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Compiled by: Mo Mo, edited by: xiaojunzhu, Jiang shunyao.
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The uremic symptoms of patients with renal failure may be caused by intestinal microorganisms. The purpose of this study was to investigate the relationship between intestinal microbial components, uremic toxins and symptoms of renal failure in patients with end-stage renal disease (ESRD). The characteristics of intestinal microflora, serum and fecal metabolisms and human phenotypes of 223 ESRD patients and 69 healthy controls were collected. The association between these datasets and the rodent model of chronic kidney disease (CKD) was revealed by multidimensional data integration to detect the effect of intestinal microflora on toxin accumulation and disease severity.
The results showed that a group of microorganisms enriched in ESRD patients were closely related to the clinical variables of patients, encoding the functions related to toxin and secondary bile acid synthesis; the relative abundance of functional microorganisms was related to the concentration of these metabolites in serum or feces. Compared with the control group, the transplantation of intestinal microorganisms from ESRD patients to aseptic mice or rats with antibiotic treated renal injury can induce the production of uremic toxin in serum, and aggravate renal fibrosis and oxidative stress. Two of them, eggerthella lenta and Fusobacterium nucleatum, promote the production of uremic toxins and the development of kidney diseases in CKD rats. Probiotic bifidobacteria reduce the abundance of these harmful microorganisms, reduce the level of toxins and delay the severity of disease. Abnormal intestinal flora in ESRD patients can lead to poor metabolism and promote the development of disease, suggesting that intestinal flora is an ideal target for the treatment of uremia.
Paper ID
Original name: aberrant got microbiota alterers host metallic and impacts real failure in humans and roads
Abnormal intestinal flora changes host metabolome and affects renal failure in humans and rodents
Journal: gut
IF：17.94
Published on: April 2, 2020
Correspondence Author: Ren Kaizheng, Yu Zhengli; Stanislav dusko Ehrlich
Correspondence Author: Department of food science and engineering, School of agriculture and biology, Shanghai Jiaotong University
Preface
End-stage renal disease (ESRD) is the late stage of chronic kidney disease (CKD). It has high incidence rate and high mortality worldwide. At present, the cost of ESRD treatment is staggering, and the cost in the United States alone is as high as $34 billion a year. The progression of CKD to ESRD and its complications are closely related to the accumulation of toxic metabolites in blood and other metabolic tissues. A large part of these toxins are derived from intestinal flora and cannot be effectively removed by dialysis. The significant changes of intestinal microflora structure in CKD patients and the destruction of blood and fecal metabolic components in ESRD hemodialysis patients indicate that there is a metabolic disorder based on microflora in CKD patients. However, the mechanism of ESRD related metabolites (such as uremic toxins) from microorganisms and the changes of ESRD metabolites mediated by intestinal flora has not been fully studied. As a recent study revealed, the regulation of specific intestinal microorganisms can regulate the concentration of circulating uremic toxin indole sulfate, providing the possibility of finding new treatment methods.
In this study, we conducted a comprehensive study, through a large-scale cohort study of 223 hemodialysis patients and 69 healthy controls (matched by age, weight and diet patterns) and an independent validation cohort of 24 patients, to obtain intestinal microorganisms, serum and fecal metabolism groups, data (phenotypes) based on clinical and questionnaire surveys, and integrate them into a multi-dimensional data set.
Result
1. The serum metabolisms of ESRD patients and healthy people were analyzed by non-target mass spectrometry (MS), and 180 kinds of annotated serum metabolisms were obtained. There were significant differences in serum metabolism between ESRD group and control group (Fig. 1a); 134 of 180 metabolites had significantly different abundances. In view of the heterogeneity caused by primary diseases, ESRD was divided into three groups: glomerulonephritis (n = 76), diabetic nephropathy (n = 73) and others (n = 74), and compared with the control group. The differences of metabolism groups in the three groups are similar. Although ≥ 97% of serum metabolites are different in the whole population, only a small amount of metabolites (& lt; 9%) have significantly different abundances in different groups. This shows that ESRD serum metabolize group has nothing to do with the primary disease to a great extent. Interestingly, we found that gender had a moderate and statistically significant effect on the serum metabolism of ESRD patients (P = 0.018, R2 = 1.7%). Consistent with this, ESRD status is the main cause of the difference in serum metabolism between patients and healthy people (Figure 1b), because it explains nearly 11% of the difference, while other biological clinical variables (such as gender, weight and total blood cholesterol concentration) jointly explain an additional 8.5%; the three main types of primary diseases have no significant impact on serum metabolism.
The ESRD serum metabolome is characterized by the accumulation of nine uremic toxins and an imbalance in the composition of bile acids (for example, conjugated and unconjugated bile acids and primary and secondary bile acids (SBA)) (Figure 1c). The accumulation of uremic toxins in 60 patients (ESRD patients, n = 40; healthy control group, n = 20) with ESRD was confirmed by quantizing the target metabolites in the subset randomly selected. It is reported that in addition to trimethylamine oxide (TMAO) produced by choline and carnitine, other toxins are produced by the degradation of aromatic amino acids (AAAS) and phenol derived from diet by intestinal microbiota. Similarly, the circulating composition of bile acids is associated with kidney disease and is known to be affected by intestinal microorganisms. We conducted cluster analysis of serum metabolites, and studied the correlation between cluster abundance and clinical indicators (such as serum creatinine and glomerular filtration rate) used to evaluate the progress of CKD. Importantly, uremic toxins and bile acids were closely associated with relevant clinical indicators across the cohort; significant correlations were also observed in individual patients and in the control group. These findings, consistent with previous studies, illustrate the physiological importance of these circulating metabolites for the clinical status of patients.
