CN116042866A

CN116042866A - Microbial marker for evaluating fecal fungus transplanting curative effect of patients with type II diabetes and application thereof

Info

Publication number: CN116042866A
Application number: CN202111419850.1A
Authority: CN
Inventors: 丁大法; 畅航; 毛建华
Original assignee: Berkeley Nanjing Medical Research Co ltd; 2nd Affiliated Hospital of Nanjing Medical University
Current assignee: Berkeley Nanjing Medical Research Co ltd; 2nd Affiliated Hospital of Nanjing Medical University
Priority date: 2021-08-02
Filing date: 2021-11-26
Publication date: 2023-05-02
Also published as: CN113337630A

Abstract

The invention discloses an intestinal tract macro genome characteristic as a screening mark of the fecal transplanting curative effect of a patient with type II diabetes, wherein the intestinal tract microbial macro genome characteristic is intestinal flora of the family rinkenellictaceae and the genus Anaerotyruncus, and the patient with type II diabetes suitable for fecal transplanting treatment is selected according to the expression level of the specific intestinal flora markers. According to the biological markers of the intestinal flora and different detection technology platforms, corresponding detection kits are designed and developed. The system and product can be used for precise treatment of type II diabetes based on individualization.

Description

Microbial marker for evaluating fecal fungus transplanting curative effect of patients with type II diabetes and application thereof

Technical Field

The invention belongs to the technical field of microorganism detection, and particularly relates to a group of intestinal flora markers related to human type II diabetes fecal bacteria transplanting curative effect and application of the intestinal flora markers in clinical accurate medicine.

Background

Diabetes is one of the important chronic diseases currently threatening the world, and drugs play an important role in the course of diabetes treatment. Recently, many target drugs, such as GLP-1 receptor agonists, DDP-4 inhibitors, SGLT-1, 2 inhibitors, etc., have been developed according to the pathophysiological mechanism of the onset of type II diabetes. However, individual differences in the response of type II diabetes to drug therapy are prevalent during the course of treatment. The occurrence mechanism is related to genetics, sex, age, height, weight, life eating habit, disease state, combined administration and other factors. Although pharmacogenomics determines the use of personal genetic information, it plays an increasingly important role in clinical personalized medicine and assessing the risk of adverse drug reactions. However, the "precise treatment of the genotyping" of the diabetic drugs is not so much, although it is reported that polymorphism of the organic cation transporter 1 (OCT 1) gene affects the uptake of metformin, thereby affecting the efficacy and metabolism of the drugs. Thiazolidinedione pharmacogenomics research is mainly focused on CYP450 enzymes and adiponectin gene polymorphism. Recent studies have found that changes in the composition of host intestinal microorganisms affect the metabolism and therapeutic effects of diabetic drugs, and that patient's heterogeneous response to treatment may be due to differences in the intestinal microbiome. Thus, a priori knowledge of the individual's microbial composition may be helpful in predicting the outcome of treatment and/or suggesting an optimal treatment strategy. Gu et al demonstrated that intestinal microbiomes can classify newly developed patients with type II diabetes (T2D) into two clusters, cluster P (dominant by Prevoltella) and B (dominant by Bactoides), and found that acarbose treatment was more pronounced in patients with diabetes three months later than in group B. These findings indicate that quantifying the microbial composition in a patient's stool sample helps to predict treatment outcome and classify the patient as potentially responders or non-responders, particularly the therapeutic impact of diabetic drug and gut flora interactions on type two diabetes is not yet clear. So the interaction between the hypoglycemic agent and the intestinal microorganisms is explored, and the better accurate treatment of the type II diabetes has important clinical significance.

