Variations of bile bacterial community alongside gallstone disease progression and key taxa involved in poor outcomes after endoscopic surgery

Gallstone disease is a prevalent cause of hospitalization in many regions of the world, which may occur at any location of the gallbladder and biliary tract [1]. Certain ethnic groups develop gallstone disease more frequently than others [2]. For example, approximately 10–15% of the American adult population (20–25 million) develops gallstone disease [3‐5], while only 3% of the adult population develops the disease in many parts of Africa [6]. It has been observed that gallstone disease annually contributes to the highest medical equipment costs ($4.3 billion) and the second highest physician costs ($0.75 billion) among all digestive diseases [7, 8]. Although approximately 80% of people with gallstones in the biliary system present asymptomatic [2, 9], acute inflammation caused by this disease results in a strong cramp-like visceral pain in the right upper abdomen [10]. Other complications include gallbladder inflammation (cholecystitis), pancreas inflammation (pancreatitis), jaundice obstruction, and bile duct infection (cholangitis) [10]. Specifically, gallstones in the gallbladder (i.e., gallbladder stones, GBS) can often progress and migrate into the common bile duct, causing the formation of common bile duct stones (CBDS). Furthermore, the chronic inflammation caused by gallstone disease may progress to malignant biliary diseases such as gallbladder cancer and bile duct cancer [11].

In recent years, microbiota, especially bacteria, have been recognized as vital environmental factors that are associated with gallstone disease and its complications while being related to the progression of the disease [8, 12]. For example, bacterial infection with gallstone disease causes chronic inflammation in the biliary system, which has been acknowledged as a risk factor for the development of bile duct cancer (i.e., cholangiocarcinoma) [13, 14] and has been linked to a high incidence of gallbladder cancer [11, 15]. Consequently, knowledge of bacterial community dynamics in the bile of gallstone patients and healthy people may help prevent the development of gallstone diseases and associated complications. Currently, the microbial residents of the gut tract and some biological fluids in different locations of our body have been extensively studied, and their correlations to the pathological state of the host have been well recognized during the last two decades; however, such studies on bile are limited [16, 17]. Enterobacteria have been documented as frequently isolated from the bile fluids of cholelithiasis patients, and have been suggested to contribute to gallstone formation [18]. Very recently, high-throughput sequencing technology revealed that Enterobacteriaceae were abundant in the biliary tract of patients with acute cholecystitis and gallstones [19, 20]. In addition, the genera Prevotella, Streptococcus, Veillonella, Fusobacterium, and Haemophilus are prevalent in the bile ducts of patients with primary sclerosing cholangitis [21]. These previous findings demonstrated that different bacterial communities were present in diseased biliary systems, which may correlate with the etiology of the disease. Some studies discovered biliary disease-enriched bacteria—such as Enterobacteriaceae, Bacterioidaceae, Prevotellaceae, Porphyromonadaceae, and Veillonellaceae—in chronic cholecystitis and gallbladder cancer [22, 23]. Nevertheless, to date, only a few studies have explored the bile bacterial communities in individuals without any bile or liver-related disorders [22, 23]. Furthermore, the bacterial assemblage variations in gallstone disease formation and progression (i.e., Healthy Controls (HCs)→GBS→ CBDS→Stricture of the Common Bile Duct (SCBD)) have not yet been studied.

For the treatment of gallstone diseases, the gallstones in GBS and CBDS patients can be removed using endoscopic approaches, such as natural orifice transluminal endoscopic surgery (NOTES) and endoscopic retrograde cholangiopancreatography (ERCP), respectively [24]. Bacteremia and acute pancreatitis are potential complications, particularly in patients who have previously undergone ERCP, and the bile microbiota have been suggested to be contaminated with the duodenal microbiota during the procedure [25], whereas this has not been studied for NOTES. Furthermore, associations between bile bacteria and the clinical indexes of specific biliary diseases remain under-studied.

In this study, bile samples from healthy liver donors and gallstone patients at different stages who have undergone ERCP or NOTES were collected sterilely, and 16S rRNA amplicon sequencing was performed to determine the bile bacterial community variations between these different pathological states to find the key taxa involved in these diseases or endoscopic surgery treatments. Moreover, the correlation between bacteria and clinical indexes was explored and discussed to identify the bacteria that may be involved in post-endoscopic complications.

