Shotgun metagenomics reveals significant gut microbiome features in different grades of acute pancreatitis

Comparative study of gut microbiota and metabolite variations between severe and mild acute pancreatitis patients at different stages

Acute pancreatitis (AP) is influenced by interactions between gut microbiota and metabolic products, though the mechanisms remain unclear. This study investigates variations in gut microbiota and metabolites between severe (SAP) and mild acute pancreatitis (MAP) patients to assess their impact on disease progression. Using a cross-sectional cohort design, gut microbiota and metabolite profiles were compared in SAP and MAP patients over two weeks post-diagnosis. 16S rRNA gene sequencing and metabolomic analyses, including KEGG pathway assessments and Spearman correlation, were employed, along with Mendelian Randomization (MR) to assess the influence of specific microbiota on AP. Results showed that SAP patients had significantly reduced gut microbiota diversity, which further declined in the second week. This was marked by increases in pathogenic bacteria like Stenotrophomonas and Enterobacter and decreases in beneficial bacteria such as Blautia. Key changes included a rise in Proteobacteria and a decline in Ruminococcaceae, Enterococcus, and Faecalicatena. Metabolic shifts included lipid metabolite upregulation and antioxidant downregulation. Correlation analysis linked Stenotrophomonas to short-chain fatty acid and amino acid metabolism, highlighting its role in disease progression. MR analysis confirmed negative causal relationships between Enterococcus B, Faecalicatena torques, and AP, suggesting protective effects. Variations in Blautia species indicated differing influences on AP. This study underscores the critical role of gut microbiota and metabolites in AP progression and suggests the need for further research to confirm these findings and explore targeted therapeutic interventions.

What is the role of parenteral nutrition in the management of the patient with severe acute pancreatitis?

Severe acute pancreatitis often presents as a complex critical illness associated with a high rate of infectious morbidity, multiple organ failure, and in-hospital mortality. Breakdown of gut barrier defenses, dysbiosis of intestinal microbiota, and exaggerated immune responses dictate that early enteral nutrition (EN) is preferred over parenteral nutrition (PN) as the primary route of nutrition therapy. EN, however, is not feasible in all cases because of intolerance, risk of complications, or a direct contraindication to enteral feeding. For these patients, PN can be provided in a manner that is safe, is metabolically appropriate, and follows the principles of modern critical care nutrition. Adherence to goal-directed fluid resuscitation, provision of trophic doses of PN to meet 20%-25% of protein and/or calorie requirements through the acute phases of illness, use of less-inflammatory intravenous lipid emulsions, and close monitoring of electrolytes, triglyceride levels, and signs of refeeding syndrome all serve to optimize the response to this route of nutrition support. For these reasons, prescribing PN remains an important strategy in the management of this difficult population of patients.

The composition of the stent microbiome is associated with morbidity and adverse events during endoscopic drainage therapy of pancreatic necroses and pseudocysts

Background

Development of pancreatic necroses or pseudocysts are typical complications of pancreatitis and may require endoscopic drainage therapy using metal or plastic stents. Microbial infection of these lesions poses a major challenge. So far, the composition and significance of the microbial colonization on drainage stents are largely unknown although it may impact outcomes during endoscopic drainage therapy.

Methods

A total of 26 stents used for drainage of pancreatic lesions were retrieved and the stent microbiome was determined by 16S rRNA gene sequencing. Additional analysis included comparison of the stent microbiome to the intracavitary necrosis microbiome as well as scanning electron microscopy (SEM) and micro-computed tomography (μCT) imaging of selected metal or plastic stents.

Results

The stent microbiome comprises a large proportion of opportunistic enteric pathogens such as Enterococcus (14.4%) or Escherichia (6.1%) as well as oral bacteria like Streptococcus (13.1%). Increased levels of opportunistic enteric pathogens were associated with a prolonged hospital stay (r = 0.77, p = 3e-06) and the occurrence of adverse events during drainage therapy (p = 0.011). Higher levels of oral bacteria were associated (r = -0.62, p = 8e-04) with shorter durations of inpatient treatment. SEM and μCT investigations revealed complex biofilm networks on the stent surface.

Conclusion

The composition of the stent microbiome is associated with prolonged hospital stays and adverse events during endoscopic drainage therapy, highlighting the need for effective infection control to improve patient outcomes. In addition to systemic antibiotic therapy, antimicrobial stent coatings could be a conceivable option to influence the stent microbiome and possibly enhance control of the necrotic microflora.

