CN110878349A - End stage renal disease biomarker and application thereof - Google Patents
End stage renal disease biomarker and application thereof Download PDFInfo
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- CN110878349A CN110878349A CN201911245044.XA CN201911245044A CN110878349A CN 110878349 A CN110878349 A CN 110878349A CN 201911245044 A CN201911245044 A CN 201911245044A CN 110878349 A CN110878349 A CN 110878349A
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- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
The invention provides a final stage nephropathy biomarker and application thereof. Wherein the end-stage nephropathy biomarker is Ackermanella muciniphila, Exiguobacter finnii, Exiguobacter sarmentosum, Bacteroides cellulolyticus, Bacteroides fragilis, Bifidobacterium dentium, Clostridium difficile, Clostridium saccharolyticum, Vibrio desulforicus, Eggerthella lenta, enterococcus faecalis, enterococcus faecium, Flavolyticus Perot, Fusobacterium nucleatum, Enteromomonas butyricum, Lactobacillus amylovorus, Lactobacillus casei, Lactobacillus fermentum, Lactobacillus plantarum, Streptococcus infantis, Streptococcus thermophilus, Clostridium butyricum, Eubacterium procum, and Clostridium prasukii. Whether a subject has or is susceptible to end stage renal disease can be effectively determined by determining these microbial markers in the subject's intestinal flora.
Description
Technical Field
The invention relates to the field of biomedicine, in particular to a final stage nephropathy biomarker and application thereof.
Background
End-stage renal disease (ESRD) is an advanced consequence of Chronic Kidney Disease (CKD) and is one of the leading causes of morbidity and mortality worldwide. The cost of ESRD treatment is currently prohibitive, exceeding $ 500 billion per year in the united states alone. The progression of CKD and its complications are closely related to the accumulation of toxic metabolites in the circulation. A large proportion of these toxins are produced by intestinal microorganisms and are not normally removed efficiently by dialysis. In humans, a clear association between microbial composition, metabolic disorders and chronic kidney disease remains to be established. Significant alterations in the microbial structure of the gut in CKD patients and disruption of the metabolic composition of blood and stool in hemolytic ESRD patients indicate a microbial-based metabolic imbalance in CKD. However, the microbial origin of ESRD related metabolites such as uremic toxins and the mechanisms of gut microbiota-mediated ESRD metabolome changes have not been well studied, and these studies may lead to therapeutic insights. Currently, the study of end-stage renal disease (ESRD) remains to be improved.
Disclosure of Invention
The present application screens biomarkers highly correlated with end stage renal disease by studying intestinal flora, and can accurately diagnose end stage renal disease using the markers, and can be used to detect therapeutic effects.
According to one aspect of the invention, the invention provides a group of isolated microorganisms. According to an embodiment of the present invention, the group of microorganisms comprises Ackermanella muciniphila (Akkermansia muciniphila), Arthrobacter xylinum (Alisterides finegoldii), Arthrobacter saxatilis (Alisterides shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium dentis (Bifidobacterium dendum), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulfuricola (Desulfuricus), Escherichia tarkii (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Lactobacillus thermophilus (Lactobacillus thermophilus), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum strain (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum strain (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus strain (Lactobacillus plantarum), Lactobacillus strain (Lactobacillus plantarum), Lactobacillus strain (Lactobacillus strain 3), Lactobacillus plantarum), Lactobacillus strain (Lactobacillus plantarum), Lactobacillus strain (Lactobacillus plantarum), Lactobacillus strain (Lactobacillus strain), Lactobacillus plantarum), Lactobacillus strain (Lactobacillus plantarum), Lactobacillus strain (Lactobacillus), Lactobacillus strain, Eubacterium recta (Eubacterium rectangle), Clostridium prausnitzii (Clostridium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus torques (Ruminococcus torques). Can be used as a biomarker for end stage renal disease, can effectively determine whether a subject has or is susceptible to end stage renal disease by determining the presence or absence of at least one of these microorganisms in the subject's intestinal flora, and can be used to monitor the efficacy of treatment in patients with end stage renal disease. In addition, according to embodiments of the present invention, the relative abundance of at least one of these microorganisms in the gut flora may also be detected, whereby the resulting relative abundance value may be compared to a predetermined threshold (cutoff) value to improve the efficiency of determining whether a subject is suffering from or susceptible to end stage renal disease, and for monitoring the efficacy of treatment in patients with end stage renal disease.
According to yet another aspect of the invention, a method of determining an abnormal state in an object is presented. According to an embodiment of the invention, the method comprises the steps of: determining the presence or absence of Ackermanella muciniphila (Akkermansia muciniphila), Arthrobacter xylinum (Alisips finegoldii), Arthrobacter saxatilis (Alisips shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium (Bifidobacterium dense), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulforicus (Desulfuricus vibrio vibriosis), Escherichia coli (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterobacter faecalis), Enterococcus faecium (Enterobacter), Lactobacillus faecium), Lactobacillus casei flavobacterium (Lactobacillus thermophilus), Lactobacillus casei (Lactobacillus casei), Lactobacillus plantarum (Lactobacillus plantarum 3), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus casei), Lactobacillus casei (Lactobacillus casei), Lactobacillus casei (Lactobacillus casei), Lactobacillus casei (Lactobacillus casei) and Lactobacillus casei (Lactobacillus casei), Lactobacillus casei (Lactobacillus casei), Lactobacillus casei (, Eubacterium recta (Eubacterium rectangle), Clostridium prausnitzii (Clostridium prausnitzii), Vibrio rokii (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus) and Ruminococcus torques (Ruminococcus torques) can be used as biomarkers for end-stage renal disease, and further, according to the embodiment of the present invention, the relative abundance of these microorganisms in the intestinal flora can be determined by using the method, and thus, the relative abundance value obtained can be compared with a predetermined critical value, thereby improving the efficiency of determining whether a subject suffers from or is susceptible to type II diabetes and monitoring the therapeutic effect of a type II diabetic patient.
According to yet another aspect of the invention, a method of determining an abnormal state in an object is presented. According to an embodiment of the invention, the method is: determining the presence or absence of Ackermanella muciniphila (Akkermansia), Arthrobacter xylinum (Alisipes finegoldii), Arthrobacter saxatilis (Alisiphiahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium lactis (Bifidobacterium dendum), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulphuricus (Desulfuricus), Escherichia coli (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterobacter faecalis), Lactobacillus faecium (Enterobacter faecalis), Lactobacillus casei (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum) producing strain (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus plantarum) and Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus plantarum) or Lactobacillus (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus plantarum) and Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus), eubacterium recta (Eubacterium rectangle), Clostridium prausnitzii (Clostridium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus torques (Ruminococcus torques). In addition, according to embodiments of the present invention, using this method, the relative abundance of these microorganisms in the gut flora can be determined, whereby the resulting relative abundance value can be compared to a predetermined threshold value, thereby improving the accuracy of determining whether a subject has end stage renal disease, and the efficiency of the treatment for monitoring patients with end stage renal disease.