A large number of microorganisms are planted in human intestinal tracts, the intestinal flora cells are more than 3500 bacteria, the number of the intestinal flora cells is about 10 times of that of the human body cells, the weight of the bacteria is about 1.5kg, and the number of the huge bacteria is 100 times of that of the human body self genes. The sum of genome information of intestinal flora is called intestinal metagenome, which is a second genome of human beings for controlling human health, and has important regulation and control effects in physiological and pathological processes such as metabolism, immunity, inflammation and the like. There is growing evidence that abnormalities in the intestinal flora are closely linked to disorders of glucose metabolism, lipid metabolism, insulin sensitivity, inflammatory systems, etc. Scientists are studying which bacteria are beneficial, how to promote them, hopefully in the future to be able to combat diseases such as irritable bowel syndrome, obesity, type two diabetes by controlling intestinal bacteria. At present, more and more researches show that intestinal flora is closely related to occurrence and development of metabolic diseases such as obesity, type II diabetes and the like, and the intestinal flora is taken as an entry point to explore pathogenesis of the type II diabetes and accurate targeted therapy of medicines, so that the intestinal flora becomes a new research hot spot internationally. The interaction between human intestinal flora and type II diabetes is first reported and published in nature 2012, and the study shows that the relative abundance of main butyric acid producing clostridium bacteria such as Enterobacter (Roseburia) and Clostridium tenella (Faecaliberium) in type II diabetes patients is significantly lower than that in normal populations, while the levels of lipopolysaccharide, hydrogen sulfide pro-inflammatory function and branched-chain amino acid transport function are significantly higher in the population of Enterobacteriaceae species that are conditionally pathogenic. Subsequently, dr Fredrik

And teams thereof found in 2013 that similar intestinal dysbacterioses exist in women of european age, in diabetic patients and pre-diabetic populations with impaired glucose tolerance, such as a significant enrichment of Streptococcus species. Furthermore, in a number of independent studies, researchers found that the significant characteristics of changes in intestinal flora before and after metformin administration were consistent in healthy persons or in type II diabetics. Intervention or reconstitution of host intestinal flora may be a new therapeutic strategy for metabolic diseases such as diabetes and obesity. However, the current research on the relationship between the composition change of the intestinal flora and the type II diabetes is complex, the intestinal flora causes the type II diabetes and (or) the type II diabetes causes the intestinal flora to be disordered, the current research results are not consistent, and the environment of different areas has obvious influence on the intestinal flora of a host. Especially explore intestinal flora and metabolites as early warning of type II diabetes, diagnosis and treatment targets and interaction with hypoglycemic drugs, and lack of clinical related data. The fecal bacteria transplantation (fecal microbiota transplantation, FMT) is to transplant functional flora in the feces of a healthy person into the intestinal tract of a patient, rebuild the intestinal flora with normal functions, and treat intestinal and parenteral diseases. To date, FMT has been used for the treatment of recurrent clostridium difficile infection, refractory inflammatory bowel disease, refractory constipation, metabolic syndrome, and other diseases. In 2017, cell metabolism reports the influence of FMT on blood sugar and insulin functions of metabolic syndrome patients for the first time, and results show that FMT can remodel intestinal flora of patients, increase beneficial bacteria, improve insulin resistance of the patients and improve insulin sensitivity. This provides a new idea for future research of metabolic diseases caused by intestinal flora and development of probiotics for treatment. However, to date, fecal Microorganism Transplantation (FMT) from healthy donors has not been evaluated to determine whether it would benefit type two diabetics. The second affiliated hospital digestion medical center of the university of south Beijing medical science established a standardized FMT (comprising standardized fecal bacteria library) laboratory system as early as 2012, and used the standardized FMT to rescue and treat a variety of refractory bowel diseases, registered clinical trials (NCT 01790061, NCT01790711, NCT 01793831), and obtained good research results. The subject group is in Jiangsu province in early stageUnder the support of the key research and development (social development) project (under the host of No. BE2016800, ding Dafa), the medical key talent project of the Jiangsu province "science education Jiang Wei" of young people (under the host of No. QNRC2016674, ding Dafa), partial originality discovery is achieved. By researching intestinal flora of healthy people and type II diabetics in Nanjing area of Jiangsu province, the important clinical significance of the earlier-stage subject research is as follows: 1) Further enriches the disturbance of intestinal flora, which is a key factor for the occurrence and development of type II diabetes; 2) The first international report on FMT treatment of patients with type II diabetes, reestablishing intestinal flora and obtaining good clinical effects; 3) The individual difference of host intestinal flora is found to determine the curative effect response of FMT in treating type II diabetes, so that clinical indications and treatment strategies are indicated for FMT in treating type II diabetes, and ideas and directions are provided for later-stage research of FMT in accurately treating type II diabetes.

