61 results about "Microbial genome" patented technology

The invention discloses a construction method and application of a pathogenic microorganism genome database. The method comprises the steps of genome acquisition, genome screening, target region grabbing, strain verification, target region sequence clustering, redundancy elimination and database merging. The construction method of the pathogenic microorganism genome database is suitable for targeted high-throughput sequencing, and the corresponding amplification relationship between the primer and the corresponding microorganism genome sequence is obtained through the operations of screening, filtering, simulation amplification and the like on pathogenic microorganism genome data; the risk of wrong identification of pathogenic species can be reduced by constraining the corresponding relationship.

The invention discloses a small CRISPR (clustered regularly interspaced short palindromic repeats)-Cas gene editing system and application thereof. According to the invention, based on microbial genome and metagenome data, a class of CRISPR-Cas family protein is mined through a biological information method, and is named as Cas12r. A CRISPR-Cas12r editing tool constructed on the basis of the gene can realize gene editing in prokaryotic or eukaryotic cells. The CRISPR-Cas12r gene editing system obtained by the invention has the characteristics of miniaturization and various PAM types.

The invention provides a PCR (polymerase chain reaction) method for rapidly screening effective donors for FMT (fibronectin) treatment of depression, which comprises the following steps: (1) collecting excrement samples of the donors, and extracting total microbial genome DNA (deoxyribonucleic acid) of the excrement samples; (2) designing six primer pairs according to a specific conserved sequence of a target strain; (3) taking the extracted donor excrement DNA as a PCR (Polymerase Chain Reaction) template, and adding a primer pair for amplification; (4) observing a PCR result through electrophoresis; and if each target band is positive in the PCR electrophoresis result of the donor sample, determining that the donor contains the target strain, and determining that the donor is an effective donor for FMT treatment of depression. The effective donor suitable for FMT treatment of depression is screened out by detecting whether the donor faeces contain three key probiotics closely related to depression symptom relieving or not, a basis is provided for microbial therapy of mental diseases such as depression, and important clinical application value is achieved.

The invention relates to the technical field of construction of genome databases, in particular to a construction method of a pathogenic microorganism genome database. The method comprises the following steps: carrying out pathogen characteristic point location analysis on a pathogen microorganism genome sequence to obtain pathogen characteristic point location data; carrying out physiological and biochemical characteristic analysis on a pathogenic microorganism genome sequence according to the pathogenic characteristic point data, carrying out genome evolution relation simulation, and then carrying out prepositive relation linkage identification to obtain prepositive relation linkage data; performing relation nested structure analysis on the prepositive relation linkage data, and performing relation coding index construction to obtain a linkage relation coding index; and carrying out dynamic retrieval condition matching on the linkage relationship coding index, and carrying out genome database construction to obtain the pathogenic microorganism genome database. The construction technology of the genome database is improved, so that the construction technology of the genome database is more perfect.

The invention discloses an astragalus sinicus breeding genetic data mining system based on bioinformatics, and particularly relates to the technical field of data mining. The method comprises the following steps: acquiring and synchronizing original sequencing data of an astragalus sinicus host genome and a rhizobium symbiotic microorganism genome to generate a standardized genetic information data set; the method comprises the following steps: identifying sequence cross contamination sites between a host genome and a symbiotic microorganism genome, and eliminating genetic information interference of a microorganism source, so as to obtain purified host genome data without microorganism interference; analyzing the contribution degree of the microbial genome to the target character of the astragalus sinicus to obtain a microbial effect weight; integrating the purified host genome data and the microbial effect weight, constructing an astragalus sinicus character association analysis model, and positioning character association sites; and finally, screening candidate breeding markers based on character associated site information to obtain a precise breeding genetic marker set. According to the method, the accuracy and efficiency of milk vetch breeding are improved.