2. The patients' fecal metabolism group changed and was significantly related to the serum metabolism group. The fecal metabolism group of ESRD group and the control group was significantly different (Figure 1D). Specifically, 98 of the 255 labeled fecal metabolites showed significant difference in abundance between the two groups. Uremic toxin precursors and secondary bile acids were enriched in feces of patients, while primary bile acids, short chain fatty acids (SCFAs) and SCFA derivatives (such as methyl butyric acid and methylpropionic acid) were significantly reduced; these compounds accounted for 49.6% of the changes in fecal metabolism. As for the fecal metabolism group, two of the three primary groups (glomerulonephritis and others) had very similar differences with the control group. The similarity of diabetic nephropathy is slightly lower, even though most 64% of fecal metabolites are still recovered. The difference of diabetic nephropathy metabolism group was confirmed by the comparison between groups. The metabolic products of 23% (58 out of 255 cases) had different abundances. However, except for p-cresol, there was no significant difference in uremic toxin precursor or bile acid, and p-cresol was more abundant in diabetic nephropathy. Gender had no significant effect on fecal metabolism in ESRD patients (P = 0.463, R2 = 0.43%), but had significant effect on serum metabolism. It should be noted that ESRD is the main reason for the difference in fecal metabolism between patients and control group again, even though it explains a small proportion of the difference (4.2%), other biological clinical variables (such as clinical indicators, drugs, etc.) only explain the other 5.8% difference. The state of diabetes is also an important factor causing the difference.
Proctor's analysis showed a strong synergy between serum and fecal metabolism profiles (Fig. 1F). Most importantly, serum uremic toxins are closely related to their fecal precursors, which indicates that metabolic changes in the intestine of ESRD patients promote the accumulation of uremic toxins in serum.
To further validate our metabonomics results, we designed a separate cohort consisting of 12 ESRD patients and 12 healthy controls. The accumulation of uremic toxins in ESRD patients was confirmed in the new cohort; similarly, in ESRD patients' faeces, an increase in toxin precursors was observed, accompanied by a significant decrease in SCFAs and SCFA derivatives. Most (8 / 13) but not all metabolites were statistically significant (Q & lt; 0.1), which may be related to the small size of the validation queue.
Figure 1: characteristics of serum and fecal flora associated with ESRD.
3. Classification and functional characteristics of intestinal flora in ESRD patients
In order to study whether the intestinal microflora mediates the metabonomics changes of ESRD patients, we analyzed the intestinal microflora by shotgun method. On the illuminahiseq platform, each fecal sample produced an average of 74.7 million reads (11.2 GB data). Using sequencing data, we collected 11.4 million gene catalogs of non redundant genes, which represent the microbiome of our cohort. These genes have been annotated into 11867 functional classifications of KEGG and organized into 900 sub genomic species (MGS), of which about 66% can be assigned to known genera, highlighting a considerable novelty to be explored.
Using gene map, we first found that there were significant differences in microbial diversity, taxonomic composition and functional potential between ESRD patients and healthy people. About 269 enriched MGS and 188 deletions were found in ESRD patients (Fig. 2a); 164 taxonomies at species and / or genus level were listed in table 10 of supplementary materials. As more than half of the species in our cohort changed significantly (457 / 900 MGSS, 51%), we concluded that ESRD status significantly affected the microbiota. The most abundant species in ESRD patients include eggerthellalenta, flavifractor spp (mainly f. plautii), alistipes spp (mainly a. finegoldii and a. shahii), ruminoccus spp and Fusobacterium spp (Fusobacterium spp) (Figure 2b). Species with reduced abundance include Prevotella, Clostridium and several butyrate producing bacteria (Roseburia spp, faecalibacterium praussnii and eucterium retele; FIG. 2). The decrease of SCFAs in the feces of ESRD patients may be due to the decrease of the microorganism producing SCFA.
The functional expression of ESRD intestinal flora in oxidative stress resistance is obvious, which may be due to the high degree of inflammation in patients. The functions needed for amino acid biosynthesis and degradation are depleted and enriched, respectively, which may reflect the increase of amino acid utilization in ESRD patients. The functional modules and enzymes related to AAA degradation and SBA biosynthesis were enriched, which was consistent with the enrichment of uremic toxin precursor and SBA in fecal metabolome. In addition, these functions were significantly correlated with the concentrations of the corresponding ESRD related metabolites in serum and feces (Figure 2C). Our conclusion is that uremic toxin enrichment in ESRD patients is related to intestinal microbiota mediated AAA degradation and microbial SBA biosynthesis.
Figure 2: correlation between characteristics of intestinal flora and changes of serum and fecal metabolites in ESRD patients
4. the changes of intestinal microbiome mediate the changes of metabonomics in patients with ESRD. In order to further explore the relationship between intestinal microbiome and metabonomics, we studied the changes of intestinal MGSs and serum