CN107217089B - Method and device for determining individual state - Google Patents
Method and device for determining individual state Download PDFInfo
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- CN107217089B CN107217089B CN201610165864.8A CN201610165864A CN107217089B CN 107217089 B CN107217089 B CN 107217089B CN 201610165864 A CN201610165864 A CN 201610165864A CN 107217089 B CN107217089 B CN 107217089B
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Abstract
The invention discloses a ankylosing spondylitis microbial marker, which consists of the following microorganisms: actinomycetes (Actinomyces sp.icm47), Bifidobacterium breve (Bifidobacterium breve), Bifidobacterium bifidum (Bifidobacterium sp.12_1_47BFAA), Bifidobacterium longum (Bifidobacterium longum), corynebacterium aerogenes (collinella aerociens), Bifidobacterium bifidum (Bifidobacterium bifidum), Bifidobacterium pseudocatenulatum (Bifidobacterium pseudopetatus), eggplantus lentus (egghella lentia), Bifidobacterium catenulatum (Bifidobacterium catenulatum) and Bifidobacterium adolescentis (Bifidobacterium adolescentis). The so-called ankylosing spondylitis markers were significantly enriched in the population of ankylosing spondylitis patients compared to the healthy population.
Description
Technical Field
The invention relates to the field of biomarkers, in particular to a method and a device for determining the state of an individual, and more particularly to an ankylosing spondylitis marker, application of the ankylosing spondylitis marker, a method for determining the state of the individual by using the ankylosing spondylitis marker, a device for determining the state of the individual by using the ankylosing spondylitis marker, a method for classifying a plurality of individuals by using the ankylosing spondylitis marker, a medicine for treating ankylosing spondylitis and a method for preparing the medicine for treating ankylosing spondylitis.
Background
Ankylosing Spondylitis (AS) is a chronic progressive inflammatory disease that mainly invades the spine and involves the sacroiliac and peripheral joints. The disease is mostly male with 15-30 years old, the ratio of male to female is 2: 1-3: 1, the cause of ankylosing spondylitis is not completely clear at present, and the research results in recent years show that the disease is related to factors such as genetic predisposition, infection, immunity and the like.
Ankylosing spondylitis is usually insidious in onset and has no clinical symptoms in the early stage, and some patients can show mild general symptoms in the early stage, such as hypodynamia, emaciation, long-term or intermittent low fever, anorexia, mild anemia and the like. Because of the mild condition, most patients cannot find the disease early, so that the condition is delayed and the optimal treatment time is lost.
Ankylosing spondylitis is closely related to human leukocyte antigen HLA-B27, according to epidemiological investigation, the positive rate of HLA-B27 of ankylosing spondylitis patients is as high as 90-96%, while the positive rate of HLA-27 of common people is only 4-9%; the incidence rate of ankylosing spondylitis of HLA-B27 positive people is about 10% -20%, while the incidence rate of common people is 1-2 per mill, and the difference is about 100 times. Although the HLA-B27 test is helpful for diagnosis of ankylosing spondylitis, most patients are diagnosed by medical history, signs and X-ray examination. At present, the early diagnosis of ankylosing spondylitis is mainly examined by imaging such as CT, radioactive nuclear scanning, magnetic resonance and the like, and the examination process is complex.
With the completion of human genome sequencing and the high-speed development of high-throughput sequencing technology, gene screening becomes the direction of ankylosing spondylitis diagnosis, and has advantages for discovering groups with potential ankylosing spondylitis. Studies have shown that more than 70% of ankylosing spondylitis patients suffer from intestinal inflammation, and 5-10% of these patients have severe intestinal inflammation and may develop clinical Inflammatory Bowel Disease (IBD) or Crohn's Disease (CD) (miellants et al, 1985). Some marker genes for Crohn's Disease (CD) are associated with ankylosing spondylitis (Parkes et al, 2013), suggesting that both diseases may have similar pathogenesis, possibly associated with gut disorders. Studies have shown that multiple genes associated with ankylosing spondylitis play an important role in gut immunity, such as genes involved in the interleukin IL-23 pathway, in regulating gut health (Wellcome et al, 2007). Compared to healthy controls, ankylosing spondylitis patients and their orthotopic intestinal permeability is increased, again illustrating the important role of intestinal microbes in ankylosing spondylitis (miellents et al, 1991). To date, there are no reports of intestinal microbial markers for patients with ankylosing spondylitis.
Disclosure of Invention
The present invention aims to solve at least one of the above technical problems to some extent or at least to provide a commercial choice.
According to a first aspect of the present invention, there is provided a microbial marker for ankylosing spondylitis, the marker consisting of the following microorganisms: actinomycetes (Actinomyces sp.icm47), Bifidobacterium breve (Bifidobacterium breve), Bifidobacterium (Bifidobacterium sp.12_1_47BFAA), Bifidobacterium longum (Bifidobacterium longum), colibacillus aerogenes (collinella aerociens), Bifidobacterium bifidum (Bifidobacterium bifidum), Bifidobacterium pseudocatenulatum (Bifidobacterium pseudopetatus), eggplants lentus (egghellanta), Bifidobacterium catenulatum (Bifidobacterium catenulatum) and Bifidobacterium adolescentis (Bifidobacterium adolescentis).
The microbial marker for ankylosing spondylitis provided by the invention is determined by comparative analysis and verification of differences of abundances of microorganisms in stool samples of a large number of individuals suffering from ankylosing spondylitis and a large number of healthy control individuals, and the microbial marker related to ankylosing spondylitis in intestinal microorganisms is determined. The method can determine the probability of an individual in a ankylosing spondylitis state or a healthy state by using the named ankylosing spondylitis marker, and can be used for non-invasive early discovery or auxiliary detection of ankylosing spondylitis.
According to a second aspect of the present invention, the present invention provides the use of the above-mentioned ankylosing spondylitis microbial marker in detecting ankylosing spondylitis, monitoring treatment of ankylosing spondylitis, preparation of a medicament for treating ankylosing spondylitis and/or preparation of a functional food.