The invention relates to a metagenome analysis method suitable for microbiota in a straw mushroom growth process, and relates to the technical field of microorganism application, and the metagenome analysis method comprises the following steps: extracting a microbial genome DNA sample in the straw mushroom growth process; detecting the quantity and the quality of the extracted DNA samples to obtain quantity and quality detection results of DNA; constructing a metagenome sequencing library with the insertion length of 400bp by using the extracted DNA samples, and sequencing to obtain original sequencing reads; the original sequencing reads are subjected to cutting treatment, and filtered reads are obtained; performing optimization processing on the filtered reads to obtain an optimization result; and performing gene data analysis on the optimization result, wherein the analysis content comprises gene prediction and gene abundance statistics. According to the method, the blank of microorganism detection in the straw mushroom growth process is filled up, and rich and comprehensive information analysis content is provided on the metagenome level.

The present application discloses a pathogenic microorganism analysis and identification system and its application. The system of the present application includes a data statistics module, a sample management module, an experiment management module, an information analysis module, a report management module, and a system management module; the information analysis module includes a sample analysis sub-module, which is used to implement data quality control steps, host removal steps, sequence classification steps, calculation of classification credibility index steps, and filtering of non-pathogenic bacteria steps; the credibility is screened according to the number of reads at the species level and genus level, the number of unique Kmers at the species level, the genome size of the corresponding species, the read coverage size, the number of windows containing reads, and the microbial genome reference genome by the number of reads. The present application realizes the automatic analysis of mNGS raw off-machine data through each module, obtains reliable classification results according to the credibility screening scheme, automatically reports the microorganism, and solves the dependence on professional technicians for the analysis of mNGS raw off-machine data.

The invention belongs to the technical field of dynamic monitoring of oil production engineering, and particularly relates to a method for analyzing and identifying inter-well connectivity based on microbial genome DNA (Deoxyribose Nucleic Acid). Comprising the following steps: acquiring liquid samples of a producing well and a water injection well and rock debris samples of a new drilled well in the same area and the same stratum as the producing well; carrying out microbial genome DNA analysis on the obtained sample to obtain dominant strain compositions of the oil producing well, the water injection well and the newly-drilled well; comparing the number of the dominant strains shared by the producing well and the water injection well and the number of the dominant strains shared by the producing well and the new drilling well, and judging the connectivity of the producing well and the water injection well according to a comparison result. The invention provides a novel inter-well connectivity identification method, which can effectively solve the problems that the water breakthrough direction of an oil production well is complicated and is difficult to identify clearly due to the influence of dominant channels, natural fractures, water injection dynamic fractures and other factors on a water injection development oil reservoir.

The invention relates to the technical field of bioinformatics and microbial genome analysis, in particular to a food-borne pathogenic bacterium typing method based on a wgMLST technology, which comprises the following steps of: preliminarily comparing a genome sequence with a constructed lightweight wgMLST database, and aiming at imperfectly matched gene loci in a comparison result, identifying the genomic sequence in the lightweight wgMLST database and identifying the genomic sequence in the lightweight wgMLST database. And expanding or cutting off the sequence according to the comparison region, predicting and extracting a potential open reading frame (ORF) sequence, and carrying out dictionary comparison on the potential ORF sequence until matching succeeds, thereby accurately judging the corresponding number of the allele. And traversing all imperfect matching sites and repeating the process to finally obtain a complete wgMLST typing spectrum. According to the method, a wgMLST typing task of large-scale high-throughput sequencing data can be efficiently processed; the complete analysis speed of single pathogenic bacteria is increased by nearly 10 times; a complete allele dictionary is introduced for secondary comparison and error correction, and it is ensured that imperfect matching site typing is correct and high in accuracy; and a technical support is provided for high-throughput strain detection and typing.