According to a further aspect of the present invention, there is provided a kit for determining an abnormal state of a subject, which is suitable for determining Ackermanella muciniphila (Akkermansia muciniphila), Acronobacter funiculorum (Alisipsizing), Acronobacter sarmentosum (Alisipes shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium dentis (Bifidobacterium dentium), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulfuricola (Desulfuricus), Escherichia coli (Escherichia coli), Lactobacillus tarkii (Lactobacillus tarkii), Lactobacillus tarkii (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum), Lactobacillus (Lactobacillus), Lactobacillus plantarum), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus plantarum), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), butyrate-producing bacteria (butyrate-producing bacteria SS3/4), Eubacterium recta (Eubacterium rectangle), Clostridium prasuvialis (Faecalibacterium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus strans (Ruminococcus torques). With the kit, the relative abundance of these microorganisms in the gut flora can be determined, whereby the relative abundance values obtained can be compared to predetermined threshold values, thereby improving the accuracy of determining whether a subject is suffering from or susceptible to end stage renal disease, and the efficiency of the treatment for monitoring patients with end stage renal disease.
According to yet another aspect of the invention, the invention proposes the use of a biomarker as a target for screening for the treatment or prevention of an abnormal condition. According to an embodiment of the present invention, the biomarker comprises Akkermansia muciniphila (Akkermansia muciniphila), Lactobacillus plantarum (Alistipes finegoldii), Lactobacillus sakei (Alistipes shahii), Bacteroides cellulolyticus (bacteria cellulolyticus), Bacteroides fragilis (bacteria fragilis), Bifidobacterium dentis (Bifidobacterium mutans), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), vibrio thiofidus (vibrio faecium), escherichia lentus (escherichia coli), Enterococcus faecalis (Enterococcus faecalis), Lactobacillus acidophilus (Lactobacillus acidophilus), Lactobacillus thermophilus (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus (Lactobacillus plantarum), Lactobacillus (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus strain, Lactobacillus strain, Butyrate-producing bacteria (butyrate-producing bacteria SS3/4), Eubacterium recta (Eubacterium rectangle), Clostridium prasuvialis (Faecalibacterium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus strans (Ruminococcus torques). According to an embodiment of the invention, the abnormal condition is end stage renal disease. According to embodiments of the present invention, the effect of a candidate drug on the viability of these microorganisms before and after use can be used to determine whether the candidate drug can be used to treat or prevent end stage renal disease.
Additional aspects and advantages of the invention will be set forth in part in the description which follows and, in part, will be obvious from the description, or may be learned by practice of the invention.
Drawings
The above and/or additional aspects and advantages of the present invention will become apparent and readily appreciated from the following description of the embodiments, taken in conjunction with the accompanying drawings of which:
FIG. 1 is a graph showing the histological and immunohistochemical results of the example of the present invention, wherein a is a study of staining and quantification of glomerulosclerosis index PAS, b is a study of changes in tubular area after F.nuclearum and E.lenta 8 weeks of lavage of immunohistochemical TGF- β and quantitative TGF- β regional CKD rats, respectively, c is a study of renal cortex 8-OH-dG immunohistochemistry and quantification of 8-OH-dG + cells.
FIG. 2 is a graph showing the histological and immunohistochemical results of the example of the present invention, wherein a is a study of staining and quantification of glomerulosclerosis index PAS and b is a study of immunohistochemistry of renal cortex 8-OH-dG and quantification of 8-OH-dG + cells.
Fig. 3 is a diagram showing quantitative PCR analysis of eggerbil tarda and fusobacterium nucleatum in rat feces using SYBR Green qPCR and the relative abundance of both bacteria normalized to per gram of feces for comparison in an example of the present invention, wherein the content of e.lenta and f.nuclearum in CKD rat intestinal flora and sham rat was quantitatively analyzed by qPCR method after 8 weeks of gavage. Data are expressed as mean ± standard deviation. ' indicates P < 0.05; ' indicates P < 0.01.
Detailed Description
Reference will now be made in detail to embodiments of the present invention, examples of which are illustrated in the accompanying drawings, wherein like or similar reference numerals refer to the same or similar elements or elements having the same or similar function throughout. The embodiments described below with reference to the accompanying drawings are illustrative only for the purpose of explaining the present invention, and are not to be construed as limiting the present invention.
Biomarkers
According to a first aspect of the invention, biomarkers of end stage renal disease are presented.
In this context, the term "biomarker" is to be understood broadly and includes any detectable biological marker capable of reflecting an abnormal state. Genetic markers, species markers (species/genus markers) and functional markers (KO/OG markers) may be included. The meaning of the gene marker is not limited to the existing gene that can be expressed as a protein having biological activity, and includes any nucleic acid fragment, which may be DNA, RNA, modified DNA or RNA, or unmodified DNA or RNA. Gene markers may also sometimes be referred to herein as signature fragments.
According to an embodiment of the present invention, stool samples of healthy population and end stage renal disease population are analyzed in batch using high throughput sequencing, and statistical tests are performed on the healthy population and the end stage renal disease population based on high throughput sequencing data to determine specific nucleic acid sequences associated with the end stage renal disease patients, comprising the steps of:
collecting and processing samples: collecting fecal samples of healthy people and end-stage renal disease patients, and performing DNA extraction by using the kit to obtain nucleic acid samples;
library construction and sequencing: constructing and sequencing a DNA library by using high-throughput sequencing so as to obtain a nucleic acid sequence for distinguishing the intestinal microorganisms contained in the sample;
the nucleic acid sequence of a specific intestinal microorganism associated with a patient with end stage renal disease is determined by bioinformatics analysis. First, the sequenced sequences (reads) are aligned with a reference gene set (which may be a newly constructed gene set or a database of any known sequences, e.g., using a non-redundant gene set of known human intestinal microflora). Next, based on the alignment results, the relative abundance of each gene in the nucleic acid samples from the stool samples of the healthy population and the end stage renal disease patient population, respectively, is determined. By comparing the sequencing sequence with the reference gene set, the corresponding relation between the sequencing sequence and the genes in the reference gene set can be established, so that the number of the corresponding sequencing sequence can effectively reflect the relative abundance of the genes aiming at the specific genes in the nucleic acid sample. Thus, the relative abundance of genes in the check sample can be determined by comparison results, according to conventional statistical analysis. Finally, after the relative abundance of each gene in the nucleic acid sample is determined, the relative abundance of each gene in the nucleic acid sample from the stools of the healthy population and the end stage renal disease patient population is statistically examined, whereby it can be judged whether there is a gene whose relative abundance is significantly different in the healthy population and the end stage renal disease population, and if there is a gene that is significantly different, the gene is regarded as a biomarker of an abnormal state, i.e., a gene marker.
In addition, for a known or newly constructed reference gene set, the reference gene set usually comprises gene species information and functional annotations, so that on the basis of determining the relative abundance of the genes, the species information and the functional annotations of the genes can be further classified, thereby determining the species relative abundance and the functional relative abundance of each microorganism in the intestinal flora, and further determining the species marker and the functional marker of the abnormal state. Briefly, the method of determining a species marker and a functional marker further comprises: comparing the sequencing sequences of the healthy population and the end stage renal disease patient population with a reference gene set; respectively determining the species relative abundance and the functional abundance of each gene in the nucleic acid samples of the healthy population and the terminal renal disease patient population based on the comparison result; and determining species markers and functional markers, respectively, that show significant differences in relative abundance between nucleic acid samples from the healthy population and the population of patients with end stage renal disease. According to embodiments of the present invention, statistical tests, such as weighting, averaging, median value, etc., of the relative abundance of genes from the same species and of genes with the same annotations can be employed to determine the functional relative abundance and the species relative abundance.