The ankylosing spondylitis microbial marker is determined by analyzing the abundance of various intestinal microorganisms in stool samples of ankylosing spondylitis disease groups and healthy groups through difference comparison and verifying a large number of stool samples in known states. The ankylosing spondylitis marker is significantly enriched in patients with ankylosing spondylitis compared with the healthy group, and the significant enrichment refers to that the abundance of various microorganisms contained in the ankylosing spondylitis marker is statistically significantly higher or obviously and substantially higher than that in the healthy group compared with that in the healthy group. The substance capable of reducing the abundance of the substance can be used for treating the ankylosing spondylitis or beneficial to patients with the ankylosing spondylitis to take, the substance capable of reducing the abundance of the substance is not limited to a medicament for treating the ankylosing spondylitis and a functional food beneficial to intestinal flora balance, and the ankylosing spondylitis marker provided by the invention can be used for preparing a medicament for treating the ankylosing spondylitis and/or preparing a functional food, a health-care medicament and the like beneficial to intestinal flora balance.
According to a third aspect of the present invention, there is provided a method of determining the status of an individual using the aforementioned ankylosing spondylitis microbial marker, the method comprising: (1) determining the abundance of various microorganisms in the ankylosing spondylitis marker in a stool sample of the individual; (2) comparing the abundances of the various microorganisms in the ankylosing spondylitis marker determined in (1) with those in a control group consisting of stool samples of one or more groups of individuals of the same state, the state including suffering from ankylosing spondylitis and not suffering from ankylosing spondylitis, respectively, and determining the state of the individual according to the obtained comparison result. The ankylosing spondylitis marker is determined by analyzing the abundance of various intestinal microorganisms in stool samples of ankylosing spondylitis disease groups and healthy groups through difference comparison and verifying a large number of stool samples in known states.
The method of the aspect of the invention is based on detecting the abundance of various microorganisms in the ankylosing spondylitis microorganism marker in the stool sample of the individual, respectively comparing the detected abundance of various microorganisms with the abundance of the microorganisms in the control group, and determining the probability that the individual is an ankylosing spondylitis individual or a healthy individual according to the obtained comparison result. Provides a non-invasive auxiliary detection method for early detection of ankylosing spondylitis.
All or a part of the steps of the method for determining the state of an individual using the ankylosing spondylitis microbial markers according to the aspect of the present invention described above may be performed using an apparatus/system including the respective unit function modules detachably, or the method may be programmed, stored in a machine-readable medium, and executed by a machine.
According to a fourth aspect of the present invention, there is provided an apparatus for determining a state of an individual using the aforementioned ankylosing spondylitis microbial marker, the apparatus being adapted to perform all or part of the steps of the method of determining a state of an individual using ankylosing spondylitis microbial markers according to an aspect of the present invention, the apparatus comprising: a data input unit for inputting data; a data output unit for outputting data; a processor for executing an executable program, the executing of the executable program comprising performing all or a portion of the steps of the above-described method for determining a status of an individual using ankylosing spondylitis; and the storage unit is connected with the data input unit, the data output unit and the processor and is used for storing data, wherein the storage unit comprises the executable program. The above description of the technical features and advantages of the method for determining the status of an individual using ankylosing spondylitis microbial markers according to an aspect of the present invention is equally applicable to the device according to this aspect of the present invention, and will not be described herein again.
According to a fifth aspect of the present invention, there is provided a system for determining a state of an individual using the aforementioned ankylosing spondylitis microbial marker, the system being adapted to perform all or part of the steps of the method for determining a state of an individual using ankylosing spondylitis microbial markers according to an aspect of the present invention, the system comprising: a microorganism abundance determination unit for determining the abundance of various microorganisms in the ankylosing spondylitis marker in a stool sample of the individual; and an individual state determination unit for respectively comparing the abundances of various microorganisms in the ankylosing spondylitis marker from the microorganism abundance determination unit with the abundances of the microorganisms in a control group, and determining the state of the individual according to the obtained comparison result, wherein the control group consists of one or more groups of stool samples of individuals in the same state, and the state comprises the state with ankylosing spondylitis and the state without ankylosing spondylitis. The above description of the technical features and advantages of the method for determining the status of an individual using ankylosing spondylitis markers according to an aspect of the present invention is equally applicable to the system according to this aspect of the present invention, and will not be repeated herein.
According to a sixth aspect of the present invention, there is provided a method of classifying a plurality of individuals using the aforementioned ankylosing spondylitis microbial marker, the method comprising: determining the state of each individual by using the method for determining the state of the individual according to the aspect of the invention; and classifying the individuals according to the obtained states of the individuals. The method can distinguish a plurality of individuals or a plurality of unknown stool samples according to different states of the individuals, and is convenient for classification and marking management. In addition, the above description of the technical features and advantages of the method for determining the status of an individual using the ankylosing spondylitis microbial marker of one aspect of the present invention is equally applicable to the method of this aspect of the present invention, and will not be repeated herein.
According to a seventh aspect of the present invention, there is provided a medicament for treating ankylosing spondylitis, which causes a decrease in the abundance of each of the microorganisms in the aforementioned ankylosing spondylitis microorganism markers. The ankylosing spondylitis microbial marker is determined by differential analysis of abundance of various intestinal microbes in stool samples of ankylosing spondylitis disease groups and healthy groups and verification of a large number of stool samples in known states. Compared with the healthy group, the ankylosing spondylitis marker is remarkably enriched in the ankylosing spondylitis disease group, and the remarkable enrichment refers to that the abundance of various microorganisms contained in the ankylosing spondylitis marker is statistically significantly higher or obviously and substantially higher than that in the healthy group. The substance with reduced abundance can be used for treating ankylosing spondylitis or beneficial to patients with ankylosing spondylitis, and can be used as a medicine for treating ankylosing spondylitis.
The medicament or the functional food of the invention reasonably and effectively applies the determined ankylosing spondylitis microbial marker, supports the growth of beneficial bacteria in the intestinal tract and/or inhibits potential pathogenic bacteria in the intestinal tract, and has important significance for assisting in reducing the blood endotoxin level and/or relieving the clinical symptoms of ankylosing spondylitis.