The invention discloses a method and system for synchronously detecting host chromatin openness and in-vivo microbiome based on transposase, and belongs to the technical field of biological sequencing data analysis. According to the method, transposase is used for selectively fragmenting an open chromatin region of a host, and a microbial genome is almost randomly cut, so that synchronous enrichment of host and microbial DNA is realized; after high-throughput sequencing library construction and double-end sequencing, sequencing data is split into host source and non-host source reads through bioinformatics analysis, host chromatin state and microorganism composition are analyzed respectively, and a microorganism-host epigenetic regulation network is constructed; the invention further provides a matched DNA sequencing library and an analysis system, multi-scene research of infectious diseases, intestinal microecology, tumor microenvironment and the like is supported, a public database can be reanalyzed, and potential microbial interaction signals are mined. According to the method, the host-microorganism interaction research efficiency is remarkably improved, and a high-sensitivity and integrated technical scheme is provided for epigenetic regulation mechanism analysis.

The application discloses a gene editing system CRISPR-Cas12p and application thereof. Based on microbial genomes and metagenomic data, the CRISPR-Cas12p protein of the CRISPR-Cas protein family is obtained by preliminary screening by using a Prodigal gene prediction tool, a Pfam database and HMMER software, and a gene editing system CRISPR-Cas12p is constructed. PAM preference and interference function identification show that the editing system has a PAM preference of 5'-TTC-3', can effectively realize targeted cutting by using long transcripts and double RNA hybrid chain transcripts respectively, and can realize editing of a target gene in prokaryotic and eukaryotic cells. The CRISPR-Cas12p gene editing system obtained by the application has a small protein component, is beneficial to delivery, can realize gene editing in prokaryotic and eukaryotic cells, and has a wide application prospect.

The invention relates to the technical field of biochemistry, and discloses a hydrolase for splitting bacterial peptidoglycan causing chronic inflammatory diseases, the hydrolase is separated from a human intestinal microbe genome, and the hydrolase can hydrolyze a peptidoglycan layer of gram-positive pathogenic bacteria in a targeted manner, so that the bacterial peptidoglycan has the advantages that the bacterial peptidoglycan has a good anti-inflammatory effect, and the bacterial peptidoglycan has a good anti-inflammatory effect. The compound has high efficiency, specificity and low drug resistance and has a synergistic effect with existing antibiotics; the preparation method of the hydrolase comprises the following steps: according to an amino acid sequence, selecting escherichia coli preferred codons, and artificially synthesizing a gene sequence for coding the hydrolase; cloning the synthetic gene into an expression vector to construct a recombinant expression plasmid; transforming the recombinant expression plasmid into escherichia coli, and carrying out induced expression; the hydrolase is obtained through a separation and purification step. According to the hydrolase for splitting the bacterial peptidoglycan causing the chronic inflammatory disease, a peptidoglycan layer of gram-positive bacteria can be efficiently hydrolyzed through the hydrolase, so that the bacteria are rapidly split, and the antibacterial effect is improved.

The invention provides a method for batch detection of viruses in a single-cell microbial genome. According to the method, by constructing the comprehensive reference index and the independent reference index and combining the two-stage detection strategy, high-throughput, batch and automatic analysis is achieved, whether all viruses / plasmids in a database exist in a sample or not can be detected at the same time through one-time operation, correlation analysis with all strains is automatically completed, and the detection efficiency is greatly improved.

The present invention provides a method, system and device for removing contamination in the results of single-cell microbial genome species assembly based on classification feature gene sets. Based on the regularity of the appearance of feature gene sets in species genomes, the present invention gradually searches for the best combination of length threshold and coverage threshold, which is used to filter the results of single-cell microbial genome species assembly, thereby removing contaminated contigs assembled from background reads. The method provided by the present invention not only overcomes the defect of the prior art that the length threshold cannot be automatically determined, but also does not need to assume that the coverage of the contigs of the species is normally distributed or multi-peaked when determining the contig coverage threshold, thereby achieving high-throughput detection and automatic removal of multi-cell contamination and background contamination in the results of single-cell genome assembly, and obtaining the best contamination removal results as much as possible.