In view of the fact that no intestinal flora marker and scoring system for predicting the fecal flora transplanting curative effect of the patients with the diabetes mellitus worldwide can be used for guiding the accurate selection of the patients with the diabetes mellitus to benefit, the provided type-II diabetes mellitus microorganism marker has the advantages of good specificity, high sensitivity and important significance for the accurate prediction and selection ability of the patients with the diabetes mellitus.

Disclosure of Invention

The invention develops a group of flora markers by adopting a multi-step bioinformatics strategy based on comprehensive intestinal microbiology data of the patients with the diabetes. Multivariate random forest analysis shows that the marker can predict and evaluate the fecal fungus transplanting curative effect of the type II diabetes patient.

The sample in the invention is excrement of a type II diabetes patient, DNA is separated from the excrement sample, the expression level of two intestinal flora markers is measured, and then the type II diabetes patient suitable for fecal bacteria transplantation treatment is screened through a prediction model. The two flora markers are rinkenella laceae and Anaerotyruncus (Ruminococcea family), and the control flora is total intestinal flora.

In order to achieve the above object, the present invention provides the following technical solutions:

in embodiments, the invention provides a set of microbial markers for assessing the efficacy of fecal transplantation in treating patients with type II diabetes, including the rinkenella laceae and the Ruminococcea family.

Preferably, the microorganism of the family Ruminococaceae is of the genus Anaerotyruncus.

In another embodiment, the invention provides a microbial marker for use in constructing a model for assessing the efficacy of fecal transplantation in treating patients with type II diabetes.

In some embodiments, the method of determining the relative content of a microbial marker described above includes quantitative PCR, gene chip, second generation high throughput sequencing, panomics, or Nanostring techniques.

Preferably, the relative amounts of the above-mentioned microbial markers can be determined by quantitative PCR, gene chip, second generation high throughput sequencing, and by the Panomics or Nanostring technique, by 16S rRNA sequencing.

In another embodiment, the invention provides the use of a microbial marker in the preparation of a therapeutic test agent for fecal transplantation efficacy in type II diabetics.

In another embodiment, the invention provides a set of microbial probes or primers for use in a fecal transplant therapeutic test agent for type II diabetes patients, the microbial probes capable of generating hybridization signals by molecular hybridization in combination with the target microorganism, and the primers capable of amplifying the target microorganism by PCR-based techniques.

In some embodiments, the microbial probes or primers described above can be used to detect a microbial marker by quantitative PCR, gene chip, second generation high throughput sequencing, panomics, or Nanostring techniques.

Preferably, the microbial probes or primers can be used for detecting the expression level of the microbial markers in the feces of the patients with the type II diabetes by quantitative PCR, gene chip, second generation high throughput sequencing, panomics or Nanostring technology.

In another embodiment, the present invention provides a composition for assessing the efficacy of a type II diabetes fecal transplant comprising the microbial probe or primer described above.

In another embodiment, the invention provides a kit for assessing the efficacy of a type II diabetic fecal transplant comprising the composition described above.

The term "biomarker" as used herein is to be understood in a broad sense and includes any detectable biological indicator, which may comprise genetic markers, species markers (species/genus/family markers) and functional markers (KO/OG markers). The meaning of the marker is not limited to a gene that can express a protein having biological activity, but includes any nucleic acid fragment, and may be modified DNA or RNA, or unmodified DNA or RNA.

The terms "microbial probe" and "primer" as used herein refer to an oligonucleotide, preferably a single stranded deoxyribonucleotide, including natural (naturally occurring) dNMP (dAMP, dGMP, dCMP and dTMP), deformed nucleotides or unnatural nucleotides, and may further comprise ribonucleotides.

The microbial probes and marker primers utilized in the present invention comprise hybridizing nucleotide sequences complementary to the target location of the target nucleic acid. The term "complementary" means substantially complementary to a target nucleic acid sequence that selectively hybridizes to the primer or probe under hybridization conditions, and has the meaning of including substantially complementary (substantially complementary) and fully complementary (perfectly complementary) in their entirety, preferably fully complementary. The term "substantially complementary sequence" as used herein includes not only a completely identical sequence but also a sequence which can function as a primer on a specific target sequence and is partially inconsistent with a sequence to be compared.