According to an eighth aspect of the present invention, there is provided a method for preparing or screening a medicament for treating ankylosing spondylitis according to one aspect of the present invention described above, comprising the step of preparing or screening a substance capable of inducing a decrease in the abundance of each of the microorganisms in the ankylosing spondylitis marker according to one aspect of the present invention described above as the medicament.
By utilizing the method for producing or screening the medicament for treating the ankylosing spondylitis, disclosed by the invention, the determined ankylosing spondylitis biomarker is reasonably and effectively applied to screening, so that the medicament capable of supporting the growth of beneficial bacteria in an intestinal tract and/or inhibiting potential pathogenic bacteria in the intestinal tract can be obtained, and the method has important significance for assisting in reducing the blood endotoxin level and/or relieving the clinical symptoms of the ankylosing spondylitis.
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 schematic illustration of the experimental analysis procedure for screening and identifying the microbial markers of ankylosing spondylitis in an example of the present invention.
Fig. 2 is a schematic diagram showing the results of AUC evaluation of a microbial species marker as a diagnostic index in the example of the present invention.
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 reference numerals refer to the same or similar elements or elements having the same or similar functions 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. It should be noted that the terms "first" or "second", etc. are used herein for convenience of description only and are not to be construed as indicating or implying any relative importance or order between them.
In the description of the present invention, "a plurality" means two or more unless otherwise specified. In this document, unless expressly stated or limited otherwise, the terms "connected" and "connected" are to be construed broadly, e.g., as meaning either a fixed connection or a removable connection or an integral connection; can be mechanically or electrically connected; they may be connected directly or indirectly through intervening media, or they may be interconnected between two elements.
A biological marker is a cellular, biochemical or molecular change that can be detected from a biological medium. Biological media include various body fluids, tissues, cells, feces, hair, breath, and the like.
The abundance of a certain microorganism refers to the abundance of that microorganism in a certain population of microorganisms, for example, the abundance of that microorganism in a population of gut microorganisms, and can be expressed as the amount of that microorganism in that population.
The identity (identity) and similarity (similarity) of sequences are referred to as the degree of identity or similarity, respectively, between sequences.
According to one embodiment of the invention, the ankylosing spondylitis biomarker is provided, and the detection of the change of the biomarker can determine the relative probability that an individual suffers from ankylosing spondylitis. The ankylosing spondylitis microbial marker consists of the following microorganisms: actinomycetes (Actinomyces sp.ICMs 47), Bifidobacterium breve (Bifidobacterium breve), Bifidobacterium sp.12_1_47BFAA, Bifidobacterium longum (Bifidobacterium longum), Coriolus versicolor (Collinsela aerofaciens), Bifidobacterium bifidum (Bifidobacterium bifidum), Bifidobacterium pseudocatenulatum (Bifidobacterium erudocatentum), Escherichia tarda (Eggerthella lenta), Bifidobacterium catenulatum (Bifidobacterium catenulatum), and Bifidobacterium adolescentis (Bifidobacterium adolescentis).
The microbial marker for ankylosing spondylitis is determined by differential comparative analysis and verification of the abundance of microbes in fecal samples of a large number of ankylosing spondylitis individuals and a large number of healthy control individuals, and the microbial marker related to ankylosing spondylitis in intestinal microbes is determined. The probability that an individual is in the ankylosing spondylitis state or in the healthy state can be determined by using the ankylosing spondylitis marker, and the method can be used for non-invasive early discovery, auxiliary detection of ankylosing spondylitis and the like.
According to one embodiment of the invention, the provided ankylosing spondylitis microbial marker is used for detecting ankylosing spondylitis, monitoring and treating ankylosing spondylitis, preparing medicines for treating ankylosing spondylitis and/or preparing functional foods. The microbial marker of ankylosing spondylitis is determined by analyzing the abundance of various intestinal microorganisms in stool samples of ankylosing spondylitis disease groups and healthy groups through difference comparison by the inventor and verifying a large number of stool samples in known states. Compared with the healthy population group, the ankylosing spondylitis microbial marker is remarkably enriched in the ankylosing spondylitis disease group, and the remarkable enrichment refers to that the abundance of various microorganisms contained in the ankylosing spondylitis marker is statistically meaningfully higher or is remarkably and substantially higher than that in the healthy group.
The substance capable of reducing the abundance of the named ankylosing spondylitis marker can be used for treating ankylosing spondylitis or beneficial to patients with ankylosing spondylitis to take, the substance capable of reducing the abundance of the named ankylosing spondylitis marker is not limited to a medicine for treating ankylosing spondylitis and a functional food beneficial to intestinal flora balance, and the ankylosing spondylitis marker provided by the embodiment can be used for preparing a medicine for treating ankylosing spondylitis and/or preparing a functional food, a health-care medicine and the like beneficial to intestinal flora balance.
According to another embodiment of the present invention, there is provided a method for determining the status of an individual using the ankylosing spondylitis marker of the above embodiment, the method including the following steps (1) and (2):
(1) determining the abundance of the ankylosing spondylitis microbial marker in the individual to be tested.
Determining the abundance of various microorganisms in the ankylosing spondylitis microorganism markers in the stool sample of the individual to be tested.
According to an embodiment of the invention, the following is performed to accomplish this step: obtaining sequencing data for a nucleic acid sequence in a fecal sample of the individual, the sequencing data comprising a plurality of reads; aligning the reads to genomes of various microorganisms in the markers to obtain alignment results; determining the abundance of each microorganism in the marker according to the comparison result.
The sequencing data is obtained by sequencing nucleic acid sequences in a sample, and the sequencing can be selected from but not limited to semiconductor sequencing technology platforms such as PGM, Ion Proton and BGISEQ-100 platforms, synthetic sequencing technology platforms such as Hiseq and Miseq sequence platforms of Illumina and single molecule real-time sequencing platforms such as PacBio sequence platform according to different selected sequencing platforms. The sequencing mode can be single-ended sequencing or double-ended sequencing, and the obtained off-machine data are sequencing and reading fragments which are called reads (reads).