Finally, microorganisms were identified in which there was a significant difference in relative abundance between the stool samples of the healthy population and the end stage renal disease patient population. i.e.Ackermanobacter muciniphila (Akkermansia muciniphila), Ackerobacter flexneri (Alisips finegoldii), Ackerobacter sargentii (Alisips shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium (Bifidobacterium lactis), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulforicus (Fusarium cellulolyticum), Escherichia coli (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterococcus faecalis), Flavonoides flavobacterium (Flavonica), Lactobacillus thermophilus (Lactobacillus plantarum), Lactobacillus plantarum 3, Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum, Lactobacillus plantarum, Lactobacillus, eubacterium recta (Eubacterium rectangle), Clostridium prausnitzii (Clostridium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus torques (Ruminococcus torques). Thus, the presence or absence of at least one of the above-mentioned microorganisms is detected to effectively determine whether a subject has end stage renal disease, and can be used to monitor the efficacy of treatment in patients with end stage renal disease. The term "presence" as used herein is to be understood in a broad sense and refers to both qualitative analysis of the presence of a corresponding target in a sample and quantitative analysis of the target in the sample, and further to statistical analysis or any known mathematical operation of the quantitative analysis results obtained with reference, e.g. quantitative analysis results obtained by parallel tests on samples with known states. According to the embodiment of the invention, the accuracy of determining whether the subject suffers from or is susceptible to end stage renal disease and the efficiency of the treatment for monitoring patients with end stage renal disease can be improved by determining the relative abundance of the microorganisms in the intestinal flora and comparing the obtained relative abundance value with a predetermined critical value.
According to the examples of the present invention, Ackermanella muciniphila (Akkermansia muciniphila), Arthrobacter xylinum (Alisips finegoldii), Arthrobacter saxatilis (Alisips shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium lactis (Bifidobacterium dense), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulphuricus (Desulfurivibrio vibrio failurensis), Escherichia lentus (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterobacter faecalis), Lactobacillus faecium, Lactobacillus plantarum (Lactobacillus thermophilus), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus strain, Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus strain, Lactobacillus), Lactobacillus (Lactobacillus strain, Lactobacillus (Lactobacillus), Lactobacillus strain, Lactobacillus (Lactobacillus strain, Lactobacillus), Lactobacillus strain, Lactobacillus (Lactobacillus strain, Lactobacillus (Lactobacillus strain, Lactobacillus, and thus may be collectively referred to herein as pest markers. Butyrate-producing bacteria (butyrate-producing bacteria SS3/4), Eubacterium recta (Eubacterium rectangle), Clostridium prasuvialis (Faecalibacterium prausnitzii), Vibrio reuteri (Roseburia intestinalis), Ruminococcus bicincans (Ruminococcus bicirtus) and Ruminococcus contortus (Ruminococcus torques) are enriched in healthy persons (control group) and thus may be collectively referred to herein as beneficial biomarkers.
By detecting the presence or absence of at least one of the above-mentioned microbial species in the intestinal flora of the subject, in particular, Ackermanella muciniphila (Akkermansia muciniphilii), Arthrobacter xylinum (Alisipes finegoldii), Arthrobacter sakii (Alisipes shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium dentis (Bifidobacterium dense), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio (Desulfuricus), Escherichia coli (Eggeria gonorrhoeae), Enterococcus faecalis (Enterococcus faecalis), Lactobacillus thermophilus (Eggeria), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus fermentum (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus (Lactobacillus plantarum), Lactobacillus (Lactobacillus), Lactobacillus plantarum) and Lactobacillus (Lactobacillus strain), Lactobacillus plantarum), Lactobacillus (Lactobacillus strain, Lactobacillus plantarum), Lactobacillus (Lactobacillus strain, Lactobacillus), Lactobacillus strain, Lactobacillus (Lactobacillus strain, Lactobacillus plantarum), Lactobacillus (Lactobacillus strain, to effectively determine whether a subject is suffering from or susceptible to end stage renal disease, and can be used to monitor the efficacy of treatment in patients with end stage renal disease.
Method for detecting abnormal state in object
According to yet another aspect of the invention, a method of determining an abnormal state in an object is presented. According to an embodiment of the invention, the method comprises determining the presence or absence of at least one polynucleotide sequence, i.e. at least one of said genetic, species and functional markers, in the gut flora of the subject.
According to one embodiment of the invention, the abnormal condition is end stage renal disease. According to embodiments of the present invention, it may be determined whether a subject has or is predisposed to end stage renal disease by determining whether at least one of the above-mentioned markers is present in the subject's intestinal flora, and may be used to monitor the efficacy of treatment in patients with end stage renal disease.
According to one embodiment of the present invention, the presence or absence of Achromobacter muciniphila (Akkermansia muciniphila), Arthrobacter xylinum (Alisteries finegoldii), Arthrobacter sakii (Alisterides shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium dentis (Bifidobacterium dense), Clostridium difficile (Clostridium difficile), Clostridium saccharivorans (Clostridium saccharolyticum), Vibrio desulphuricus (Desulfuricus vibrio vibriosis), Escherichia lentus (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium faecalis (Enterobacter), Lactobacillus thermophilus (Lactobacillus), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus (Lactobacillus), Lactobacillus plantarum), Lactobacillus (Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus (Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus strain (Lactobacillus), Lactobacillus strain, Lactobacillus), Lactobacillus strain (Lactobacillus strain, at least one of butyrate-producing bacteria (SS 3/4), Eubacterium recta (Eubacterium receale), clostridium praerusni (Faecalibacterium praerusni), vibrio rhodesi (rosebria intestinalis), Ruminococcus bicans (Ruminococcus bicucus) and Ruminococcus contortus (Ruminococcus torques). Further comprising: DNA library construction from the excreta, and sequencing. Sequencing results may be obtained to determine whether at least one of the above microorganisms is contained in the excreta. Therefore, nucleic acid data of the intestinal flora of the subject can be effectively obtained through sequencing, so that whether the gene marker exists in the nucleic acid information can be effectively determined.
According to embodiments of the present invention, the means of performing sequencing is not particularly limited. According to one embodiment of the invention, the sequencing is performed using a second generation sequencing method or a third generation sequencing method. The sequencing is preferably performed using at least one selected from the group consisting of HiSeq 3000, HiSeq X, NovaSeq, MiniSeq, BGISEQ, PacBio, Nanopore, and single molecule sequencing devices. Therefore, the characteristics of high-throughput and deep sequencing of the sequencing devices can be utilized, so that the subsequent sequencing data can be analyzed, and the accuracy and the precision are particularly good when statistical inspection is carried out.
According to an embodiment of the present invention, the obtained sequencing result may be compared with a reference genome, for example, known genomic information of a microorganism to be detected is contained in the reference genome, in such a manner as to determine the presence or absence of the microorganism. According to an embodiment of the invention, said step of aligning is performed using at least one selected from SOAP2, MAQ, BWA. This can improve the efficiency of alignment, and thus can improve the efficiency of detection of abnormal conditions such as end stage renal disease. According to the embodiments of the present invention, a plurality of (at least two) biomarkers can be simultaneously detected, so that the efficiency of detecting an abnormal state such as end-stage renal disease can be improved.
Species and functional markers one skilled in the art can also determine the presence or absence of said species and function in the gut flora by conventional species identification means and biological activity testing means. For example, species identification can be performed by 16S rRNA sequencing.
