Sepsis refers to a lethal organ dysfunction that is attributed to the dysregulated responses of the host to infections, serving as a leading reason for morbidity and mortality worldwide, so the World Health Organization has recognized it as a global health emergency. The pathogenesis of sepsis remains unclear to date (Anggraini et al. 2022), including imbalance of inflammatory response, immune dysfunction, coagulation dysfunction, and other aspects. The process of its onset is a gradual sequential reaction, and further development may lead to the development of multiple organ dysfunction syndrome. The gastrointestinal tract is the most unique among them. On the one hand, the gastrointestinal tract is the organ first affected by sepsis, and it is affected by both endogenous and exogenous factors, leading to functional disorders. On the other hand, the gastrointestinal tract can act as an intermediate hub, causing damage to other distant organs and accelerating the progression of sepsis (Longhitano et al. 2020).
The microbiota distributed in the gastrointestinal tract is commonly referred to as the gut microbiota (GM), which exerts an essential effect on the maintenance of physiological functions such as metabolism, immunity, and endocrine in the human body (Klingensmith and Coopersmith 2023). There is increasing evidence that the imbalance of GM leads to a higher risk of sepsis and worse outcomes (Adelman et al. 2020; Kang and Thomas 2021; Kullberg et al. 2021; Miller et al. 2021; Niu and Chen 2021). Recent evidence has demonstrated that gut microbiota regulates host physiological homeostasis mediators. Therefore, maintaining or restoring microbiota and metabolite composition might be a therapeutic or prophylactic target against critical illness (Niu and Chen 2021). Fecal microbiota transplantation and supplementation of probiotics are microbiota-based treatment methods that are limited in evidence-based efficacy. The detailed roles of these microorganisms in the sepsis pathophysiology need further investigation.
The causality involving outcomes together with exposure was probed into through a Mendelian randomization (MR) study with instrumental variables (IVs) selected from single-nucleotide polymorphisms (SNPs). Compared to randomized controlled trials, MR analysis can more quickly and more economically determine the cause and effect involving exposure factors plus outcomes (Skrivankova et al. 2021). The correlation of GM with sepsis has not been investigated using MR analysis so far. Therefore, the causal relationship between GM and sepsis, as well as the concrete functions of diverse GM taxa in sepsis, deserves in-depth investigation. Therefore, this MR study was performed by virtue of massive summary statistics from genome-wide association studies (GWASs) concerning GMs and sepsis to distinguish GM taxa with possible influences on sepsis to give support to current evidence while providing novel opinions for the treatment plus prevention of sepsis.
A two-sample MR study was carried out to exploit the association of GM with sepsis. Fig. 1 illustrates the whole design of our research.
The MiBioGen study provided GM-related GWAS data (Kurilshikov et al. 2021), a multiethnic genome-wide meta-analysis on GM with most enormous scale. In this study, the sequencing profiles for 16S rRNA gene targeting the variable regions such as V4, V3–V4, and V1–V2, together with the data of whole-genome genotyping collected from 18,473 individuals (with a predominant proportion of European ancestry) in 25 cohorts, were utilized. Finally, 122,110 host genetic variants were obtained from GWASs, which were mapped to the abundance-associated genetic loci in 211 taxa (16 classes, 131 genera, 20 orders, 9 phyla, and 35 families) through the analysis of variations in GM taxa among diverse populations and GWAS analysis by taxa step by step.
MR-Base database (
The other two from the FinnGen database (
Details of data sources.
Trait | Population | Sample_size | Case | Control | |
---|---|---|---|---|---|
ieu-b-5088 | Sepsis (under 75) | European | 462,869 | 11,568 | 451,301 |
ieu-b-4980 | Sepsis | European | 486,484 | 11,643 | 474,841 |
ieu-b-69 | Sepsis | European | 462,918 | 10,154 | 454,764 |
finn-b-O15_PUERP_SEPSIS | Puerperal sepsis | European | 121,441 | 2,286 | 119,155 |
finn-b-ASTHMA_PNEUMONIA_AND_SEPSIS | Asthma-related pneumonia or sepsis | European | 140,994 | 5,545 | 135,449 |
A procedure integrating distance < 500 kb, European ancestry, and LD r2 < 0.3 was applied to determine the GM-associated lead SNPs at the genome-wide significance level (
R-based “TwoSampleMR” package (version v0.5.6) (Hemani et al. 2018) was employed to accomplish the two-sample MR analysis, with five models in total, namely, MR-Egger, Wald ratio, weighted median, inverse-variance-weighted (IVW), and weighted mode established. The lead SNPs, after clumping, were employed as IVs. For the purpose of guaranteeing the robustness of data and the precision of results, the IVs for the models in this study were selected based on three major principles: 1) IVs had relationships to GM taxa (
Our study used the IVW approach as a primary analytical method when there were two or more instrumental variables, and the Wald ratio model was utilized for data analysis with merely one IV existing. If the IVW model produced a significant result, the GM taxa would be assumed to have a causal link with sepsis. The other three models were also utilized as references, and if the favorable outcomes were reproduced, we considered the results more reliable. Cochran Q test plus MR-Egger regression were employed to evaluate the heterogeneity and pleiotropic effect, respectively, to avoid violating MR assumptions. Causal effects were considered credible in the case of
R 4.0.2 software (R Core Team 2020) was used for statistical analysis.