Exploring the Microbial Landscape: Gut Dysbiosis and Therapeutic Strategies in Pancreatitis-A Narrative Review

The gut microbiota is emerging as an important contributor to the homeostasis of the human body through its involvement in nutrition and metabolism, protection against pathogens, and the development and modulation of the immune system. It has therefore become an important research topic in recent decades. Although the association between intestinal dysbiosis and numerous digestive pathologies has been thoroughly researched, its involvement in pancreatic diseases constitutes a novelty in the specialized literature. In recent years, growing evidence has pointed to the critical involvement of the pancreas in regulating the intestinal microbiota, as well as the impact of the intestinal microbiota on pancreatic physiology, which implies the existence of a bidirectional connection known as the "gut-pancreas axis". It is theorized that any change at either of these levels triggers a response in the other component, hence leading to the evolution of pancreatitis. However, there are not enough data to determine whether gut dysbiosis is an underlying cause or a result of pancreatitis; therefore, more research is needed in this area. The purpose of this narrative review is to highlight the role of gut dysbiosis in the pathogenesis of acute and chronic pancreatitis, its evolution, and the prospect of employing the microbiota as a therapeutic intervention for pancreatitis.

The Interaction of Microbiome and Pancreas in Acute Pancreatitis

Acute pancreatitis (AP) is a common acute abdomen disease characterized by the pathological activation of digestive enzymes and the self-digestion of pancreatic acinar cells. Secondary infection and sepsis are independent prognosticators for AP progression and increased mortality. Accumulating anatomical and epidemiological evidence suggests that the dysbiosis of gut microbiota affects the etiology and severity of AP through intestinal barrier disruption, local or systemic inflammatory response, bacterial translocation, and the regulatory role of microbial metabolites in AP patients and animal models. Recent studies discussing the interactions between gut microbiota and the pancreas have opened new scopes for AP, and new therapeutic interventions that target the bacteria community have received substantial attention. This review concentrates on the alterations of gut microbiota and its roles in modulating gut-pancreas axis in AP. The potential therapies of targeting microbes as well as the major challenges of applying those interventions are explored. We expect to understand the roles of microbes in AP diagnosis and treatment.

Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis

Acute pancreatitis (AP) is a type of digestive system disease with high mortality. Previous studies have shown that gut microbiota can participate in developing and treating acute pancreatitis by affecting the host's metabolism. In this study, we followed 20 AP patients to generate longitudinal gut microbiota profiles and activity during disease (before treatment, on the third day of treatment, and 1 month after discharge). We analyzed species composition and metabolic pathways' changes across the treatment phase, severity, and etiology. The diversity of the gut microbiome of patients with AP did not show much variation with treatment. In contrast, the metabolic functions of the gut microbiota, such as the essential chemical reactions that produce energy and maintain life, were partially reinstated after treatment. The severe AP (SAP) patients contained less beneficial bacteria (i.e., Bacteroides xylanisolvens, Clostridium lavalense, and Roseburia inulinivorans) and weaker sugar degradation function than mild AP patients before treatment. Moreover, etiology was one of the drivers of gut microbiome composition and explained the 3.54% variation in species' relative abundance. The relative abundance of pathways related to lipid synthesis was higher in the gut of hyperlipidemia AP patients than in biliary AP patients. The composition and functional profiles of the gut microbiota reflect the severity and etiology of AP. Otherwise, we also identified bacterial species associated with SAP, i.e., Oscillibacter sp. 57_20, Parabacteroides johnsonii, Bacteroides stercoris, Methanobrevibacter smithii, Ruminococcus lactaris, Coprococcus comes, and Dorea formicigenerans, which have the potential to identify the SAP at an early stage. IMPORTANCE Acute pancreatitis (AP) is a type of digestive system disease with high mortality. Previous studies have shown that gut microbiota can participate in the development and treatment of acute pancreatitis by affecting the host's metabolism. However, fewer studies acquired metagenomic sequencing data to associate species to functions intuitively and performed longitudinal analysis to explore how gut microbiota influences the development of AP. We followed 20 AP patients to generate longitudinal gut microbiota profiles and activity during disease and studied the differences in intestinal flora under different severities and etiologies. We have two findings. First, the gut microbiota profile has the potential to identify the severity and etiology of AP at an early stage. Second, gut microbiota likely acts synergistically in the development of AP. This study provides a reference for characterizing the driver flora of severe AP to identify the severity of acute pancreatitis at an early stage.