The primer sequences of the microbial probe and the marker need not have a sequence completely complementary to a part of the sequence of the template, as long as they have sufficient complementarity within a range capable of hybridizing with the template to exert their inherent functions. Therefore, the microorganism probe and primer of the present invention need not have a sequence completely complementary to the above-mentioned nucleotide sequence as a template, and may have sufficient complementarity within a range capable of hybridizing with the template to exert its inherent function. The design of PRIMERs and probes is within the skill of those skilled in the art, and may utilize, for example, PRIMER design procedures (e.g., prime 3 procedure).

The determination of the expression level of the flora in the present invention can be performed by methods well known in the art, including but not limited to quantitative PCR, gene chip, second generation high throughput sequencing, panomics or Nanostring techniques.

The invention provides a prediction diagnosis kit for the curative effect of the fecal bacteria transplantation of a patient with diabetes containing the flora marker primer pair. In the kit of the present invention, tools and/or reagents known in the art for PCR reaction may be added in addition to the primers or probes for the two colony markers. The kit of the present invention may further contain, if necessary, a tube for mixing the components, a microplate, and instructions describing the method of use.

Advantageous effects

The invention successfully discovers two specific biomarker flora for predicting the fecal fungus transplanting curative effect of the type II diabetes patient, and establishes a curative effect prediction system based on the expression level of the flora for the first time. Multivariate random forest analysis shows that the multivariate random forest analysis has accurate prediction and selection capability for benefited patients, can be used for selecting benefited individuals with faecal fungus transplantation for treating type II diabetes, and can be used for treatment selection, so that excessive medical treatment is avoided, and the purpose of individual medical treatment is achieved.

Drawings

Fig. 1: the invention is applied to clinical test design schemes.

Fig. 2a-2c: intestinal flora differences between healthy and type II diabetics at the family (family) level. (FIG. 2 a) relative abundance of major microbiology in T2DM patients and healthy controls; (FIG. 2 b) PCA at the intestinal flora grade of T2DM patients, 17T 2DM samples (crosses) and 20 control samples (open circles), p-values were obtained from a permutation of multiple variance analysis (PERMANOVA); (FIG. 2 c) a relatively rich box plot of 12 families shows significant differences between T2DM patients and healthy controls, p-values were obtained by the Mann-Whitney test, boxes representing the median and quartile ranges between the first and third quartiles, and points representing outliers.

Fig. 3a-3b: correlation between intestinal flora at the genus (genus) level and clinical parameters related to diabetes. (FIG. 3 a) Spearman correlation coefficient plot between genus richness and clinical factors, p <0.05 in T2DM patients and healthy control samples; * P < 0.01; (FIG. 3 b) random forest analysis evaluates the correlation between microbial abundance at the genus level and clinical factors, with significant levels indicated by grey lines (p < 0.05).

Fig. 4a-4f: effects of fecal transplantation treatment on patient intestinal flora and clinical parameters. (FIG. 4 a) PCA of intestinal microbiota of T2DM patients before and after FMT treatment, microbiome samples after FMT treatment were separated from microbiome samples before FMT treatment, and sample microbiome of beneficiaries before treatment and non-beneficiaries were clearly separated. (FIGS. 4b-4 f) box plots show clinical factor changes in beneficiaries and non-beneficiaries before and after FMT treatment, p-values were obtained by Mann-Whitney test.

Fig. 5a-5f: and (5) comparing the change of clinical parameters of patients before and after the fecal transplantation treatment. (FIG. 5 a) fasting blood glucose; (FIG. 5 b) postprandial blood glucose; (FIG. 5 c) hemoglobin A1c (HbA 1 c); (FIG. 5 d) uric acid; (FIG. 5 e) fasting C-peptide; (FIG. 5 f) postprandial C peptide.

Fig. 6a-6b: the expression level of two intestinal flora biomarkers in healthy people and type II diabetes patients (before and after fecal bacteria transplantation treatment). (FIG. 6 a) Rikenella ceae; (FIG. 6 b) Anaerotyruncus genus.

Fig. 7: the prediction effect of the invention on the fecal transplantation curative effect of the type II diabetes patient can predict the reaction of the patient to the FMT treatment according to the abundance of the intestinal bacteria of the Rikenella ae family and the Anaerotyruncus genus in the fecal sample before treatment through a trained model.