Given the number of IVs remaining below 10, R2 equals to:
In other cases, the formula can be changed to:
In subsequent investigations, the IVs for exposure were determined as the SNPs at genomewide statistical significance threshold (
Table II exhibited the MR results of various causality evaluation methods for GM and sepsis. The results of IVW analysis demonstrated that Actinobacteria and
Mendelian randomization (MR) analysis of gut microbiota on sepsis at genome-wide significance level (
Classification | Bacterial taxa | Outcome | No. SNP | MR method | Beta | SE | OR | 95% CI | Horizontal pleiotropy | Heterogeneity | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Actinobacteria | phylum | ieu-b-4980 | 4 | IVW | −0.222 | 0.1 | 0.801 | 0.658–0.975 | 0.027 | 190.05 | 0.47 | 0.76 |
4 | Weighted median | −0.245 | 0.116 | 0.783 | 0.623–0.983 | 0.035 | ||||||
ieu-b-5088 | 4 | IVW | −0.23 | 0.099 | 0.795 | 0.655–0.964 | 0.02 | 190.04 | 0.6 | 0.94 | ||
4 | Weighted median | −0.25 | 0.109 | 0.779 | 0.629–0.965 | 0.022 | ||||||
ieu-b-69 | 4 | IVW | −0.338 | 0.101 | 0.713 | 0.585–0.869 | 0.001 | 190.04 | 0.55 | 0.74 | ||
4 | Weighted median | −0.367 | 0.118 | 0.693 | 0.550–0.873 | 0.002 | ||||||
ieu-b-69 | 6 | IVW | −0.231 | 0.071 | 0.794 | 0.691–0.912 | 0.001 | 352.59 | 0.44 | 0.02 | ||
6 | Weighted median | −0.241 | 0.089 | 0.786 | 0.660–0.936 | 0.007 | ||||||
order | ieu-b-4981 | 7 | IVW | 1.051 | 0.368 | 2.861 | 1.391–5.885 | 0.004 | 390.71 | 0.18 | 0.3 | |
7 | Weighted median | 1.024 | 0.49 | 2.783 | 1.065–7.276 | 0.037 | ||||||
ieu-b-69 | 7 | IVW | −0.199 | 0.065 | 0.819 | 0.722–0.930 | 0.002 | 388.52 | 0.55 | 0.74 | ||
7 | Weighted median | −0.208 | 0.081 | 0.812 | 0.692–0.952 | 0.01 | ||||||
ieu-b-69 | 7 | IVW | −0.231 | 0.071 | 0.819 | 0.722–0.930 | 0.001 | 388.52 | 0.55 | 0.74 | ||
7 | Weighted median | −0.208 | 0.082 | 0.812 | 0.691–0.954 | 0.012 | ||||||
ieu-b-69 | 9 | IVW | −0.204 | 0.065 | 0.815 | 0.724–0.912 | 0.002 | 441.31 | 0.83 | 0.9 | ||
9 | Weighted median | −0.226 | 0.079 | 0.798 | 0.683–0.931 | 0.004 | ||||||
genus | finn-b-ASTHMA_PNEUMONIA_AND_SEPSIS | 1 | Wald ratio | −0.371 | 0.174 | 0.69 | 0.490–0.970 | 0.033 | – | – | – | |
Gastranaerophilales | order | finn-b-015_PUERP_SEPSIS | 1 | Wald ratio | −0.526 | 0.265 | 0.59 | 0.352–0.992 | 0.047 | – | – | – |
Beta – estimated causal effect coefficient in different MR methods, CI – confidence interval,
The causal correlation of sepsis with GM was evaluated through two-sample MR analyses in this study, the first research using MR analyses to assess this relationship. We found that at different taxa levels, Actinobacteria and
Sepsis substantially threatens the public health due to its high morbidity and mortality. Unfortunately, over the past decades, antibiotics and supportive care represent the only established targeted therapy of sepsis (Evans et al. 2021). As shotgun metagenomic sequencing, 16S rRNA, and other culture-independent methods are emerging and developing (Durazzi et al. 2021), increasing evidence now suggests that the GM exerts crucial effects on sepsis from the aspect of the pathophysiological process (Chancharoenthana et al. 2023). Sepsis can significantly influence the composition, diversity, and balance of normal GM due to the pathophysiological changes such as gut hypoperfusion and impaired mucosal integrity and the clinical interventions, including antibiotics for treating sepsis. At the same time, its development may be facilitated by these factors in turn, forming a vicious cycle (Miller et al. 2021). GM alteration increases sepsis susceptibility before sepsis onset via multiple mechanisms, such as stimulating the pathogenic intestinal bacteria to expand, initiating strong proinflammatory responses of the immune system, and inhibiting beneficial microbial products (short-chain fatty acids and so on) from generation. Once sepsis is on set, GM disruption is exacerbated while the susceptibility to end-organ dysfunction is enhanced. According to finite evidence, the reduction of sepsis risk plus the improvement of sepsis outcomes may be attributed to selective decontamination of the digestive tract, prebiotics, fecal microbial transplantation, probiotics, and other microbiome-based therapies, while the safety of such therapies has been rarely considered (Adelman et al. 2020). Research on specific microbiome changes during sepsis and the mechanism of action on sepsis have therefore been identified as a critical problem to explore.