Current status and advancements in research of gut microecology in acute pancreatitis

Acute pancreatitis (AP) is one of the most common acute abdominal conditions in clinical practice, with increasing incidence and substantial healthcare burden. In recent years, substantial research with high-throughput sequencing technologies has revealed the imbalance between beneficial and pathogenic microbiomes as well as their metabolites during the clinical course of AP. Furthermore, disruption of the intestinal barrier and microbial translocation have been identified as important factors exacerbating systemic inflammatory response and subsequent infectious complications in AP. Maintaining a stable gastrointestinal microecology in patients may help prevent gut-derived infection and attenuate the "second hit" of inflammation induced by AP, thereby improving patient outcomes. This article provides a systematic review of the role of intestinal microbiota and microbial metabolites in the progression of AP, as well as potential therapeutic strategies, in order to offer insights into the understanding of AP pathogenesis and the identification of novel therapeutic targets.

Altered gut microbiota in the early stage of acute pancreatitis were related to the occurrence of acute respiratory distress syndrome

Background

Acute respiratory distress syndrome (ARDS) is the most common cause of organ failure in acute pancreatitis (AP) patients, which associated with high mortality. Specific changes in the gut microbiota have been shown to influence progression of acute pancreatitis. We aimed to determine whether early alterations in the gut microbiota is related to and could predict ARDS occurrence in AP patients.

Methods

In this study, we performed 16S rRNA sequencing analysis in 65 AP patients and 20 healthy volunteers. The AP patients were further divided into two groups: 26 AP-ARDS patients and 39 AP-nonARDS patients based on ARDS occurrence during hospitalization.

Results

Our results showed that the AP-ARDS patients exhibited specific changes in gut microbiota composition and function as compared to subjects of AP-nonARDS group. Higher abundances of Proteobacteria phylum, Enterobacteriaceae family, Escherichia-Shigella genus, and Klebsiella pneumoniae, but lower abundances of Bifidobacterium genus were found in AP-ARDS group compared with AP-nonARDS groups. Random forest modelling analysis revealed that the Escherichia-shigella genus was effective to distinguish AP-ARDS from AP-nonARDS, which could predict ARDS occurrence in AP patients.

Conclusions

Our study revealed that alterations of gut microbiota in AP patients on admission were associated with ARDS occurrence after hospitalization, indicating a potential predictive and pathogenic role of gut microbiota in the development of ARDS in AP patients.

From Genomics to Metagenomics in the Era of Recent Sequencing Technologies

Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.

The gut-lung axis in severe acute Pancreatitis-associated lung injury: The protection by the gut microbiota through short-chain fatty acids

The role of gut microbiota in regulating the intestinal homeostasis, as well as the pathogenesis of severe acute pancreatitis-associated lung injury (PALI) is widely recognized. The bioactive functions of metabolites with small molecule weight and the detail molecular mechanisms of PALI mediated by "gut-lung axis" have gradually raised the attentions of researchers. Several studies have proved that short-chain fatty acids (SCFAs) produced by gut microbiome play crucial roles and varied activities in the process of PALI. However, relevant reviews reporting SCFAs in the involvement of PALI is lacking. In this review, we firstly introduced the synthetic and metabolic pathways of SCFAs, as well as the transport and signal transduction routes in brief. Afterwards, we focused on the possible mechanisms and clues of SCFAs to participate in the fight against PALI which referred to the inhibition of pathogen proliferation, anti-inflammatory effects, enhancement of intestinal barrier functions, and the maintenance and regulation of immune homeostasis via pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). In addition, the latest reported pathological and physiological mechanisms of the gut-lung axis involved in PALI were reviewed. Finally, we summarized the potential therapeutic interventions of PALI by targeting SCFAs, including dietary fiber supplementation, direct supplementation of SCFAs/prebiotics/probiotics, and drugs administration, which is expected to provide new sights for clinical use in the future.

Intestinal Microbiota - An Unmissable Bridge to Severe Acute Pancreatitis-Associated Acute Lung Injury

Severe acute pancreatitis (SAP), one of the most serious abdominal emergencies in general surgery, is characterized by acute and rapid onset as well as high mortality, which often leads to multiple organ failure (MOF). Acute lung injury (ALI), the earliest accompanied organ dysfunction, is the most common cause of death in patients following the SAP onset. The exact pathogenesis of ALI during SAP, however, remains unclear. In recent years, advances in the microbiota-gut-lung axis have led to a better understanding of SAP-associated lung injury (PALI). In addition, the bidirectional communications between intestinal microbes and the lung are becoming more apparent. This paper aims to review the mechanisms of an imbalanced intestinal microbiota contributing to the development of PALI, which is mediated by the disruption of physical, chemical, and immune barriers in the intestine, promotes bacterial translocation, and results in the activation of abnormal immune responses in severe pancreatitis. The pathogen-associated molecular patterns (PAMPs) mediated immunol mechanisms in the occurrence of PALI via binding with pattern recognition receptors (PRRs) through the microbiota-gut-lung axis are focused in this study. Moreover, the potential therapeutic strategies for alleviating PALI by regulating the composition or the function of the intestinal microbiota are discussed in this review. The aim of this study is to provide new ideas and therapeutic tools for PALI patients.