Gallstone disease and its endoscopic treatment may result in several complications that severely lower the quality of life of the patient; the progression of the disease can even contribute to biliary cancers [32]. Bacterial infections are common complication causatives during the disease or endoscopic treatment process. In this study, we compared bile bacterial communities between the HCs and three groups of gallstone patients at different pathological states (i.e., GBS, CBDS, and SCBD). The results show that the bile harbors a relatively stable bacterial community as no significant differences were observed in the alpha diversity or beta diversity between each group from a global view. Of note, high heterogeneity was observed in the CBDS group and specific taxonomic variations existed between each group. The biliary taxa abundance and occurrence frequency were found to fit exponential correlations, and the majority of the taxa were intermittent or transient and low in abundance. The featured taxa identified using LDA in each group were mainly intermittent or transient taxa, among which Lachnoanerobaculum, Atopobium, Oribacterium, Peptostreptococcus, Rothia, Stomatobaculum, Klebsiella, and Prevotella showed much higher presence in the diseased groups. Moreover, patients with acute pancreatitis after endoscopic surgery displayed lower alpha diversity. Although some taxa, such as Photobacterium, Plesiomonas, Desulfatiglans and Caldithri, were not featured in any group using LDA, they were co-clustered and highly positive-correlated with microbial infection (indicated by PCT) after endoscopic surgery. However, some LDA-featured taxa in HCs, such as Vibrio metschnikovii, Enhydrobacter, Brevundimonas, and Diaphorobacter, were co-clustered and negatively correlated with biliary system inflammation and acute pancreatitis.

Studies in recent years have confirmed that the biliary system harbors a complex microbiota; among them, Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria are the most predominant phyla described in both the healthy and diseased biliary bacterial communities by many studies [23, 33, 34]. Similar to earlier reports, these phyla were most abundant in bile in this study, especially for Proteobacteria that had 60% abundance, which showed identical abundance to that described in the small intestine [35]_. For the first time, Molinero et al. [23] compared the bacterial communities between gallstone/cholelithiasis patients and individuals without any hepatobiliary pathology (i.e., liver donors), and observed that Proteobacteria were more abundant in the control group while Bacteroidota were more abundant in the cholelithiasis group at the phylum level; and a significantly higher abundance of Escherichia-Shigella was observed in the cholelithiasis group at the genus level. Similar bacterial variations between healthy controls and disease groups have also been observed in this study. For example, Proteobacteria was found to be the most abundant taxon in the control group, while Firmicutes and Bacteroidota were the most abundant in the CBDS group (Fig. 1e). At the genus level, Ralstonia was found to be the most abundant genus in the control group and its abundance decreased over 14% in the diseased groups (Fig. 1f). Previous studies have demonstrated that certain bacteria can work cooperatively by encoding specific enzymes or macromolecules, thereby facilitating gallstone formation through the synthesis of essential components [8]. For example, Clostridium perfringens and E. coli have been found to produce beta-glucuronidase, which releases free bilirubin from the bilirubin diglucuronide, the free bilirubin then precipitates with free ionized calcium ion to form calcium bilirubinate, a major component of pigment gallstones; the lipopolysaccharides produced from Gram-negative bacteria, such as Escherichia sp., Klebsiella sp., and Pseudomonas sp., can stimulate mucin secretion from dog gallbladder epithelium, which functions as an integrating factor to coagulate amorphous material into gallstones [8, 36]. We observed in this study that Escherichia-Shigella and Klebsiella were far more abundant while Ralstonia, Lactobacillus, and Neisseria were far less abundant in the CBDS patients than those in the GBS patients, indicating that with the gallstones migrating from the gallbladder to the common bile duct, the abundance of specific taxa greatly changed. Interestingly, with the disease progression, some taxa related to gallstone formation, such as Escherichia-Shigella and Klebsiella, also got increased. To the best of our knowledge, this is the first study to explore the bacterial composition differences between GBS and CBDS. In several studies, alpha diversity of the bile bacteria decreased significantly in the diseased group, and a divergent bacterial community was observed between the groups. For example, Molinero et al. reported a decreased alpha diversity in the cholelithiasis group and divergent bacterial communities between the healthy and cholelithiasis groups (indicated by beta diversity) [23]. Dangtakot et al. [14] found a decreased bacterial richness and increased diversity between CBDS and cholangiocarcinoma (CCA) patients. However, paradoxical results exist as no significant differences were observed in the alpha diversity or beta diversity between each group in this study and some other studies. For example, Kim et al. [33] recently reported that no significant differences existed between CBDS, benign biliary stricture, gallbladder cancer, pancreatic cancer, and distal cholangiocarcinoma (dCCA) in the bile microbiota. Chen et al. [34] observed similar bile bacterial richness between patients with dCCA and the new onset CBDS. Pereira et al. [21] revealed no significant differences in bacterial communities between early-stage primary sclerosing cholangitis (PSC) patients and non-PSC patients_. In comparison to the extensive studies, this paradox reminds us that more efforts are needed to decipher the bile microbiota, particularly those taking healthy bile samples (e.g., liver donors) as controls. In contrast, high heterogeneity was observed in CBDS and SCBD when compared with GBS or HCs, which was also observed in a previous study on patients with common bile duct stones (bile was collected via ERCP) [34], suggesting that strict standards should be kept in the ERCP surgery to reduce bacterial contamination from the intestine. Furthermore, clinical indexes relevant to the biliary pathological state, especially for microbial infection and acute pancreatitis, should be highly important and taken into consideration to obtain more creditable results concerning the involvement of the microbiota in these diseases.