Detailed Description

The present invention first identified significantly different populations of different intestinal flora levels between healthy populations of the same type of diabetes (fig. 2a-2 c), significantly varying relative abundance of taxa at family level (family) compared to healthy controls (fig. 2 a), T2DM patients and healthy controls showed separation by maximum folding metric learning (MCML) analysis of all families (fig. 2 b), and furthermore we found that the abundance of Rikenellaceae, lactobacillaceae, enterobacteriaceae, coriobacteriaceae, enterococcaceae, streptococcaceae, cytophagaceae, actinomycetaceae and erysipelotorich families significantly increased while the abundance of ruminococceae significantly decreased (fig. 2 c).

Then confirming the correlation between the intestinal flora and the clinical parameters related to diabetes, and finding that the abundance of Dorea is obviously positively correlated with the level of glucose and hemoglobin A1c (HbA 1 c) in blood under empty stomach at the level of genus (genus) through data depth analysis and Spearman calculation, and the abundance of Megasphaera is also obviously positively correlated with the level of HbA1c (fig. 3 a); at the family level, rikenellaceae, enterobacteriaceae, enterococcaceae, erysipelotrichaceae abundance correlated significantly positively with fasting glucose levels, while none of the family levels correlated significantly with HbA1c levels; no significant correlation between uric acid levels and abundance was found at the genus and family levels (fig. 3 a); random forest analysis further confirmed these observations (fig. 3 b), confirming the intestinal flora as etiological basis for type two diabetes.

The present invention incorporates 17T 2DM patients (ChiCTR-ONC-17011792) with clinical outcome assessment after FMT treatment (fig. 1) by clinical trials for treatment of type two diabetes using autonomous dominant fecal fungus transplantation, 17T 2DM patients had clinical symptoms of 1 year or longer, and neither insulin injection twice daily in combination with metformin treatment was adequately controlled. Subjects were evaluated prior to fecal transplant treatment and fecal matter was retained as well as blood samples. Clinical evaluation showed significantly higher blood glucose and hemoglobin A1c (HbA 1 c) levels in these patients compared to the 20 healthy control groups (table 1).

17T 2DM patients received two FMTs by midgut TET technique (FIG. 1), and T2DM patients and healthy controls were subjected to 16S rRNA sequencing using Illumina MiSeq for a total of 37 stool samples, and differences between microbiome samples after FMT treatment and microbiome samples before FMT treatment were seen (FIG. 4 a), confirming that FMT reconstituted the gut microbiome of T2DM patients. Analysis was performed using a multi-step bioinformatics method, and clinical outcome of all patients was assessed by measuring the levels of hemoglobin (HbA 1 c) and other clinical markers associated with T2 DM. Then, FMT treatment efficacy was assessed by patients whose clinical criteria were defined as responsive (fig. 4a-4f, fig. 5a-5f, table 2, table 3, table 4), and 11 out of 17T 2DM patients were found to be responsive to FMT treatment (fig. 4b-4 f), with significantly reduced fasting blood glucose, postprandial blood glucose, hbA1C and uric acid levels, and significantly increased postprandial C peptide (C-peptide) levels in 11 beneficiaries (fig. 4b-4 f); whereas in 6 non-responders, these clinical parameters did not change (FIGS. 4b-4 f).

Finally, comparison of intestinal flora in type II diabetics with intestinal flora between healthy groups after faecal fungus transplantation treatment by random forest deep predictive model analysis, among 6 beneficiaries who did not respond to FMT treatment, rikenella and Anaerotyruncus (Ruminococcea) had similar levels of abundance before treatment to healthy controls, whereas of 11 beneficiaries who responded to FMT treatment, riceneraceae and Anaerotyruncus had significantly higher abundance before treatment than healthy controls, and FMT treatment could adjust their abundance to healthy levels (FIGS. 6a-6 b), indicating that Rikenella and Anarounctucus are causally related to FMT treatment T2DM patients.

The invention provides a fecal fungus transplanting effect evaluation system for first-case diabetics in the world, and provides accurate medical basis for fecal fungus transplanting treatment of type II diabetes.