Belonging to the Actinobacteria phylum, Bifidobacteriales order, and
We found that the Gastranaerophilales order was negatively connected with sepsis, but the mechanism is unclear. The Gastranaerophilales order lacks the genes essential for aerobic respiration so that it can grow in human and animal guts with low or nearly no oxygen. It can be classified as non-photosynthetic Cyano-bacteria (Melainabacteria class) (Hu and Rzymski 2022). The proportion of Cyanobacteria phylum in the GM is less than 1%. Di Rienzi et al. (2013) utilized the human gut and groundwater to assemble the whole genomes of non-photosynthetic cyanobacterium-like organisms for the first time in 2013. Even though the correlations of diverse diseases with the composition of human GM have been explored in numerous studies, the association between health and intestinal Cyanobacteria and Gastranaerophilales in humans should be researched in detail. In the past years, a couple of researches indicated that gut Cyanobacterial abundance increased in many diseases, such as amyotrophic lateral sclerosis (Di Gioia et al. 2020), neurodevelopment disorder (Zhang et al. 2021), acute gastroenteritis (Xiong et al. 2021), Wilson’s Disease (Cai et al. 2020) and allergy rhinitis (Zhu et al. 2020). However, there is no observational study on the correlation between sepsis and Gastranaerophilales. We infer that the mechanism by which Gastranaerophilales participates in sepsis may be related to the metabolism of tryptophan, which belongs to the crucial amino acids supplied to human bodies by diets, containing the structure of an indole and metabolized by GM to produce indole and indole derivatives. Rosario et al. (2021) found Gastranaerophilales can contribute to increased concentrations of indole, which could be converted into indole-3-propionic acid (IPA). It is argued that IPA conjugates with the aromatic hydrocarbon receptor of intestinal epithelium cells or pregnane X receptor of lymphocytes to activate the immune system, thereby stimulating the intestinal hormone secretion along with gastrointestinal motility, enhancing the intestinal epithelial barrier, putatively modulating GM composition, and exerting anti-inflammatory, anti-oxidative or toxic effects on systemic circulation (Zhang et al. 2022). As Fang et al. (2022) uncovered, IPA ameliorates sepsis-induced mortality and decreases the serum levels of proinflammatory cytokines by modulating intestinal microbiota, which could provide a new potential therapeutic approach for sepsis. Consistent with the abovementioned research, Huang et al. (2022) also found that the IPA level in the feces of septic patients is significantly lower than in controls, and a lower IPA level was about poorer clinical outcomes. It was also discovered from animal models that there was a relationship between the survival of mice with sepsis and GM-derived IPA, and the treatment with IPA was able to prevent sepsis-related mortality while mitigating the organ injury plus bacterial burden resulting from sepsis.
In addition, we identified
Compared with that in patients without Crohn’s disease, the abundance of
Moreover, one study showed that a higher intake of saturated fatty acids and trans-fatty acids leads to a prominently raised relative abundance of
In general, our study had several limitations. First, while most participants in the GWASs providing summary data for this study had European ancestry, a minority of GM data came from collections acquired through other ethnic groups, possibly leading to racial bias. Secondly, merely the genus level, instead of more specific levels like strain and species, was selected to explore bacterial taxa. More detailed and accurate results may be obtained by analyzing microbiome GWAS via more advanced shotgun metagenomic sequencing. Thirdly, genus was set as the lowest taxonomic level for the data about exposure, and suc a limitation prohibited further investigation into the causality between GM and sepsis from the aspect of species.
To sum up, the results of this study provide evidence for underlying causal protective effects of different taxa levels Actinobacteria and