Current studies investigating bile bacteria alterations between different pathological states are devoted to describing taxa abundance or diversities, which may underestimate the importance of the occurrence frequency of specific taxa between different groups. Previous studies have reported that the majority of taxa are low in abundance while the minority are high in abundance in a specific ecosystem. Zhang et al. [37] reported that 25.5% of the top abundant genera accounted for 89.1% of the cumulative abundances in the microbial communities of activated sludge from 14 wastewater treatment plants across Asia and North America. This microbiota assemblage pattern has also been observed in other studies [38]. In this study, the top 9.52% and 18.63% abundant taxa showed 89.41% and 84.71% accumulative abundances at the phylum and genus levels, respectively, indicating that the bile microbiota assembly pattern was similar to other ecosystems. Moreover, the best model of taxa abundance and occurrence frequency in the bile was calculated to be fitting for the exponential correlations, which have been found in other communities [29, 37]. The LEfSe analysis indicates that the most featured taxa between the different pathological groups were intermittent or transient. The only highly represented taxa in CBDS were two persistent taxa (i.e., Klebsiella and Prevotella). Furthermore, two persistent genera (i.e., Pseudomonas and Veillonella) are highly represented in SCBD. In previous studies, Klebsiella increased significantly in CBDS when compared with the healthy group and was associated with severe cholangitis [22, 39]. Prevotella was previously identified as the dominant biliary genera in gallstone patients and aligned with salivary microbiota [34, 40], which was also a pathogen causing chronic endodontic infection [41]. In another study, Pseudomonas was more abundant in CCA than that in gallstone patients [14]. Although these four taxa were frequently enriched in the diseased biliary bacterial community, in this study, they were persistent between the healthy and diseased groups (Table 2), which makes it more possible for them to be the results of the biliary diseases but not the drivers.