In the present invention, the sample is excrement of a patient, preferably feces. The flora marker for the treatment effect prediction of the fecal bacteria transplantation of the type II diabetes patient can be detected through different detection technology platforms, including but not limited to quantitative PCR, gene chips, second-generation high-throughput sequencing, panomics and Nanostring technologies, and corresponding flora primers (quantitative PCR) and probes (gene chips, second-generation high-throughput sequencing, panomics and Nanostring technologies) are designed aiming at different technology platforms. Preferably, the expression level of the target bacterial flora is detected, and more preferably, the expression level of the target bacterial flora is quantitatively detected. In order to detect the expression level, it is necessary to isolate DNA from the tissue of the sample, and methods known in the art for isolating DNA from the sample can be used. The random forest prediction model we define is described above.

In another aspect, the present invention provides a composition for predicting and diagnosing the efficacy of fecal transplantation in a patient suffering from diabetes, comprising as an active ingredient a bacterial group probe or primer directed to the aforementioned genus Anaerotyroso and family Rikenella.

In another aspect, the invention provides a kit for predicting and diagnosing the effect of fecal transplantation in a patient with diabetes, which comprises the composition.

The present invention is further illustrated in the accompanying drawings and detailed description which are to be understood as being merely illustrative of the invention and not limiting of its scope, and various modifications of the invention, which are equivalent to those skilled in the art upon reading the invention, will fall within the scope of the invention as defined in the appended claims.

Example 1DNA extraction and sequencing

The DNA extraction method comprises the following steps: genomic DNA was extracted from a 0.25 gram stool sample using a QIAamp PowerFecal Pro DNA kit according to the manufacturer's instructions. The treated sample was added to the bead jumper tube. Rapid and thorough homogenization is achieved using mechanical and chemical methods. Once the cells are differentiated, IRT is used to remove the inhibitor. The total genomic DNA was captured on a silicon membrane in spin column format. The DNA is then washed and eluted, ready for downstream use.

Samples were subjected to 16S rRNA sequencing using an Illumina Miseq.

Example 2 identification of biomarkers

The identification and screening of biomarkers requires that the following 3 conditions be met simultaneously:

1. the relative abundance of this bacterium is statistically different between healthy individuals and those with diabetes who are effectively treated by fecal transplantation (prior to fecal transplantation); furthermore, there was no statistical difference between healthy people and diabetics who were effectively treated with fecal transplantation (after fecal transplantation).

2. The relative abundance of the bacteria is not statistically different between healthy people and diabetics who are not effective in fecal transplantation therapy (prior to fecal transplantation); furthermore, there was no statistical difference between healthy people and diabetics who were not effective in fecal transplantation therapy (post fecal transplantation).

3. The relative abundance of this bacterium is statistically different between those with diabetes who are effective in fecal transplantation (before fecal transplantation) and those with diabetes who are ineffective in fecal transplantation (before fecal transplantation).

Example 3 model training

The classifier constructed is a random forest. Using the relative abundance of the species as a risk value, the area under the curve AUC is estimated, the larger the AUC, the higher the diagnostic capacity. Random forest classification based on relatively rich levels of riconellaceae and anaeroruncus gave a prediction accuracy of about 82.4% and an AUC of about 0.83 (fig. 7). The trained model can predict patient response to FMT treatment based on the abundance of rikenella ceae and anaerotrurus in the patient's FMT pre-treatment fecal sample.

Example 4 design of clinical experiments

Patient qualification

Patients with the following conditions were aged 18-71 years and BMI of 22-30kg/m ² And at the time of group entry, insulin (MDI) and metformin (6.5% or more and HbA1c or less and 8.5% or less) are injected multiple times per day, and type two diabetes mellitus (T2 DM) cannot be sufficiently controlled, and the disease persists for 1 year or longer; the 20 non-diabetic participants in the hospital physical examination center served as healthy controls, matched to the diabetic participants by gender, BMI and other clinical parameters. Prior to administration, patients must receive a stable insulin and metformin regimen and employ a stable insulin management regimen for more than 12 weeks. Detailed inclusion and exclusion criteria are described below:

the inclusion criteria were: (i) 18 to 71 years old; (ii) The last 12 months met the standard definition of the american diabetes association T2 DM; (iii) There were no systemic and metabolic diseases other than T2DM, and no infections in the past 3 months; (iv) No diets or drugs, such as glucocorticoids or antibiotics, that might interfere with glucose homeostasis were ingested during the past 3 months; (v) HbA1c lower than 8.5%.