According to an embodiment of the present invention, the method may further include the steps of: achromobacter determined muciniphilus (Akkermansia muciniphila), Achromobacter flexneri (Alisips finegoldii), Achromobacter sarkii (Alisips shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium (Bifidobacterium lactis), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulforicus (Desufovibrio falciparundinaceus), Escherichia tarkii (Eggerthella lenta), Enterococcus faecalis (Enterobacter faecalis), Enterococcus faecium (Enterobacter faecium), Lactobacillus paracasei (Flavonoides), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus plantarum 3), Lactobacillus plantarum (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus plantarum (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus plantarum, Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus paracasei), the relative abundance of at least one of Eubacterium rectal (Eubacterium rectangle), clostridium praerumtzii (clostridium praerumtzii), vibrio rhodesiae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus strabilis (Ruminococcus torques), and the resulting relative abundance may be compared with a predetermined threshold value. Thus, it is possible to determine whether the object is in an abnormal state based on the difference between the relative abundance and the predetermined threshold value. According to an embodiment of the present invention, the predetermined cut-off value may be obtained by routine experimentation, e.g. by determining the relative abundance of the biomarker in a sample of a subject of a known physiological state from a subject of a known physiological state by parallel experiments, thereby obtaining the predetermined cut-off value. According to an embodiment of the invention, the cut-off values used are as shown in the table below, wherein for a beneficial biomarker (orientation defined as 0) a relative abundance value below the cut-off value is diagnosed as a disease state; for a pest marker (orientation defined as 1), a relative abundance value greater than a threshold value is diagnosed as a disease state.
According to embodiments of the present invention, butyrate-producing bacteria (SS 3/4), Eubacterium rectile (Eubacterium recoverale), clostridium pratense (Faecalibacterium prausnitzii), vibrio rhodesiae (Roseburia intestinalis), Ruminococcus biceps (Ruminococcus bicinums), and Ruminococcus contortus (Ruminococcus torques) may be used as beneficial bacteria for the treatment or prevention of end stage renal disease, for example, they may be used in food products. According to an embodiment of the present invention, there is provided a food or pharmaceutical composition comprising at least one of a butyrate-producing bacterium (butyrate-producing bacterium SS3/4), a Eubacterium rectorum (Eubacterium recipient), a Clostridium praerussitum (Faecalizii), a Vibrio rhodinii (Roseburia intestinalis), a Ruminococcus bicincanus (Ruminococcus bicincanus), and a Ruminococcus toruloides (Ruminococcus torques). The food or pharmaceutical composition can be used for effectively preventing or treating end stage renal disease. Further, according to an embodiment of the present invention, there is provided a use of at least one of butyrate-producing bacteria (butyrate-producing bacteria SS3/4), Eubacterium rectal (Eubacterium repeat), clostridium pratensis (Faecalibacterium prausnitzii), vibrio rhodesiae (Roseburia intestinalis), Ruminococcus bicinctus (Ruminococcus bicircus) and Ruminococcus contortus (Ruminococcus torques) for the manufacture of a medicament for the prevention/treatment of end stage renal disease. Also, according to an embodiment of the present invention, there is provided a method for treating end stage renal disease, including administering at least one of butyrate-producing bacteria (SS 3/4), Eubacterium rectorum (Eubacterium recoverie), clostridium pratensis (clostridium pratensiti), vibrio rhodesi (Roseburia intestinalis), Ruminococcus bicinctus (Ruminococcus bicucus), and Ruminococcus contortus (Ruminococcus torques) to a subject in need thereof.
Others
According to another aspect of the invention, the invention provides a kit for determining an abnormal state of a subject. According to an embodiment of the invention, the kit comprises reagents suitable for detecting at least one of the aforementioned biomarkers. For example, for the genetic marker, the kit comprises a nucleic acid sequence suitable for detecting Achromobacter muciniphila (Akkermansia muciniphila), Arthrobacter xylinum (Alisterides finegoldii), Arthrobacter sakii (Alisterides shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium dentis (Bifidobacterium dendum), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulfuridus (Desulfuricus), Escherichia lentus (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Lactobacillus plantarum (Lactobacillus thermophilus), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus strain (Lactobacillus), butyrate-producing bacteria (butyrate-producing bacteria SS3/4), Eubacterium recta (Eubacterium recycle), Clostridium pratense (Faecalibacterium prausnitzii), Vibrio rosenbergii (Roseburia intestinalis), Ruminococcus bicinctus (Ruminococcus bicinctus) and Ruminococcus stractii (Ruminococcus torquus), in particular, Achromobacter muciniphilus (Akkermanicola), Achromobacter fengeri (Alisiperium fingiii), Achromobacter sarmentosum (Alitists shahii), Bacteroides cellulolyticus (bacteriodes cellulolyticus), Bacteroides fragilis (bacterioides), Bifidobacterium fragilis (bacteriodes), Bifidobacterium bifidum (Bifidobacterium bifidum), Clostridium difficile (Clostridium difficile), Bacillus coli (Clostridium difficile), Bacillus bifidulus (Clostridium difficile), Bacillus bifidum) and Bacillus bifidum (Clostridium difficile (Bacillus bifidum) and Bacillus bifidum (Bacillus bifidum) are, The reagent for at least one of Lactobacillus casei (Lactobacillus casei), Lactobacillus fermentum (Lactobacillus fermentum), Lactobacillus plantarum (Lactobacillus plantarii), Streptococcus infantis (Streptococcus infantis), Streptococcus thermophilus (Streptococcus thermophilus), and Bacillus bifidus (Streptococcus finegolensis), by which it is possible to effectively determine whether a subject contains Achromobacter muciniphilus (Akkermaniphila), Bacillus bifidus (Alistevensis finegoldii), Bacillus sarsonii (Aliskili), Bacteroides cellulolyticus (Bacillus cellulolyticus), Bacteroides (Bacillus fragilis), Bifidobacterium denticola (Bifidobacterium denticola), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium sporogenes), Bacillus bifidum (Lactobacillus), Bacillus bifidum (Bacillus subtilis), Clostridium difficile (Clostridium bifidum), Clostridium difficile (Clostridium difficile), Bacillus bifidum (Clostridium bifidum), Bacillus flavobacterium (Clostridium bifidum), Bacillus acidovorans (Clostridium bifidum), Bacillus acidovorus (Clostridium difficile), Bacillus bifidum (Bacillus subtilis), Bacillus bifidum (Bacillus bifidum), Bacillus bifidus (Bacillus bifidus), Bacillus bifidus, Clostridium difficile (Bacillus bifidus), Bacillus bifidus (Bacillus bifidus, Bacillus bifidu, Lactobacillus amyloliquefaciens (Lactobacillus amylovorus), Lactobacillus casei (Lactobacillus casei), Lactobacillus fermentum (Lactobacillus fermentum), Lactobacillus plantarum (Lactobacillus plantarum), Streptococcus infantis (Streptococcus infantis), Streptococcus thermophilus (Streptococcus thermophilus), Clostridium butyricum (butyricum-producing bacterium SS3/4), Eubacterium rectale (Eubacterium rectale), Clostridium pratensis (Lactobacillus pratensiti), Vibrio rozekii (Roseburia intestinalis), Micrococcus bicolor (Staphylococcus bicinctus) and Streptococcus mutans (Clostridium torulos), especially Streptococcus thermophilus (Bacillus licheniformis), Lactobacillus acidophilus (Bifidobacterium bifidum), Lactobacillus bifidus (Bifidobacterium bifidum), Clostridium difficile (Clostridium difficile), Bacillus bifidum (Clostridium difficile), Clostridium difficile (Clostridium difficile), Bacillus bifidum (Clostridium difficile), Bacillus bifidum, Clostridium difficile (Clostridium difficile), Bacillus bifidum (Clostridium difficile), Bacillus bifidum, Bacillus difficile (Clostridium difficile), Bacillus bifidum, Bacillus, Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterococcus faecium), Flavonidus perniciae (Flavonidor planutiii), Fusobacterium nucleatum (Fusobacterium nucleatum), Enteromonas butyricum (Enteromonas butyricumproducers), Lactobacillus amylovorus (Lactobacillus amylovorus), Lactobacillus casei (Lactobacillus casei), Lactobacillus fermentum (Lactobacillus fermentum), Lactobacillus plantarum (Lactobacillus plantarum), Streptococcus infantis (Streptococcus infantis), Streptococcus thermophilus (Streptococcus thermophilus) to determine an abnormal state of the subject. According to an embodiment of the present invention, the abnormal condition referred to herein is a disease, preferably, the abnormal condition is end stage renal disease.