Alongside gallstone disease progression, some persistent and harmless taxa in the bile may become pathogenic. For example, Veillonella is an opportunistically pathogenic commensal commonly found in the oral, genitourinary, respiratory, and intestinal tract of humans, while it may cause various rare infections in immunocompromised host [42]. Moreover, Veillonella was found increased in PSC patients when compared with that in HCs [43]. Our study identified Veillonella as a persistent bacterium in the biliary bacterial community, and its abundance increased sequentially alongside HCs→GBS→CBDS→SCBD (Table 2). While it remains speculative to propose that Veillonella becomes pathogenic during disease progression, further investigation is warranted to explore this possibility. In contrast, six LDA featured genera that were transient or intermittent in HCs but persistent in the diseased groups have also been reported in previous studies. Interestingly, five of them were abundant and frequently isolated in the oral cavity. For example, Lachnoanerobaculum has been isolated from human saliva and found to induce bacteremia in a patient with leukemia [44]. Atopobium increased in patients with pancreatic cancer [45], and was frequently isolated from the oral cavity [46]. Rothia, aligned more with the salivary microbiota of patients, increased in patients with pancreatic cancer, and was dominant in patients with gallstone diseases [46, 47]. Oribacterium in the oral cavity has been suggested as a biomarker for pediatric-onset PSC diagnosis or pancreatic head cancer [48]. Stomatobaculum in the saliva was correlated with gastroesophageal reflux disease [49]. In addition, Peptostreptococcus, which resides in the intestine, participated in the oxidation and epimerization of bile acids and led to the formation of gallstones, and may be potentially involved in gallbladder cancer progression [32]. Noticeably, the abundances of four out of the five oral cavity-aligned taxa (i.e., Lachnoanerobaculum, Atopobium, Oribacterium, and Stomatobaculum) increased sequentially during disease progression (i.e., HCs→GBS→CBDS→SCBD) (Table 2), and belonged to the phyla Firmicutes and Actinobacteriota (Additional file 1: Table S3). Collectively, bacteria translocation from the oral cavity may play a vital role in gallstone formation and progression, which could be developed as effective diagnostic biomarkers for biliary disease or indicators for disease progression (Additional file 2: Fig. S5). The overgrowth or undergrowth of persistent bacteria within the biliary system could also contribute, but they are less likely to be the drivers. In the future, strain-level taxonomic assignment analysis should be conducted to further confirm the underlying pathogenic mechanisms of these featured taxa.

Under clinical conditions, poor outcomes of endoscopic surgery, such as pancreatitis and microbial infections frequently occur, although antibiotics are administered before the procedure. To our knowledge, the variations in the bile bacterial community between good outcomes and poor outcomes have not been explored. Using Spearman’s correlation analysis, acute pancreatitis after endoscopic surgery was found to correlate with lower bacterial diversity (Additional file 2: Fig. S2). This result reminds us that when comparing bile bacterial community variations between different diseased groups, the clinical indexes should be taken as parameters for grouping. We further found that the specific taxa that were mostly correlated with poor outcomes were not featured by LDA score between the disease groups (Fig. 3 and Fig. 5). This result implies that although some taxa were increased or decreased significantly in the diseased groups, they are not the cause of poor outcomes after endoscopic surgery. Of note, among the module yellow taxa, which are mostly correlated with poor outcomes, two (Photobacterium and Plesiomonas), have been identified as human pathogens causing wound tissue and intestinal infections [50‐52], while there is no evidence of the pathogeny of the other five; however, they should be critically considered when acute pancreatitis or microbial infections are observed after endoscopic surgery. For the taxa presenting 100% in HCs (Pseudomonas, Brevundimonas, and Diaphorobacter) and featured in HCs by LDA score, their loss in the diseased biliary system may result in a higher probability of developing acute pancreatitis after endoscopic surgery, as they are negatively correlated with ALP or AMY/LIPA. As indicated in Fig. 5, the majority of the taxa that positively correlated with infections are intermittent taxa, which may be contaminations from the upper digestive tract or small intestine during the endoscopic surgery process.

In conclusion, we compared the bile bacterial community variations between different pathological states in gallstone disease progression and revealed that the bile harbors a relatively stable bacterial community during disease progression. However, specific taxa variations were observed between the HCs, benign gallstone disease patients, and malignant gallstone disease patients. A few taxa consist of the core taxa in the bile, accounting for most of the abundance. Moreover, exponential correlations exist between bacterial abundance and occurrence frequency. Notably, abundance alteration of the persistent taxa may not be the cause of gallstone formation and progression, while bacterial translocation and colonization from the oral cavity plays a vital role. Furthermore, the bacterial group that causes infection or inflammation after endoscopic surgery is not the same as that correlated with disease development or progression and may result in a reduction in biliary bacterial diversity. This study extends our knowledge of potential bacterial contributions to gallstone disease progression and outcomes after endoscopic surgical treatment. However, limitations exist because of the low sampling volume and non-strain level taxa assignment, and some of the generated results were speculative, which warrants further studies.