The exclusion criteria were: (i) Significant systemic diseases of clinical significance, including malignant tumors; (ii) Serious diabetic complications (diabetic retinopathy, diabetic neuropathy, diabetic nephropathy, and diabetic foot); (iii) Antibiotics are continuously used for more than 3 days in the first 3 months of the selection; alcohol abuse, defined as men >80g/d, women >40g/d; continuously taking weight-reducing medicine for more than 1 month; (iv) Serious organic diseases including coronary heart disease, myocardial infarction or stroke; (v) Acute disease, acute or chronic inflammation, infectious disease; (vi) Mental illness, which makes it impossible for participants to understand the nature, scope and possible consequences of the study.

The study was approved by the ethical committee of the second affiliated hospital of the university of south Beijing medical science, south China (protocol number: 2015 KY 044), which was registered with the China clinical trial registry (ChiCTR-ONC-17011792). A schematic of the study design and 37 participants is shown in figure 1.

Fecal fungus transplanting treatment process

The fecal donor is recruited according to the standard, and the screening of the donor should comprehensively consider the influence of genetic factors, dietary and life habit and other environmental factors and health conditions on the intestinal flora of the donor. The Chinese faecal bacteria library comprehensively screens healthy donors from 8 aspects of age, physiology, pathology, psychology, authenticity, time factors, living environment and recipient state.

All T2DM participants received FMT treatment by a new technique called "trans-endoscopic intestinal (TET)", 200ml once a week, and a total of 50-60 g were transplanted, and blood glucose levels of the participants were monitored for 12 weeks.

Blood glucose monitoring and insulin dosage adjustment

Insulin dosage is adjusted based on the patient's blood glucose level to reduce the patient's hyperglycemia. During the 12 week period of treatment, the patient is instructed to inject insulin analogue or pre-mix insulin analogue based doses to achieve pre-breakfast blood glucose levels of 4.4 to 6.7mmol/L and the patient is instructed to adjust the insulin injection doses to achieve pre-noon, pre-evening and pre-bedtime blood glucose levels of 4.4 to 6.7mmol/L. Researchers can use judgment in proposing to adjust insulin dosage based on their own knowledge of the patient's personal history, requiring the patient to record daily blood glucose measurements and insulin dosage at specified time points to assess patient compliance with insulin dosage.

Sample collection

Plasma and stool samples were collected from type two diabetics and normal control populations 3 months before and after FMT treatment, and clinical and biochemical data were compared for different periods before and after FMT treatment.

Blood sample: blood was collected within 2 hours after breakfast after 10 hours on an overnight fast. The blood samples were left at room temperature for 30 minutes and then centrifuged at 3000Xg for 20 minutes to obtain serum, which was stored at-20 ℃ (conditioned at-80 ℃).

Fecal sample: fecal samples were collected on the same day as blood samples were collected, flash frozen in dry ice, and stored at-80 ℃ until analysis.

17T 2DM patients received two FMTs by midgut TET technique (FIG. 1), and the T2DM patients and healthy controls were subjected to 16S rRNA sequencing using Illumina MiSeq for a total of 37 stool samples, confirming that FMT reconstituted the intestinal microbiome of the T2DM patient (FIG. 4 a). Analysis was performed using a multi-step bioinformatics method, and clinical outcome of all patients was assessed by measuring the levels of hemoglobin (HbA 1 c) and other clinical markers associated with T2 DM.

The efficacy of FMT treatment was assessed by patients whose clinical criteria were defined as responsive (fig. 4a-4f, fig. 5a-5f, table 2, table 3, table 4), and 11 out of 17T 2DM patients were found to be responsive to FMT treatment (fig. 4b-4 f), with significantly reduced fasting blood glucose, postprandial blood glucose, hbA1C and uric acid levels, and significantly increased postprandial C peptide levels, and significantly improved islet secretion function in 11 beneficiaries (fig. 4b-4 f); whereas in 6 non-responders, these clinical parameters did not change (FIGS. 4b-4 f).