The alignment can be performed by using known alignment software, such as SOAP, BWA, TeraMap, etc., in the alignment process, the alignment parameters are generally set, one or a pair of reads (reads) is set to allow at most s base mismatches (mismatches), for example, s is set to be less than or equal to 2, and if more than s bases in the reads are mismatched, it is considered that the reads cannot be aligned (aligned) to the assembled fragment. The obtained alignment result includes the alignment of each read with the genome of each species, including information as to whether the read can align with the genome of a certain species or species, uniquely align with only one species or with the genomes of multiple species, align with the position of the genome of a species, align with unique position or multiple positions of the genome of a species, and the like. According to one embodiment of the invention, alignment was performed using SOAPalign 2.21 with the setting parameter-r 2-m 100-x 1000.
The genome of the microorganism refers to a predetermined sequence of the species of the microorganism, and may be any reference template of a biological category to which a sample to be tested belongs or contains, which is obtained in advance, for example, the target is the microorganism in the sample to be tested, the reference sequence may be a reference genome of various microorganisms in an NCBI database and/or a DACC enteric genome disclosed in HMP and MetaHIT projects, and further, a resource library containing more reference sequences may be configured in advance, for example, a more similar sequence is selected or determined to be assembled as the reference sequence according to factors such as the state of an individual from which the sample to be tested is derived, a region, and the like. According to one embodiment of the invention, reference genomes for various microorganisms are obtained from public databases, typically, reference genomes for a microorganism in multiple versions, i.e., a microorganism in multiple public genomes.
reads are aligned to the reference genome of the species, which can be divided into two parts: a) unique reads (U): uniquely aligning the genome of the previous species; these reads are referred to as unique reads. That is, if the genomes on the reads alignments are from the same species, the reads are defined as unique reads. b) Multiple reads (M): aligning the genomes of more than one species, defined as multiple reads. That is, if the genomes on the reads alignments are from at least two species, these reads are defined as multiple reads.
According to one embodiment of the invention, said determining the abundance of each microorganism in said marker from the alignment results according to sequencing data comprises determining the abundance of microorganism species S using the following formula: abundance of microbial species S Ab (S) ═ Ab (us) + Ab (ms), where Ab (U)S)＝US/lS，USFor the unique alignment of the number of reads of this species of microorganism S,/SFor the microorganism on the comparisonThe length of the genome of substance S,
MSfor the number of reads of this species of microorganism S in the non-unique alignment, i denotes the number of reads of this species of microorganism S in the non-unique alignment, CoiThe abundance coefficients corresponding to reads i of this species of microorganism S are not uniquely aligned,
n is the number of species of the microorganism in the read alignment of the microorganism S in the non-unique alignment, j is the number of species in the read alignment of the microorganism S in the non-unique alignment, UjNumber of reads for microbial species j being the only alignment.
For a given microbial species S, the abundance is Ab (S), in relation to the Unique reads and Multiple reads, Ab (U) and Ab (M) in the above formulas are the abundances contributed by the Unique reads and Multiple reads, respectively, of that species S. Each multiple read has a specific species abundance coefficient Co, and assuming that one multiple read is aligned to the top N species, the Co of the multiple read can be calculated using the following formula:
that is, for such multiple reads, the sum of the abundances of unique reads of the N species to which they are aligned is used as the denominator.
(2) Abundance comparisons to determine individual status.
Comparing the abundances of the various microorganisms in the ankylosing spondylitis marker determined in (1) with those in a control group consisting of stool samples of one or more groups of individuals of the same state, respectively, the state including a state with ankylosing spondylitis and a healthy state, and determining the state of the individual according to the obtained comparison result. The ankylosing spondylitis marker is determined by analyzing the abundance of various intestinal microorganisms in stool samples of ankylosing spondylitis disease groups and healthy groups through difference comparison and verifying a large number of stool samples in known states.
The abundance of each microorganism in the marker in the control group may be determined simultaneously with or sequentially with the individual to be tested. According to one embodiment of the present invention, the abundance of each microorganism in the marker in the control group is pre-determined and stored as a basis for setting the threshold. And comparing the abundance of the microorganisms in the marker in the sample of the individual to be tested with a threshold value, and determining the state of the individual to be tested based on the difference degree of the two. The threshold may be a value or range of values, for example, based on the mean abundance of a microorganism in a control group, the corresponding threshold for that microorganism may be set to a 95% confidence interval of the mean abundance.
According to an embodiment of the present invention, the control group consists of stool samples of a plurality of individuals with ankylosing spondylitis, and the step (2) includes: determining the individual as suffering from ankylosing spondylitis when the abundance of each microorganism in the ankylosing spondylitis marker determined in step (1) is not different from that in the control group. According to an embodiment of the invention, the indifference is that the abundance of each microorganism in the ankylosing spondylitis marker from the microorganism abundance determining unit falls within a first predetermined confidence interval of its abundance in the control group, optionally the first predetermined confidence interval is a 95% confidence interval.
The term non-difference is said to mean that the abundance of each microorganism in the ankylosing spondylitis marker determined in step (1) falls within a first predetermined confidence interval of its abundance in the control group. The confidence interval is referred to as the estimation interval of the overall parameter constructed from the sample statistics. In statistics, the Confidence interval (Confidence interval) of a probability sample is an interval estimate for some overall parameter of this sample. The confidence interval exhibits the extent to which the true value of this parameter has a certain probability of falling around the measurement. The confidence interval indicates the degree of plausibility of the measured value of the measured parameter, i.e. the "certain probability" required above. This probability is called the confidence level.
According to an embodiment of the invention, the control group consists of stool samples from a plurality of healthy individuals, the step (2) comprising: when the abundance of each microorganism in the ankylosing spondylitis marker determined in step (1) is not different from that in the control group, determining that the individual is in a state without ankylosing spondylitis. Said no difference is that the abundance of each microorganism in the ankylosing spondylitis marker identified in (1) falls within a second predetermined confidence interval of its abundance in the control group, optionally said second predetermined confidence interval is a 95% confidence interval.
It should be noted that, depending on the purpose or requirement, there may be different requirements on the confidence level of the result of determining the state of an individual, and a person skilled in the art may choose different significance levels (α), i.e. different probabilities of making errors, such that the confidence level of the determined state of an individual is 1- α. For example, it is reliable to determine that the individual is 95% in the determined state using this embodiment.