In addition, according to the embodiment of the invention, the invention also provides a drug screening method. Therefore, according to the embodiment of the invention, the markers closely related to the end stage renal disease are used as drug design targets to screen drugs, and discovery of new end stage renal disease drugs is promoted. For example, whether a candidate drug is a drug for the treatment or prevention of end-stage renal disease can be determined by detecting changes in biomarker levels before and after exposure to the candidate drug. For example, it is tested whether the level of the pest marker is known to decrease after exposure to the drug candidate and whether the level of the beneficial biomarker is elevated after exposure to the drug candidate. In addition, it is also possible to treat Ackermanella muciniphila (Akkermansia), Arthrobacter xylinum (Alisipes finegoldii), Arthrobacter saxatilis (Alisiphiahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium (Bifidobacterium dendum), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulphuricus (Desulfurivibrio falciparus), Escherichia coli (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterobacter faecalis), Lactobacillus faecium (Enterobacter faecalis), Lactobacillus casei (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus plantarum strain (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus (Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus plantarum (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus), Lactobacillus strain (Lactobacillus strain, Eubacterium recta (Eubacterium rectangle), Clostridium praerussitum (Clostridium praerussitrix), Vibrio rozekii (Roseburia intestinalis), Ruminococcus bicinctus (Ruminococcus bicinctus) and Ruminococcus strans (Ruminococcus torques), especially Achromobacter muciniphila (Akkeramifera), Lactobacillus plantarum (Alisiphe fingolensis), Lactobacillus gasseri (Alisiphe shii), Clostridium sarmentosum (Alisiphe shahii), Bacteroides (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides), Bifidobacterium dentis (Bifidobacterium), Clostridium difficile (Clostridium difficile), Clostridium saccharophilum (Clostridium sarcinalis), Lactobacillus casei (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus), Lactobacillus plantarum), Lactobacillus paracasei (Lactobacillus plantarum), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus paracasei (Lactobacillus paracasei), Lactobacillus, The direct or indirect effect of the biological activity of at least one of Lactobacillus plantarum (Lactobacillus plantarum), Streptococcus infantis (Streptococcus infantaris), Streptococcus thermophilus (Streptococcus thermophilus) is used to screen whether a candidate compound can be used as a medicament for the treatment or prevention of end stage renal disease. Thus, according to an embodiment of the present invention, the present invention also proposes the use of a biomarker for end stage renal disease in the screening of a medicament for the treatment or prevention of end stage renal disease.
The present invention is described below with reference to specific examples, which are intended to be illustrative only and are not to be construed as limiting the invention.
Unless otherwise indicated, the techniques used in the examples are conventional and well known to those skilled in the art, and may be performed according to the third edition of the molecular cloning, laboratory Manual, or related products, and the reagents and products used are also commercially available. For the purpose of describing the various processes and methods in detail, which are conventional in the art, the sources, trade names, and where necessary, constituents of the reagents used are identified at the time of first appearance, and the same reagents used thereafter, unless otherwise specified, are identical to those first identified.
Example 1: sample collection
223 hemodialysis patients (21-72 years old) were from four hemodialysis centers, Beijing, China. All participants were diagnosed as end-stage renal disease (ESRD) according to the global prognostic organization for renal disease (KDIGO) clinical practice guidelines and stable hemodialysis (1-3 times per week). Among 223 ESRD patients, 77 cases of glomerulonephritis (34.5%), 73 cases of end-stage renal disease (32.7%), 32 cases of hypertensive nephrosclerosis (14.3%), 6 cases of polycystic kidney (2.7%), 12 cases of interstitial nephritis (5.4%), 5 cases of kidney transplant failure (2.2%), and 19 cases of renal failure of unknown cause (8.5%).
The control group (age 26-71, BMI < 29.9kg/m2 < 18.5) included 69 healthy volunteers who underwent physical examinations each year to the Beijing space center hospital. Exclusion criteria for the control group included hypertension, end-stage renal disease, obesity, metabolic syndrome, Inflammatory Bowel Disease (IBD), cancer, liver and kidney dysfunction, dyslipidemia. The individual is excluded if the antibiotic is taken within 3 months or the probiotic product is taken within 14 days.
Example 2: DNA extraction and sequencing
2.1 collecting and storing of stool samples
Fresh faeces were collected at home or in a hospital. All participants were asked to drain the feces on a special collection paper (developed by nikken chemical limited, japan) and to separate the feces in sterile tubes. Fresh excrement in the test tube is put into an ice bag, and the excrement is put into a laboratory within 2 hours after the excrement is put into the ice bag. A stool sample was soaked in sterile DNA protective solution (pH 5.2, 0.01mol/L EDTA, 0.025mol/L Na)3C6H5O7And 5.3mol/L Na2SO4) The tubes were stored at 4 ℃ until DNA extraction and metagenomic analysis. Other stool samples were immediately frozen and stored at-80 ℃ until use.
2.2DNA extraction
Total DNA was extracted from about 180-200 mg of feces using standard methods. Fresh genomic DNA samples were mechanically fragmented to-400 bp with bio. The DNA fragments were selected using a magnetic bead-based method according to a standard protocol (AgencourtAMPure XP).
2.3DNA library construction and metagenomic sequencing
The library was prepared using the NEBnext II DNA library pretreatment kit (New England Biolabs). 2X 150bp double-ended whole genome sequencing (WMS) was performed using the Illumina HiSeq X platform.
Example 3: identification of biomarkers
3.1 basic processing of sequencing data
And under a sequencing platform, performing basic processing on WMS data based on system default parameters. Low quality reads are defined to include: 1) reads over 30% bases estimate error rate > 1%; or 2) ambiguous "N" >15 bp. These reads are deleted in pairs. Human genomic DNA reads were identified by SOAP2 and deleted if they shared > 95% of the sequence with the human genomic reference sequence (hg 19).
3.2 updating Gene lists
A new gene catalogue was created based on WMS data of all samples. High quality WMS data were assembled and gene predicted using IDBA-UD (version 1.1.2). Any two genes from different samples are classified as redundant genes if the similarity reaches or exceeds 95% in 90% of the region. After deleting all redundant genes, we obtained a list of non-redundant genes, including 11473498 microbial genes.