The invention discloses a method for detecting microbial genome RNA based on an mNGS technology. The invention provides a method for constructing an RNA sequencing library, which comprises the following steps: A1) fragmenting an RNA sample to obtain fragmented RNA; a2) carrying out reverse transcription and terminal repair reaction on the fragmented RNA in the following multi-enzyme reaction system to obtain double-chain cDNA (complementary deoxyribonucleic acid) with flat terminal and containing A basic group; and A3) sequentially carrying out joint connection and PCR amplification on the double-chain cDNA with the flat tail end and containing the A basic group to obtain the RNA sequencing library. According to the technical scheme, operation is easy, time consumption is short, reaction conditions and DNA library construction are the same, operation and reaction can be conducted at the same time, the initial amount of RNA is 100 pg, and daily requirements of microbiological detection are met.

The invention belongs to the technical field of biological medicines, and particularly relates to an oral microbial gene marker for noninvasive diagnosis of esophageal cancer patients and application of the oral microbial gene marker. The invention provides an oral microbial gene marker for distinguishing esophageal cancer patients from healthy people, which consists of six microbial genes as shown in SEQ ID NO: 1-6, and the microbial genes are enriched in the oral cavity of a human body. The microbial gene distinguishing model disclosed by the invention has good distinguishing ability in esophageal cancer patients and healthy control people, and the feasibility, applicability and universality of the microbial gene distinguishing model in the esophageal cancer patients are proved.

A method of constructing a microbial identification database, the method comprising: (ST02) acquiring genome data for microorganisms from a genome database; (ST06) determining whether a criterion is satisfied by the genome data thus acquired; (ST16) for respective sets of the genome data that were determined that they satisfied the criterion, predicting proteins to be expressed; and (ST20A, 20C) constructing a mass-to-charge ratio database including mass-to-charge ratio lists, the mass-to-charge ratio lists being predicted for the respective sets of the genome data based on the proteins thus predicted.

The application discloses a specific molecular marker screening method for microbial tracing, comprising the following steps: step one, microbial genome characteristic analysis; step two, specific candidate gene screening; step three, homologous arm design and target fragment amplification; step four, recombination plasmid construction; step five, positive control system establishment; step six, specificity verification; step seven, sensitivity detection; step eight, stability evaluation; step nine, marker practicability verification; and step ten, standardization and shaping; the unique gene fragment of the target microorganism is screened through whole genome alignment, and multiple verifications such as specificity, sensitivity, stability and practicability are combined, so that the screened molecular marker has high specificity, can effectively distinguish the target microorganism from the non-target microorganism close to the target microorganism, and cross reaction is avoided.

The invention provides a rapid analysis method of metal corrosive microorganism sulfate reducing bacteria, and belongs to the technical field of biology.The rapid analysis method comprises the steps that a to-be-detected microorganism genome DNA sample and a photosensitizer As2MoO6 atNiS are taken to jointly construct a triple asymmetric photon PCR system, asymmetric photon PCR amplification is carried out under the condition of LED light source excitation, after amplification is completed, the sample is detected, and then the sample is detected. The obtained amplification product is mixed with a photo-thermal signal probe prepared from a photosensitizer As2MoO6 coated NiS, and photo-thermal temperature change detection is carried out. The rapid analysis method provided by the invention has the characteristics of high efficiency, convenience and accuracy, and is suitable for rapid detection of sulfate reducing bacteria.

The invention provides a formula flora construction method and device, electronic equipment and a storage medium, and belongs to the field of bioinformatics, and the formula flora construction method comprises the following steps: converting a phylogenetic tree constructed by a microbial genome sequence into a weight matrix; performing center logarithm ratio transformation on the original abundance matrix and then inputting the original abundance matrix into an iterative random forest model; correcting the original feature importance into smooth feature importance by using the weight matrix so as to update the feature sampling weight of the next round; and when the model converges, extracting a high-order ecological interaction rule based on a decision path to output a candidate core flora, and further determining a target formula flora. The characteristics are smoothly corrected by introducing the phylogenetic relationship, so that the independence hypothesis of traditional abundance data is broken, the sparsity and false positive interference of high-dimensional sequencing data are effectively overcome, the evolution-driven real inter-species collaborative relationship is accurately captured and reserved, and the accuracy of the method is improved. Therefore, efficient steady-state colonization and precise targeted metabolic regulation of the formula flora in the host microenvironment are guaranteed.