The method is based on detecting the abundance of various microorganisms in the ankylosing spondylitis marker in an individual stool sample, respectively comparing the detected and determined abundances of various microorganisms with the abundances of various microorganisms in a control group, and determining the probability that the individual is an ankylosing spondylitis individual or a healthy individual according to the obtained comparison result. Provides a non-invasive auxiliary detection or auxiliary intervention treatment method for early detection of ankylosing spondylitis.
All or part of the steps of the method for determining the state of an individual using a ankylosing spondylitis marker in any one of the above embodiments may be performed using an apparatus/system including detachable function modules of respective units, or the method may be programmed, stored in a machine-readable medium, and executed by a machine.
According to an embodiment of the present invention, there is provided an apparatus for determining a state of an individual using the ankylosing spondylitis marker in the above-described embodiment of the present invention, the apparatus being configured to perform all or part of the steps of the method for determining a state of an individual using the ankylosing spondylitis marker in the above-described embodiment of the present invention, the apparatus including: a data input unit for inputting data; a data output unit for outputting data; a processor for executing an executable program, the executing of the executable program comprising performing the method of determining the status of an individual of any of the embodiments of the present invention described above; and the storage unit is connected with the data input unit, the data output unit and the processor and is used for storing data, wherein the storage unit comprises the executable program. The above description of the technical features and advantages of the method for determining the status of an individual using ankylosing spondylitis markers in any embodiment of the present invention is also applicable to the apparatus of the present invention, and will not be repeated herein.
According to an embodiment of the present invention, there is provided a system for determining the status of an individual using the ankylosing spondylitis marker in the above-described embodiment of the present invention, the apparatus being configured to perform all or part of the steps of the method for determining the status of an individual using the ankylosing spondylitis marker in any of the above-described embodiments of the present invention, the system including: a microorganism abundance determination unit for determining the abundance of various microorganisms in the ankylosing spondylitis marker in a stool sample of the individual; and an individual state determination unit for respectively comparing the abundances of various microorganisms in the ankylosing spondylitis marker from the microorganism abundance determination unit with the abundances of the microorganisms in a control group, and determining the state of the individual according to the obtained comparison result, wherein the control group consists of one or more groups of stool samples of individuals in the same state, and the state comprises the state with ankylosing spondylitis and the state without ankylosing spondylitis. The above description of the technical features and advantages of the method for determining the status of an individual using ankylosing spondylitis markers in any of the embodiments of the invention applies equally to the system of this aspect of the invention.
According to an embodiment of the present invention, the microbial abundance determination unit is configured to perform the following: obtaining sequencing data for a nucleic acid sequence in a fecal sample of the individual, the sequencing data comprising a plurality of reads; aligning the reads to genomes of various microorganisms in the markers to obtain alignment results; determining the abundance of each microorganism in the marker according to the comparison result.
The sequencing data is obtained by sequencing nucleic acid sequences in a sample, and the sequencing can be selected from but not limited to semiconductor sequencing technology platforms such as PGM, Ion Proton and BGISEQ-100 platforms, synthetic sequencing technology platforms such as Hiseq and Miseq sequence platforms of Illumina and single molecule real-time sequencing platforms such as PacBio sequence platform according to different selected sequencing platforms. The sequencing mode can be single-ended sequencing or double-ended sequencing, and the obtained off-machine data are sequencing and reading fragments which are called reads (reads).
The alignment can be performed by using known alignment software, such as SOAP, BWA, TeraMap, etc., in the alignment process, the alignment parameters are generally set, one or a pair of reads (reads) is set to allow at most s base mismatches (mismatches), for example, s is set to be less than or equal to 2, and if more than s bases in the reads are mismatched, it is considered that the reads cannot be aligned (aligned) to the assembled fragment. The obtained alignment result includes the alignment of each read with the genome of each species, including information as to whether the read can align with the genome of a certain species or species, uniquely align with only one species or with the genomes of multiple species, align with the position of the genome of a species, align with unique position or multiple positions of the genome of a species, and the like. According to one embodiment of the invention, alignment was performed using SOAPalign 2.21 with the setting parameter-r 2-m 100-x 1000.
The genome of the microorganism refers to a predetermined sequence of the species of the microorganism, and may be any reference template of a biological category to which a sample to be tested belongs or contains, which is obtained in advance, for example, the target is the microorganism in the sample to be tested, the reference sequence may be a reference genome of various microorganisms in an NCBI database and/or a DACC enteric genome disclosed in HMP and MetaHIT projects, and further, a resource library containing more reference sequences may be configured in advance, for example, a more similar sequence is selected or determined to be assembled as the reference sequence according to factors such as the state of an individual from which the sample to be tested is derived, a region, and the like. According to one embodiment of the invention, reference genomes for various microorganisms are obtained from public databases, typically, reference genomes for a microorganism in multiple versions, i.e., a microorganism in multiple public genomes.
reads are aligned to the reference genome of the species, which can be divided into two parts: a) unique reads (U): uniquely aligning the genome of the previous species; these reads are referred to as unique reads. That is, if the genomes on the reads alignments are from the same species, the reads are defined as unique reads. b) Multiple reads (M): aligning the genomes of more than one species, defined as multiple reads. That is, if the genomes on the reads alignments are from at least two species, these reads are defined as multiple reads.
According to one embodiment of the invention, said determining the abundance of each microorganism in said marker from the alignment results according to sequencing data comprises determining the abundance of microorganism species S using the following formula: abundance of microbial species S Ab (S) ═ Ab (us) + Ab (ms), where Ab (U)S)＝US/lS，USFor the unique alignment of the number of reads of this species of microorganism S,/STo compare the length of the genome of this species of microorganism S,
MSfor the number of reads of this species of microorganism S in the non-unique alignment, i denotes the number of reads of this species of microorganism S in the non-unique alignment, CoiThe abundance coefficients corresponding to reads i of this species of microorganism S are not uniquely aligned,
n is the number of species of the microorganism in the read alignment of the microorganism S in the non-unique alignment, j is the number of species in the read alignment of the microorganism S in the non-unique alignment, UjNumber of reads for microbial species j being the only alignment.