3.3 Classification of genes
Gene classification was based on the NCBI-non-redundant nucleic acid database (NCBI-NT, download 3 months 2017). Genes from the gene catalog were aligned using BLASTN with parameters "-word size 16, -even 1e-10, -max target seq 15", and at least 70% coverage per gene was required. Parameter exploration based on sequence similarity between different phylogenetic levels revealed that 95% of the similarities were assigned to the species, 85% of the similarities were assigned to the genus and 65% of the similarities were assigned to the phylum. 663 ten thousand genes of the gene catalogue can be classified and annotated by adopting the method.
3.4 functional Annotation
Functional annotation of genes the database of Kyoto encyclopedia of genomes (KEGG) was functionally annotated with Blast KOALA (v 2). Each protein was assigned a KEGG Ortholog (KO) based on the best hit genes in the database. Using this method, 39.6% of the genes in the combinatorial gene catalog can be assigned to a certain KO.
3.5 quantitative analysis of Gene
3.5.1 calculating the relative abundance of genes
The high quality sequenced sequences from each sample were aligned to a non-redundant reference gene set using SOAP2.21, with the alignment criteria being "similarity > 90%". In sequencing-based profiling, only two alignment cases were accepted: 1) the inserted double-ended sequencing sequences with correct length can be completely matched to a certain gene; 2) one of the double-ended sequencing sequences matches the tail of a certain gene, and the other matches outside the gene. In both cases, the sequence that matched was counted as one copy.
For any one sample S, the inventors calculated the relative abundance of the genes by:
step 1: calculating the copy number of each gene
Step 2: calculation of the relative abundance of Gene i
Wherein
a1Is the relative abundance of gene i in sample S; l is1The length of gene i; x is the number of1: the number of times gene i was detected in sample S (number of matching sequences); b1Represents the copy number of gene i in the sequencing data from sample S.
According to the relative abundance spectrum of the genes and the species classification and function annotation of the suppressor genes, the relative abundance spectrum and the relative abundance spectrum of the functions of the species are obtained by adding the relative abundances of the genes from the same species and the genes from the same functional units.
3.5.2 construction of species and KO composition profiles
For a species profile, we used the taxonomic assignment of each gene from the original gene catalog, and summarized the relative abundance of genes from the same species to yield the abundance of that species. The relative abundance of all species in a sample constitutes the species distribution of that sample. The KO profile was constructed using the same method. The relative abundance of an enzyme is calculated from the sum of the relative abundances of its corresponding KOs.
3.6 gut type partitioning
The method of evaluating relative abundance at genus level is the same as that of constructing KO profiles, and then enterotyping of chinese samples is performed using the relative abundance at genus level. The inventors used the same identification method described in the original text for gut type classification. In this study, the Jensen-Shannon distance was used for sample clustering.
Wherein
P (i) and Q (i) are the relative abundance of gene i in sample P, Q, respectively. Confirmation of gut type for each sample using the same method as the OG/KO relative abundance spectral data
3.7 Metagenomic species (MGS) analysis
In this study, we aggregated co-abundant genes into MGS based on the previously described method. Briefly, using algorithms that have been developed, genes are loaded into co-abundant genomes (CAG) according to their abundance distribution across all metagenomic samples. Merging two or more CAGs that satisfy the following condition: 1) the average GC bias of CAG is within 3%; 2) the average coverage difference of CAG is less than 25%; 3) CAG has the same taxonomic classification (95% homology as cut-off for species assignment). Finally, CAGs comprising more than 700 genes are considered to be different bacterial species (strains) and are considered to be metagenomic species (MGS).
As previously described, the taxonomic assignment and abundance analysis of MGS is based on the taxonomic and relative abundance of its constituent genes. In short, the assignment to a species requires 90% of the MGS genes to be identical to the species' genome, with 95% homology and 70% coverage. Assignment of MGS to a genus requires 80% genomic identity with 85% identity in the DNA or protein sequence.
3.8 screening biomarkers
Species with significant differences between ESRD patients and healthy control groups (q-value <0.05) can be defined as potential ESRD-related differential species. Based on these different species, we identified biomarkers according to the following criteria: 1) the discriminatory power (AUC) >0.6 for this species in ESRD patients and healthy controls; 2) the P-value of the rank sum test is less than 0.01.
3.9 validation of biomarkers
Sequencing data was obtained by repeating the steps of examples 1 and 2 using 233 samples, and the steps of example 3 were repeated to obtain a gene relative abundance profile, a species relative abundance profile, and a functional relative abundance profile. The community composition (species level), serum and stool metabolite abundances were determined using the two-tailed Wilcoxon rank-sum test for healthy controls and ESRD patients. FDR Regulation Using the Benjamin Hochberg method, local FDR is provided in the text. Different enriched KEGG modules were identified according to their reporter scores according to the Z scores of the respective KO groups. Modules with reporter Z scores greater than 1.65 (according to a 90% confidence of normal distribution) were considered significantly different
3.10 predictive analysis of species markers
In this study, we designed a differential population analysis method: 1) applying ROC analysis and calculating the area under ROC curve value (AUC) to assess the performance of individual MGS-based ESRD classification; 2) fold change in average relative numbers for each MGS. Calculating abundance and q-value of ESRD patients versus healthy controls (Wilcoxon rank sum test after FDR adjustment); 3) annotated MGS is shown if AUC values >0.6, q < 0.01.
For each species, a diagnostic cutoff (cutoff) is determined such that the sensitivity of the diagnosis is highest with the sum of specificity. (sensitivity is called true positive rate, which is the probability that the patient is actually diagnosed as positive by the index; specificity is called true negative rate, which is the probability that the patient is diagnosed as non-patient without actually suffering from a disease, which is the probability that the non-patient is diagnosed as invisible)
The detailed determination method of the critical value is as follows: and (3) sequencing the relative abundance of the species from low to high, then sequentially taking one value as a candidate critical value, calculating the sensitivity and the specificity under the candidate critical value, and taking the candidate critical value with the maximum sum of the sensitivity and the specificity as a final optimal critical value. For beneficial species, a relative abundance value less than a threshold value is diagnosed as end stage renal disease; for deleterious species, a relative abundance value greater than a critical value is diagnosed as end stage renal disease.
Example 4: animal experiment verification
4.1 bacterial culture, bacterial suspension culture and preparation.
Eggerthella lenta (Eggerthella lenta) VPI 0255 strain was purchased from JCM (JCM 9979) and cultured under strictly anaerobic conditions in anaerobically sterilized ATCC medium 1490(ELITE MEDIA). Fusobacterium nucleatum was purchased from CGMCC (CGMCC 1.2526) and cultured in an anaerobic sterilization medium containing peptone (AOBOX), tryptic peptide (AOBOX), yeast extract (OXOID), glucose (AOBOX), CaCl2(AOBOX), MgSO4.7H2O (AOBOX), K2HPO4.3H2O (AOBOX), KH2PO4(AOBOX), NaHCO3, KH2PO4 and KH _2PO 2. Each culture was centrifuged at 4200rpm for 15 minutes and then at 3X 109Resuspending at a concentration of CFU/ml, 3X 106CFU/ml resuspend the nucleic acid-bearing bacilli in sterile water.
4.2 animal experiments
Male SD rats (specific pathogen free grade, charles river, beijing) at 6 weeks of age were 5 per cage (filter top cage) and were free to eat (standard diet) and drink under a strict 12 hour photoperiod. They were acclimated for one week prior to receiving 5/6 nephrectomy to model typical Chronic Kidney Disease (CKD) as described previously. 5/6 two weeks after nephrectomy, rats were randomized into two groups and studied for driver species validation or probiotic intervention.