Example 5 prediction of fecal transplantation efficacy for diabetes patient

Clinically received patient faeces were collected and DNA was extracted. The expression level of the two bacterial groups is then quantitatively detected by the kit developed by the invention and corresponding instruments (such as quantitative PCR, panomics, chips, etc.). The expression levels of the two flora are input into the random forest prediction model established by the invention, and the fecal transplanting curative effect of the patient is determined.

Comparison of intestinal flora between intestinal flora and healthy groups in type II diabetics after treatment with a predictive model analysis of random forest penetration, among 6 beneficiaries who did not respond to FMT treatment, rikenella family and Anaerotyruncus genus (Ruminococcea family) had similar levels before treatment to healthy controls, whereas of 11 beneficiaries who responded to FMT treatment, riceneraceae family and Anaerotyrunctus genus had significantly higher abundance before treatment than healthy controls, FMT treatment adjusted their abundance to healthy levels (FIGS. 6a-6 b), suggesting that Rikenella family and Anarounctrouncus genus were causally related to FMT treatment T2DM patients.

Example 6 accurate selection of type II diabetes patients suitable for faecal fungus transplantation therapy

Clinically received patient faeces were collected and DNA was extracted. The expression levels of 2 colonies of the genus Rikenella and Anaerotyrunoruncus (Ruminococaceae) were then quantitatively detected using the kit developed in accordance with the present invention and a corresponding instrument. The expression level of 2 flora is input into the random forest prediction model established by the invention, and accurate selection is carried out on patients suitable for fecal fungus transplantation. The specific decision details are as follows: in the random forest modeling process, 1000 decision trees are included, and when more than half of the decision trees are considered to be effective/ineffective in treatment, the random forest makes decisions that patients are suitable for FMT treatment/unsuitable for FMT treatment. When a random forest makes a decision to be suitable for FMT treatment, the patient will receive fecal transplant treatment, otherwise other treatment regimens are recommended.

Table 1, comparison of clinical parameters for healthy people and for patients with type II diabetes

TABLE 2 comparison of clinical parameters of patients before and after faecal management

TABLE 3 comparison of clinical parameters between beneficiaries and non-beneficiaries before and after faecal fungus transplantation treatment

TABLE 4 comparison of clinical parameters between beneficiaries and non-beneficiaries before faecal fungus transplantation treatment

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Claims

1. A microbial marker for assessing the efficacy of fecal transplant therapy in a patient suffering from type two diabetes mellitus, wherein said microbial marker comprises a combination of the rinkenella laceae family and the Ruminococcaceae family.

2. The microbial marker according to claim 1, wherein the family ruminococaceae is the genus anaeroruncus.

3. The microbial marker of claim 1 or 2, wherein the microbial marker is used for constructing a model for assessing the efficacy of fecal transplantation treatment of a patient with type ii diabetes.

4. The method of claim 3, wherein the method of determining the relative content of the microbial marker comprises quantitative PCR, gene chip, second generation high throughput sequencing, panomics or Nanostring techniques.

5. The microbial marker of claim 4, wherein the relative amounts of the microbial markers can be sequenced by quantitative PCR, gene chip, second generation high throughput sequencing, panomics or Nanostring techniques.

6. Use of the microbial marker according to claim 1 or 2 for preparing a therapeutic test agent for fecal transplantation of a patient suffering from type two diabetes.

7. The use according to claim 6, wherein a set of microbial probes or primers is designed, said microbial probes being capable of generating hybridization signals by molecular hybridization in combination with target microorganisms, said primers being capable of amplifying target microorganisms by PCR-based techniques.

8. The use according to claim 7, wherein the microbial probes or primers can detect the microbial markers by quantitative PCR, gene chip, second generation high throughput sequencing, panomics or Nanostring techniques.

9. The use according to claim 8, wherein the microbial probes or primers can detect the expression level of the microbial markers in the feces of a type two diabetic patient by quantitative PCR, gene chip, second generation high throughput sequencing, panomics or Nanostring techniques.

10. A composition for assessing the efficacy of a type two diabetic fecal transplant, comprising the microbial probe or primer of claim 7.

11. A kit for assessing the efficacy of a type ii diabetic fecal transplant, comprising the composition of claim 10.