For a given microbial species S, the abundance is Ab (S), in relation to the Unique reads and Multiple reads, Ab (U) and Ab (M) in the above formulas are the abundances contributed by the Unique reads and Multiple reads, respectively, of that species S. Each multiple reads has a specific species abundance coefficient Co, say oneThe strip reads were aligned to the top N species and the Co of the strip reads was calculated using the following equation:
that is, for such multiple reads, the sum of the abundances of unique reads of the N species to which they are aligned is used as the denominator.
According to an embodiment of the invention, the control group in the individual status determination unit comprises stool samples of a plurality of individuals with ankylosing spondylitis, the individual status determination unit being adapted to perform the following: determining that the individual has ankylosing spondylitis when the abundance of each microorganism in the ankylosing spondylitis marker from the microorganism abundance determining unit is not different from that in the control group.
According to an embodiment of the invention, the indifference is that the abundance of each microorganism in the ankylosing spondylitis marker from the microorganism abundance determining unit falls within a first predetermined confidence interval of its abundance in the control group, optionally the first predetermined confidence interval is a 95% confidence interval.
According to an embodiment of the invention, the control group in the individual status determination unit comprises stool samples of a plurality of healthy individuals, the individual status determination unit being adapted to perform the following: determining that the individual is not suffering from ankylosing spondylitis when the abundances of the various microorganisms in the ankylosing spondylitis marker from the microorganism abundance determining unit are all not different from the abundances of the various microorganisms in the control group.
According to an embodiment of the invention, the indifference is that the abundance of each microorganism in the ankylosing spondylitis marker from the microorganism abundance determining unit falls within a second predetermined confidence interval of its abundance in the control group, optionally the second predetermined confidence interval is a 95% confidence interval.
According to another embodiment of the present invention, there is provided a method for classifying a plurality of individuals using the ankylosing spondylitis marker of the above-described embodiment of the present invention, the method including: determining the state of each individual by using the method for determining the state of the individual in any embodiment of the invention; and classifying the individuals according to the obtained states of the individuals. The method can distinguish a plurality of individuals or a plurality of unknown stool samples according to different states of the individuals, and is convenient for classification and marking management. In addition, the above description of the technical features and advantages of the method for determining the state of an individual by using a ankylosing spondylitis marker in the embodiment of the present invention is also applicable to the method of the aspect of the present invention, and will not be repeated herein.
According to still another embodiment of the present invention, there is provided a medicament for treating ankylosing spondylitis, which is capable of inducing a decrease in the abundance of each of the microorganisms in the ankylosing spondylitis marker according to any one of the above-described embodiments of the present invention. The ankylosing spondylitis marker is determined by differential analysis of the abundance of various intestinal microorganisms in stool samples of ankylosing spondylitis disease groups and healthy groups and verification of a large number of stool samples in known states. Compared with the healthy group, the ankylosing spondylitis marker is remarkably enriched in the ankylosing spondylitis disease group, and the remarkable enrichment refers to that the abundance of various microorganisms contained in the ankylosing spondylitis marker is statistically significantly higher or obviously and substantially higher than that in the healthy group. The substance with reduced abundance can be used for treating ankylosing spondylitis or beneficial to patients with ankylosing spondylitis, and can be used as a medicine for treating ankylosing spondylitis.
By utilizing the medicament or the functional food of the embodiment, the determined ankylosing spondylitis microbial marker is reasonably and effectively applied, the growth of intestinal beneficial bacteria is supported and/or intestinal potential pathogenic bacteria are inhibited, the defect of an intestinal barrier can be prevented, the intestinal microecological structure is improved and restored, and the medicament or the functional food has important significance for assisting in reducing the blood endotoxin level and/or relieving the clinical symptoms of ankylosing spondylitis.
According to still another embodiment of the present invention, there is provided a method for preparing or screening a drug for treating ankylosing spondylitis in the above-described embodiment, which includes the step of preparing or screening a substance capable of inducing a decrease in the abundance of each of the microorganisms in the ankylosing spondylitis marker in the above-described embodiment as the drug.
By using the method for producing or screening the medicament for treating the ankylosing spondylitis in the embodiment of the invention, the medicament capable of supporting the growth of beneficial bacteria in the intestinal tract and/or inhibiting potential pathogenic bacteria in the intestinal tract can be obtained by reasonably and effectively applying the determined ankylosing spondylitis biomarker for screening, the defect of the intestinal tract barrier can be prevented, the microecological structure of the intestinal tract can be improved and recovered, and the method has important significance for assisting in reducing the blood endotoxin level and/or relieving the clinical symptoms of the ankylosing spondylitis.
The method and/or apparatus of the present invention is described in detail below with reference to specific embodiments. Reagents, sequences (linkers, tags, and primers), software, and instruments referred to in the following examples are conventional commercial products or open sources, such as the transcriptome library construction kit from Illumina, unless otherwise submitted.
The following embodiments include a first phase and a second phase, namely a corresponding discovery phase and a verification phase. The discovery phase includes: comparing intestinal microbial composition and functional changes of 73 ankylosing spondylitis patients and 83 healthy control groups based on analysis to determine species markers; the verification phase comprises: the accuracy of the first stage results was verified using 24 AS patients and 31 healthy controls.
Example 1
In this example, the inventors performed a correlation analysis study of the microorganisms of the entire intestinal flora from stool samples of 73 ankylosing spondylitis patients and 83 healthy controls to characterize the fecal microflora and functional components. In summary, the inventors downloaded about 428.09Gb high quality sequencing data (LC healthy people) and 294Gb high quality sequencing data obtained by experimental sequencing to construct the ankylosing spondylitis reference gene set, and constructed a more complete gene set with the downloaded LC gene set and IGC gene set. Metagenomic analysis shows that 17 microbial species are closely related to ankylosing spondylitis diseases, wherein 7 bacteria are enriched in intestinal microorganisms of healthy people, and 10 bacteria are enriched in intestinal microorganisms of patients with ankylosing spondylitis.
