pathological conditions and are associated with insulin resistance and hepatic fat deposition (Mills et al., 2016). This dual nature suggests that we must carefully assess GM before clinical application.

Our results suggest that Prevotella may serve as a potential therapeutic target in the liver, which aligns with previous research. For example, Boursier (Boursier et al., 2016) et al. found that the abundance of Prevotella in non-alcoholic fatty liver disease (NAFLD) patients tends to decrease with the severity of liver damage. Shen (Shen et al., 2017) et al. further confirmed that a reduction in Prevotella levels may exacerbate NAFLD. Zhang (Zhang et al., 2023) et al. conducted an MR study that confirmed Prevotella 7 as a protective factor for chronic hepatitis B (CHB), suggesting that Prevotella 7 may reduce the risk of CHB by modulating host inflammation and immune responses; Jiang (Jiang et al., 2022) et al., in a mouse model of primary sclerosing cholangitis (PSC) induced by 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC), found that Copri enhances the FXR-related signaling pathway, leading to a significant improvement in bile stasis and liver fibrosis. It is evident that Prevotella may serve as a potential therapeutic strategy for various liver diseases. This protective mechanism may be attributed to Prevotella’s involvement in regulating intestinal immunity, enhancing the stability of the intestinal mucosal barrier, restricting the translocation of microbial metabolites, preventing the promotion of liver inflammation by metabolites, and participating in the regulation of inflammatory responses. Thereby exerting a protective effect and reducing the risk of liver diseases.

Although in this study we used MR as the research method to establish the causal relationship between GM and liver diseases, effectively eliminating the influence of confounding factors; The genetic variations of the GM were obtained from the largest GWAS meta-analysis, ensuring the strength of the instruments in the MR analysis; The utilization of MR-PRESSO and MR-Egger to eliminate horizontal pleiotropy ensured the authenticity and reliability of the study results. However, it is important to acknowledge certain limitations: 1、Although Mendelian Randomization is a powerful tool, it can only identify associations and cannot definitively determine causality. Therefore, single-cell analysis studies are necessary to further validate the causal relationship between gut microbiota and liver diseases. 2、Some Bacterial taxonomic groups were only analyzed at the order or family level, limiting further exploration. 3、The outcome data in the analysis were aggregated statistics without differentiation among different disease subtypes, precluding subgroup analysis. 4、Single-cell transcriptome sequencing and high-throughput RNA sequencing data come with certain technical limitations and interpretation challenges, such as managing data noise, identifying and annotating cell types, and data normalization. Further validation is crucial for accurately interpreting gene expression in single-cell analysis. In summary, our study results provide support for the potential causal influence of GM on liver diseases. We propose that Prevotella could be considered a liver-friendly microbial community, making treatments such as probiotics and FMT more targeted for liver disease management. While Prevotella is generally considered a beneficial bacterium, specific species and strains of Prevotella may also have varying effects on human health. Hence, there is a need for further research to explore the mechanisms by which specific species and strains of Prevotella impact liver diseases, and validation of these discoveries will rely on future RCTs. f x = a 0 + ∑ n = 1 ∞ a n ⁡ cos n π x L + b n ⁡ sin n π x L