Experiment 1: in species validation studies, rats were divided into three experimental groups: CKD + eggerella lenta (eggerthertlella lentita) rats (n-11), CKD + fusobacterium nucleatum rats (n-11) and CKD control rats (n-11). In the next ten weeks, rats were gavaged every other day with 1ml of Eggerthella lenta (3X 10)9CFU/water, dissolved in sterile water), Bacillus with nucleic acid (3X 10)6CFU/body, dissolved in sterile water) or placebo.
Experiment 2: in the study of the intervention of probiotics,rats were divided into CKD + probiotic and CKD control groups. For the next 10 weeks, rats were gavaged daily with 1ml of probiotic (4X 10)10CFU/only) or placebo. Stool specimens were collected before surgery, before gavage, 8 weeks after gavage, immediately stored at-80 ℃ for further analysis. At the end of the study (10 weeks after gavage), animals were anesthetized with ether and sacrificed for cervical dislocation. The residual kidney of each rat was excised, weighed, and cut in half. Immediately frozen in liquid nitrogen and stored at-80 ℃ for subsequent analysis. The other half was fixed with 10% formaldehyde for histological and immunohistochemical analysis.
4.3 histological and immunohistochemical analysis
To assess renal abnormalities, kidney tissue fixed in 10% formaldehyde was dehydrated at room temperature by a graded ethanol series and embedded in paraffin. The prepared tissues were cut into 5 μm sections and subjected to routine histological and morphometric studies using periodic acid-schiff (PAS) and masson trichrome staining. Glomerulosclerosis was assessed by calculating sclerosing glomeruli and calculating the glomerular sclerosis index based on PAS staining. Immunohistochemical staining was performed by heating the slide to 95 ℃ in a microwave oven for 10 minutes in 0.01M citric acid buffer (pH 6) to recover the antigen. The sections were then immunostained using ABC peroxidase method (vector laboratories) with diaminobenzidine as the enzyme substrate and hematoxylin as the counter stain.
The histological and immunohistochemical results of experiment 1 are shown in figure 1.
The histological and immunohistochemical results of experiment 2 are shown in figure 2.
4.4 real-time quantitative PCR analysis
Quantitative PCR analysis was performed on eggerbil tarda and fusobacterium nucleatum in rat feces using SYBR Green qPCR, and the relative abundance of both bacteria was normalized to per gram of feces for comparison as shown in figure 3.
Although specific embodiments of the invention have been described in detail, those skilled in the art will appreciate. Various modifications and substitutions of those details may be made in light of the overall teachings of the disclosure, and such changes are intended to be within the scope of the present invention. The full scope of the invention is given by the appended claims and any equivalents thereof.
In the description herein, references to the description of the term "one embodiment," "some embodiments," "an illustrative embodiment," "an example," "a specific example," or "some examples" or the like mean that a particular feature, structure, material, or characteristic described in connection with the embodiment or example is included in at least one embodiment or example of the invention. In this specification, the schematic representations of the terms used above do not necessarily refer to the same embodiment or example. Furthermore, the particular features, structures, materials, or characteristics described may be combined in any suitable manner in any one or more embodiments or examples.
Claims (10)
1. Use of a reagent in the manufacture of a kit, characterized in that: the reagents are suitable for use in detecting a group of microorganisms comprising: achromobacter muciniphila (Akkermansia muciniphila), Achromobacter flexneri (Alisipsizing), Achromobacter sarmentosum (Alisiples shahii), Bacteroides cellulolyticus (Bacillus cellulolyticus), Bacteroides fragilis (Bacillus fragilis), Bifidobacterium dentis (Bifidobacterium), Clostridium difficile (Clostridium difficile), Clostridium saccharivorans (Clostridium saccharolyticum), Vibrio desulfyticus (Fusarium cellulolyticum), Escherichia coli (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterococcus faecalis), Flavonoides flavivirus (Lactobacillus acidophilus), Lactobacillus thermophilus (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum 3), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum, Lactobacillus paracasei (Lactobacillus plantarum), Lactobacillus plantarum, Lactobacillus (Lactobacillus), Lactobacillus plantarum, Lactobacillus strain (Lactobacillus), Lactobacillus strain, Lactobacillus plantarum, Lactobacillus strain (Lactobacillus strain, Lactobacillus strain (Lactobacillus strain, clostridium prasudanum (Faecalibacterium prausnitzii), vibrio rhodesiae (Roseburia intestinalis), Ruminococcus bicincans (Ruminococcus bicirus) and Ruminococcus strawberrii (Ruminococcus torques), for determining end stage renal disease in a subject.
2. The use of claim 1, wherein determining whether the set of microorganisms is present further comprises: isolating a nucleic acid sample from the excreta of the subject; constructing a DNA library based on the obtained nucleic acid sample; sequencing the DNA library to obtain a sequencing result; and determining whether the set of microorganisms is present based on the sequencing result.
3. Use according to claim 2, characterized in that the sequencing step is carried out by a second generation sequencing method or a third generation sequencing method.
4. The use of claim 2, wherein determining whether the set of microorganisms is present further comprises: comparing the sequencing result to the set of microorganisms; and determining whether the set of microorganisms is present based on the comparison.
5. The use according to claim 1, further comprising the step of: determining the relative abundance of the set of microorganisms; and comparing the relative abundance to a predetermined threshold.
6. A kit for determining an abnormal state, comprising: a reagent suitable for identifying a group of microorganisms, the group of microorganisms comprising: achromobacter muciniphila (Akkermansia muciniphila), Achromobacter flexneri (Alisipsizing), Achromobacter sarmentosum (Alisiples shahii), Bacteroides cellulolyticus (Bacillus cellulolyticus), Bacteroides fragilis (Bacillus fragilis), Bifidobacterium dentis (Bifidobacterium), Clostridium difficile (Clostridium difficile), Clostridium saccharivorans (Clostridium saccharolyticum), Vibrio desulfyticus (Fusarium cellulolyticum), Escherichia coli (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterococcus faecalis), Flavonoides flavivirus (Lactobacillus acidophilus), Lactobacillus thermophilus (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum 3), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum, Lactobacillus paracasei (Lactobacillus plantarum), Lactobacillus plantarum, Lactobacillus (Lactobacillus), Lactobacillus plantarum, Lactobacillus strain (Lactobacillus), Lactobacillus strain, Lactobacillus plantarum, Lactobacillus strain (Lactobacillus strain, Lactobacillus strain (Lactobacillus strain, clostridium prasudanum (Faecalibacterium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirtus (Ruminococcus bicirtus) and Ruminococcus strabismus (Ruminococcus torques), and the abnormal state is end stage renal disease.