1. Acquisition of sequencing data
1.1 sample Collection and DNA extraction
Ankylosing spondylitis patients come from the first subsidiary hospital of the university of traditional Chinese medicine in Hangzhou Zhejiang, and 73 stool samples of ankylosing spondylitis patients in total are collected in experiments, wherein the fresh stool samples of each individual are divided into 200 mg/part and 5 parts in total, and are immediately frozen and stored in a refrigerator at the temperature of-80 ℃.
Total DNA was extracted from fecal samples of 73 patients with ankylosing spondylitis of China. DNA is extracted by a method of extracting DNA by phenol trichloromethane treatment.
1.2 library construction and sequencing, and reference data download
DNA banking was performed according to the instructions of the Instrument manufacturer (Illumina). The library was sequenced by PE100 bp. The Illumina HiSeq2000(Illumina, San Diego, CA) platform sequenced a library of 73 samples. Each sample yielded on average 4.03Gb (sd. + -0.64 Gb) high quality sequencing results, totaling 294Gb sequencing data volume.
Sequencing data for 83 healthy chinese were downloaded from EBI, access No.: ERP 005860.
Referring to the experimental procedure of fig. 1, relevant biomarkers for ankylosing spondylitis were identified, wherein omitted steps or details are well known to those skilled in the art, and several important steps are described as follows.
2. Identification of biomarkers
2.1 basic processing of sequencing data
1) Sequencing data is subjected to quality control: after obtaining the sequencing data of 73 AS samples in the first stage, the AS samples were filtered, and the quality control was performed according to the following criteria: a) (ii) removing reads greater than 50% of the low quality base (Q20); b) removing reads greater than 5N bases; c) the tail low mass (Q20) and N bases were removed. Sequences that miss pairs of reads are considered to be a single read for assembly.
2) The downloaded data of the healthy person is processed as well.
3) LC gene sets were obtained from Qin, N.et al.alternatives of the human gut microorgan imporvo sis.Nature 513,59-64 (2014.) and IGC gene sets were downloaded from ftp:// climb.genomics.cn/pub/10.5524/100001-101000/100064/1. GeneCatalogs/IGC.fa.gz.
2.2 species abundance analysis
The above processed pair-end clean reads were aligned (matched) to a redundant genome using SOAPalign 2.21, here, the so-called redundant genome is from the reference genome of the bacterium disclosed in each database. The alignment parameter is-r 2-m 100-x 1000. Reads aligned to redundant genomes, possibly divided into two parts: a) unique reads (U): reads align the genomes of only the previous species; these reads are defined as unique reads. That is, if the genomes are from the same species, reads are aligned to more than one genome and the inventors define these reads as unique reads. b) Multiple reads (M): if reads align to the genome of more than one species, they are defined as multipleads. That is, if the aligned genomes are from different species, the inventors define these reads as multiple reads.
For species S, the abundance is ab (S), related to the characteristic U reads and shared M reads, and is calculated as follows:
Ab(S)＝Ab(U)+Ab(M)
Ab(U)＝U/l
ab (U) and Ab (M) are the abundance of unique reads and multiple reads from species S, respectively, and l represents the length of the genome. Each multiple reads has a specific species coefficient Co; assuming that a multiple reads aligns to the top N species, Co for the multiple reads is calculated as follows:
for these reads, the inventors normalized the abundance of unique reads of the summed N species. That is, for multiple reads, the inventors used the sum of the abundance of unique reads for the N species against which they were aligned as the denominator.
2.3 Association analysis/screening species markers
In order to obtain the intestinal microbial species marker closely related to the ankylosing spondylitis, the inventor utilizes the abundance data of the intestinal microbial species of two groups of ankylosing spondylitis patients (73 cases) and healthy people (83 cases) to carry out a research on the correlation with diseases at the species level.
Based on the abundance table of species obtained in the above step, the inventors set criteria as follows: (1) the median abundance of the species in the ankylosing spondylitis patient group or healthy human group must be greater than 0.00001; (2) performing a Wilcoxon rank sum test by combining multiple tests of Benjamini Hochberg to obtain a p value and a q value of each species and the relevance of ankylosing spondylitis; (3) a relatively very strict threshold (q _ values <5.0E-05) is used. Then, the inventors obtained 28 intestinal microbial species closely related to ankylosing spondylitis disease. Among them, 14 species were enriched in patients with Ankylosing Spondylitis (AS), and 14 species were enriched in healthy persons (HD). The 28 microbial species markers are shown in table 1 below.
TABLE 1
Example 2
To confirm that the analysis results in example 1 can be used as a ankylosing spondylitis species marker, species abundances of 31 healthy people and 24 ankylosing spondylitis patients in a validation population are further compared, and a final microbial species marker is screened according to validation conditions. The acquisition and processing of the sequencing data of the validation population was performed with reference to example 1.
The verification results are as follows: of the 14 species enriched in healthy people, 7 were verified in the verification set to have high quality (p _ values <0.05), and the p and q values of the markers for microorganism species enriched in healthy people are shown in table 2 below. The microorganism species are, respectively, Muricidae (Lachnospiraceae bacteria 6_1_63FAA), Fusobacterium mortiferum (Fusobacterium mortiferum), Bacteroides ([ Bacteroides ] pectobacterium), Enterobacter cloacae (Enterobacter cloacae), Acidia (Eubacterium elegans), Muricidae (Lachnospiraceae bacteria 8_1_57FAA), and Clostridium (Clostridium sp.L 2-50). Bacteroides are present in the human intestinal tract and primarily help break down food to provide the nutrients and energy needed by the human body.
TABLE 2
For the 14 species enriched in ankylosing spondylitis patients, 10 of them were verified to be of high quality in the verification set (p _ values <0.05), and the cases of p and q values verified for the microbial species markers enriched in ankylosing spondylitis patients are shown in table 3 below, namely actinomycetes (actinomycetes sp.icm), Bifidobacterium breve (Bifidobacterium breve), Bifidobacterium (Bifidobacterium sp.12_1_47BFAA), Bifidobacterium longum (Bifidobacterium longum), corynebacterium aerogenes (collinesiensis), Bifidobacterium bifidum (Bifidobacterium bifidum), Bifidobacterium pseudocatenulatum (Bifidobacterium pseudocatenulatum), eggerella lenta (eggerella lenta), Bifidobacterium catenulatum (Bifidobacterium catenulatum), Bifidobacterium catenulatum (Bifidobacterium bifidum), Bifidobacterium pseudocatenulatum (Bifidobacterium adolescentis), Bifidobacterium longum (Bifidobacterium longum), and Bifidobacterium adolescentis (Bifidobacterium longum).