[The role of the microbiome in diseases of the pancreas]

BACKGROUND

The human body is inhabited by diverse microorganisms. Together, this so-called microbiome exerts important metabolic functions and contributes to the maintenance of health. At the same time, shifts in the microbiome composition may lead to disease.

OBJECTIVES

Review of the current literature about the role of the microbiome in diseases of the pancreas.

MATERIALS AND METHODS

Literature search in PubMed and Embase.

RESULTS

The exocrine pancreas is a major factor determining the composition and stability of the intestinal microbiome even in healthy people without pancreatic disease. Inflammatory diseases of the pancreas such as acute or chronic pancreatitis lead to reduced microbial diversity, loss of gut barrier stabilizing bacteria and an increase in facultative pathogens like Escherichia or Enterococcus. Even pancreatic cancer tissue harbours microbiota and mice models have shown that the growth of pancreatic cancer can be inhibited by microbiota ablation.

CONCLUSIONS

Inflammatory diseases of the pancreas lead to gut microbiome dysbiosis and tumor microbiota probably play a role in the development of pancreatic cancer. Until now, however, there is no proof that therapeutic microbiota modulation in individuals with pancreatic disease can improve mortality or quality of life. At this point, the analysis of the microbiome in pancreatic disease should only be performed in scientific studies.

[Etiology and pathogenesis of infected pancreatic necrosis]

Modern literature data confirm the central role of intestinal barrier complex not only as a target in acute necrotizing pancreatitis, but also as a trigger for septic complications. Intra-abdominal hypertension, endothelial dysfunction and gut microbiome changes following necrotizing pancreatitis might have an independent impact on acute intestinal distress syndrome and bacterial translocation. Monitoring of these conditions and early target therapy can improve the outcomes in patients with severe acute pancreatitis. Adverse outcomes of infected pancreatic necrosis including high mortality and morbidity are largely due to the prevalence of multidrug-resistant bacterial pathogens.

Spatioregional assessment of the gut microbiota in experimental necrotizing pancreatitis

BACKGROUND

Infectious complications following experimental pancreatitis involve major disruptions in the gut microbiota. The aim of this study was to characterize this disruption by examining the spatioregional distribution in microbial community structure and function following experimental pancreatitis associated with pancreatic infection.

METHODS

Mice were subjected to infusion of the pancreatic duct with either taurocholate to induce necrotizing pancreatitis or normal saline (control group). The spatial (lumen versus mucosa) and regional composition and function of the microbiota from the duodenum, ileum, caecum, colon, pancreas and blood were evaluated using 16S rRNA gene amplicon sequencing.

RESULTS

Mice that developed necrotizing pancreatitis demonstrated a decrease in microbial richness and significantly altered microbiota in distal parts of the gastrointestinal tract, compared with controls. Among the most differentially increased taxa were the mucus-degrading Akkermansia muciniphila, and there was a decrease of butyrate-producing bacteria following pancreatitis. Application of the SourceTracker tool to the generated metadata indicated that the duodenum was the most probable source of bacteria that subsequently infected pancreatic tissue in this model. The functional prediction annotation using pathway analyses indicated a diminished capacity of the caecal microbiota to metabolize carbohydrate, and fatty and amino acids.

DISCUSSION

The distal gut microbiota was significantly impacted in this model of experimental necrotizing pancreatitis. Data suggest that the duodenal microbiota might also play a role in bacterial translation and secondary infections.

Gut microbiome in acute pancreatitis: A review based on current literature

The gut microbiome is a complex microbial community, recognized for its potential role in physiology, health, and disease. The available evidence supports the role of gut dysbiosis in pancreatic disorders, including acute pancreatitis (AP). In AP, the presence of gut barrier damage resulting in increased mucosal permeability may lead to translocation of intestinal bacteria, necrosis of pancreatic and peripancreatic tissue, and infection, often accompanied by multiple organ dysfunction syndrome. Preserving gut microbial homeostasis may reduce the systemic effects of AP. A growing body of evidence suggests the possible involvement of the gut microbiome in various pancreatic diseases, including AP. This review discusses the possible role of the gut microbiome in AP. It highlights AP treatment and supplementation with prebiotics, synbiotics, and probiotics to maintain gastrointestinal microbial balance and effectively reduce hospitalization, morbidity and mortality in an early phase. It also addresses novel therapeutic areas in the gut microbiome, personalized treatment, and provides a roadmap of human microbial contributions to AP that have potential clinical benefit.