7. Use of a biomarker as a target for screening a medicament for the treatment or prevention of end stage renal disease, wherein the biomarker is a group of microorganisms comprising: achromobacter muciniphila (Akkermanomyces muciniphila), Achromobacter flexneri (Alisips finegoldii), Achromobacter sarkii (Alisiphora), Bacteroides cellulolyticus (Bacillus cellulolyticus), Bacteroides fragilis (Bacillus fragilis), Bifidobacterium dentis (Bifidobacterium dense), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulforicus (Fusarium cellulolyticum), Gracillus lentus (Eggerthella), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterococcus faecalis), Flavonoides flavivirus (Flavivipula), Clostridium thermophilus (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum) and Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus (Lactobacillus) producing strain, Lactobacillus plantarum, Lactobacillus (Lactobacillus), Lactobacillus (Lactobacillus plantarum) Lactobacillus (Lactobacillus), Lactobacillus plantarum, Lactobacillus (Lactobacillus plantarum) and Lactobacillus (Lactobacillus), Lactobacillus plantarum, Lactobacillus (Lactobacillus), Lactobacillus plantarum) producing strain (Lactobacillus), Lactobacillus plantarum) and Lactobacillus (Lactobacillus plantarum) strain (Lactobacillus), Lactobacillus (Lactobacillus plantarum) and Lactobacillus (Lactobacillus), Lactobacillus plantarum) such as strain, Lactobacillus plantarum (Lactobacillus strain, Lactobacillus strain (Lactobacillus plantarum strain, Lactobacillus strain (Lactobacillus strain, Lactobacillus (Lactobacillus strain, clostridium prasudanum (Faecalibacterium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirtus (Ruminococcus bicirtus) and Ruminococcus strabismus (Ruminococcus torques).
8. Use according to claim 7, wherein the presence of said group of microorganisms is determined by assaying a subject's excreta, wherein said excreta is feces.
9. Use of a group of microorganisms in the manufacture of a medicament for the treatment or prevention of an abnormal condition, said group comprising: achromobacter muciniphila (Akkermansia muciniphila), Achromobacter flexneri (Alisips finegoldii), Achromobacter sarkii (Alisips shahii), Bacteroides cellulolyticus (Bacteroides cellulolyticus), Bacteroides fragilis (Bacteroides fragilis), Bifidobacterium (Bifidobacterium lactis), Clostridium difficile (Clostridium difficile), Clostridium saccharolyticum (Clostridium saccharolyticum), Vibrio desulforicola (Desufovibrio vibrio philinensis), Escherichia tarda (Eggerthella lenta), Enterococcus faecalis (Enterococcus faecalis), Enterococcus faecium (Enterococcus faecium), Flavonoides (Flavobacter sphaericus), Lactobacillus casei (Lactobacillus plantarum), Lactobacillus thermophilus (Lactobacillus casei), Lactobacillus plantarum (Lactobacillus plantarum 3), Lactobacillus plantarum (Lactobacillus plantarum), Lactobacillus plantarum (Lactobacillus plantarum) and Lactobacillus plantarum (Lactobacillus plantarum) Lactobacillus), Lactobacillus plantarum (Lactobacillus) Lactobacillus strain, Lactobacillus plantarum strain (Lactobacillus), Lactobacillus plantarum (Lactobacillus strain (Lactobacillus), Lactobacillus plantarum) and Lactobacillus plantarum (Lactobacillus strain (Lactobacillus) and Lactobacillus plantarum), Lactobacillus (Lactobacillus plantarum) Lactobacillus strain (Lactobacillus) Eubacterium recta (Eubacterium rectangle), Clostridium praerumtzii (Clostridium prausnitzii), Vibrio rozae (Roseburia intestinalis), Ruminococcus bicirus (Ruminococcus bicirus), and Ruminococcus torques (Ruminococcus torques), and the abnormal state is end stage renal disease.
10. Use according to claim 9, characterized in that any one or any combination of the group of microorganisms is used.
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN112138029A (en) * | 2020-10-31 | 2020-12-29 | 中国药科大学 | Application of bacteroides ovatus in preparation of anti-renal fibrosis medicine |
| CN112294851A (en) * | 2020-12-01 | 2021-02-02 | 中国药科大学 | Application of Bacteroides fragilis in preparation of renal fibrosis resistant medicine |
| CN113957142A (en) * | 2021-12-01 | 2022-01-21 | 上海市闵行区中心医院 | Intestinal flora-based biomarker for renal anemia combined with erythropoietin resistance and application thereof |
| CN116240151A (en) * | 2023-04-17 | 2023-06-09 | 四川厌氧生物科技有限责任公司 | Fender-like bacillus and application thereof |
Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20090081713A1 (en) * | 2007-09-20 | 2009-03-26 | University Of Louisville Research Foundation, Inc. | Peptide biomarkers predictive of renal function decline and kidney disease |
| WO2010091233A1 (en) * | 2009-02-06 | 2010-08-12 | Astute Medical, Inc. | Diagnosis and prognosis of renal injury and renal failure |
| WO2015054246A1 (en) * | 2013-10-07 | 2015-04-16 | Trius Therapeutics, Inc. | Methods of treating subjects with renal impairment using tedizolid |
| CN104540962A (en) * | 2012-08-01 | 2015-04-22 | 深圳华大基因研究院 | Biomarkers for diabetes and usages thereof |
| CN108367030A (en) * | 2015-10-28 | 2018-08-03 | 麦太宝根有限公司 | Pu Shi bacillus faecalis and inertia desulfovibrio are for treating or preventing diabetes and enteropathy |
-
2019
- 2019-12-06 CN CN201911245044.XA patent/CN110878349A/en active Pending
Patent Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20090081713A1 (en) * | 2007-09-20 | 2009-03-26 | University Of Louisville Research Foundation, Inc. | Peptide biomarkers predictive of renal function decline and kidney disease |
| WO2010091233A1 (en) * | 2009-02-06 | 2010-08-12 | Astute Medical, Inc. | Diagnosis and prognosis of renal injury and renal failure |
| CN104540962A (en) * | 2012-08-01 | 2015-04-22 | 深圳华大基因研究院 | Biomarkers for diabetes and usages thereof |
| WO2015054246A1 (en) * | 2013-10-07 | 2015-04-16 | Trius Therapeutics, Inc. | Methods of treating subjects with renal impairment using tedizolid |
| CN108367030A (en) * | 2015-10-28 | 2018-08-03 | 麦太宝根有限公司 | Pu Shi bacillus faecalis and inertia desulfovibrio are for treating or preventing diabetes and enteropathy |
Non-Patent Citations (2)
| Title |
|---|
| JIANG 等: "Alteration of the gut microbiota in Chinese population with chronic kidney disease", 《SCIENTIFIC REPORTS》 * |
| 胡建广等: "高通量测序分析老年血液透析患者肠道菌群的改变", 《中国中西医结合肾病杂志》 * |
Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN112138029A (en) * | 2020-10-31 | 2020-12-29 | 中国药科大学 | Application of bacteroides ovatus in preparation of anti-renal fibrosis medicine |
| CN112294851A (en) * | 2020-12-01 | 2021-02-02 | 中国药科大学 | Application of Bacteroides fragilis in preparation of renal fibrosis resistant medicine |
| CN112294851B (en) * | 2020-12-01 | 2023-01-17 | 中国药科大学 | Application of Bacteroides fragilis in preparation of renal fibrosis resistant medicine |
| CN113957142A (en) * | 2021-12-01 | 2022-01-21 | 上海市闵行区中心医院 | Intestinal flora-based biomarker for renal anemia combined with erythropoietin resistance and application thereof |
| CN113957142B (en) * | 2021-12-01 | 2023-09-26 | 上海市闵行区中心医院 | Intestinal flora-based biological marker for renal anemia combined erythropoietin resistance and application thereof |
| CN116240151A (en) * | 2023-04-17 | 2023-06-09 | 四川厌氧生物科技有限责任公司 | Fender-like bacillus and application thereof |
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