The Bifidobacterium can prevent diarrhea and reduce constipation, i.e. bidirectional regulation. Research shows that more than 70% of ankylosing spondylitis patients suffer from intestinal inflammation, 5-10% of the patients have severe intestinal inflammation and can develop into clinical Inflammatory Bowel Disease (IBD) or Crohn's Disease (CD) (Mielants et al, 1985), and research shows that bacteroides, clostridia and sclerites in intestinal tracts of IBD patients decrease and the ratio of actinomycetes and proteobacteria increases.
TABLE 3
The inventor thinks that 7 microbial species markers enriched from healthy people can be used as a reverse index for the disease of the ankylosing spondylitis, or used as microbial preparation drug flora components for researching and developing for treating the ankylosing spondylitis, or used as a recovery index for detecting the ankylosing spondylitis and monitoring the treatment process of the ankylosing spondylitis; 10 microorganism species markers enriched for ankylosing spondylitis patients are used as positive indexes for ankylosing spondylitis diseases, and are particularly used for noninvasive detection and diagnosis of ankylosing spondylitis diseases.
The inventor utilizes the 17 microbial species markers to construct a comprehensive index, estimates the area AUC under the ROC (Receiver-operating characteristic) curve, and evaluates the diagnosis capability of the comprehensive index corresponding to the diagnosis capability of the ankylosing spondylitis if the AUC is larger. By evaluating 156 samples in the first stage (first stage) and 55 samples in the second stage (second stage), as shown in fig. 2, the diagnosis ability is very good, and the AUC obtained in the first stage is 96.62%, as shown in the left graph of fig. 2, and the confidence interval is 93.93% -99.31%; the second phase resulted in an AUC of 89.92% with a confidence interval of 81.28% -98.56% as shown in the right panel of fig. 2.
Example 3
45 stool samples were used for the detection of the individual status of the sample source.
The abundance of actinomycetes (Actinomyces sp.ICM47), Bifidobacterium breve (Bifidobacterium breve), Bifidobacterium bifidum (Bifidobacterium sp.12_1_47BFAA), Bifidobacterium longum (Bifidobacterium longum), Coriolus versicolor (Collinella aerofaciens), Bifidobacterium bifidum (Bifidobacterium bifidum), Bifidobacterium pseudocatenulatum (Bifidobacterium pseudostellatum), Escherichia lentum (Eggerthella lenta), Bifidobacterium catenulatum (Bifidobacterium catenulatum) and Bifidobacterium adolescentis (Bifidobacterium adolescentis) of Table 3 in each stool sample was determined with reference to the method of example 2, judging whether the abundances of the ten strains in each sample fall into a confidence interval of 95% of the abundances of the ten strains in the disease control group or the healthy control group, judging that the state of the individual corresponding to the sample with the abundances of the 10 strains falling into the corresponding interval of the disease group is an ankylosing spondylitis patient, and judging that the state of the individual corresponding to the sample with the abundances of the ten strains falling into the corresponding interval of the healthy group is a non-ankylosing spondylitis patient.
The result shows that the method can judge the individual state of 38 samples, and the judgment of the state of the individual corresponding to all 38 samples in the 38 samples is consistent with the recorded state of the individual from which the sample comes.
In addition, the inventors found that the combined detection of the species in table 2 and table 3, for example, the detection of the enrichment of the species markers in table 3, and the non-enrichment of the species markers in table 2, can more accurately determine and find the ankylosing spondylitis patients or susceptible people.
In the scheme of treating ankylosing spondylitis by using the markers, the inventors found that the growth of the species markers in 3 is inhibited or eliminated, and the species markers in table 2 are enriched, so that the treatment effect is excellent.
In the description herein, references to the description of the term "one embodiment," "some embodiments," "an example," "a specific example," or "some examples," etc., 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.
While embodiments of the invention have been shown and described, it will be understood by those of ordinary skill in the art that: various changes, modifications, substitutions and alterations can be made to the embodiments without departing from the principles and spirit of the invention, the scope of which is defined by the claims and their equivalents.
Claims (1)
1. A microbial ankylosing spondylitis marker, characterized in that the marker consists of the following microorganisms:
actinomycetes sp.ICM47, Bifidobacterium breve, Bifidobacterium sp.12_1_47BFAA, Bifidobacterium longum, Coriolus versicolor Alinesis, Bifidobacterium bifidum, Bifidobacterium pseudocatenulatum, Escherichia lentus Eggerthella lenta, Bifidobacterium catenulatum and Bifidobacterium adolescentis.
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| CN114085886B (en) * | 2021-11-25 | 2023-11-24 | 青岛锐翌精准医学检验有限公司 | Crohn's marker microorganism for children and application thereof |
| CN113913490B (en) * | 2021-11-25 | 2024-06-04 | 上海锐翌生物科技有限公司 | Non-alcoholic fatty liver disease marker microorganism and application thereof |
| CN114381493A (en) * | 2021-11-25 | 2022-04-22 | 青岛锐翌精准医学检验有限公司 | Inflammatory bowel disease marker microorganism and application thereof |
| CN113930479B (en) * | 2021-11-25 | 2023-11-24 | 上海锐翌生物科技有限公司 | Systemic lupus erythematosus marker microorganism and application thereof |
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| CN114317674B (en) * | 2021-12-31 | 2024-04-12 | 青岛锐翌精准医学检验有限公司 | Rheumatoid arthritis marker microorganism and application thereof |
| CN114517228A (en) * | 2021-12-31 | 2022-05-20 | 青岛锐翌精准医学检验有限公司 | Inflammatory bowel disease marker gene and application thereof |
| CN116121373A (en) * | 2022-09-14 | 2023-05-16 | 中山大学孙逸仙纪念医院 | Application of ETV4 and expression product thereof in preparation of medicines for diagnosing and treating bladder cancer |
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