The object of the present invention is to provide a gene chip for detecting Sanmen mud crabs. The present invention collects mud crabs from the main production areas of mud crab farming in the provinces along the southeast coast of China, performs 16S rRNA sequencing on their intestinal microbial genomes, and through comparative analysis, screens out the specific microbial populations in each main production area, and comprehensively designs the characteristic DNA sequences of these populations. Finally, molecular markers for identifying mud crabs in each area are obtained and developed into a gene chip with characteristics such as fast speed, high efficiency, and sensitivity. The origin of Sanmen mud crabs is identified through the gene chip, and non-Sanmen mud crabs are distinguished, thus solving the problem of identifying Sanmen mud crabs.

The invention provides a method for analyzing single-cell microorganism genome sequencing data. According to the method, species-level bins with polycellular pollution and background pollution removed and corresponding species assembly results are obtained from a single-cell microbial genome by utilizing an optimized method for assembling a species genome sequence, then strain-level bins are distinguished from the species-level bins according to species SNP characteristics, and corresponding strain assembly results are obtained after assembly. Compared with the prior art, by automatically calculating the number of assembly rounds and simplifying the process, human intervention is reduced, and the operation convenience and efficiency are improved; the pollution degree of the species bin can be effectively controlled, and the accuracy of an assembly result is ensured; the similarity matrix is calculated in groups, so that the memory consumption under the condition of high SAG number is obviously reduced, and meanwhile, the operation speed is improved; the similarity threshold value can be dynamically selected or adjusted, so that the similarity threshold value can adapt to different sample types or library quality.

A method for detecting target genomic sequences at predetermined positions in a sequenced genome of a microbial organism in the form of reads. The method comprises computing a local sequencing depth of the genome in a neighborhood of the position of a target genomic sequence, the computing including a) detecting in the reads a set of digital genomic sequences from at least one reference genome of the microbial organism, b) generating of third set of digital genomic sequences comprising reads and digital genomic sequences of the second set belonging to the neighborhood c) counting the number of copies of each digital genomic sequences of the third set of digital genomic sequences, and d) computing the local sequencing depth as being equal to the maximum of the counted numbers of copies.

This application provides a method and kit for detecting pathogenic microorganisms based on the properties of tetrastranded DNA oxidoreductase. The method utilizes isothermal amplification technology to amplify genomic fragments containing tetrastranded DNA / RNA sequences in the pathogenic microorganism genome, and then performs a colorimetric reaction by adding heme and oxidoreductase substrates, achieving rapid and visual detection of pathogenic microorganisms.

This application relates to a DNA construct for overexpressing a target gene in *Schizochytrium* microorganisms, and a method for expressing the target gene in *Schizochytrium* microorganisms using the construct. The DNA construct includes a 5' homologous arm and a 3' homologous arm capable of hybridizing to a high-expression site in the *Schizochytrium* microorganism genome.

The invention discloses a digestive tract tumor early screening system based on multi-omics data fusion, and relates to the technical field of tumor screening, the system comprises a double sample collection module, a synchronous detection module, a database support module, a fusion analysis module and a visual output module; according to the method, the accuracy and comprehensiveness of early screening of digestive tract tumors are improved through multi-omics data fusion, multi-dimensional data of fecal microbial genome DNA, metabolites, blood ctDNA and protein markers are integrated, biological information of four levels of florae, metabolism, genes and proteins is covered, and the accuracy and comprehensiveness of early screening of digestive tract tumors are improved through a three-level cross validation mechanism. According to the method, flora-metabolite synergy abnormality and gene-protein synergy abnormality can be recognized, the tumor risk value is calculated and the risk level is set in combination with positive threshold values and clinical weights in a multi-omics feature database, the detection rate of early tumors is increased, and the method has higher sensitivity especially for early digestive tract tumors without obvious symptoms.

The invention discloses endonuclease spCaslambda-2 with a wide target recognition range and application of the endonuclease spCaslambda-2. On the basis of metagenome data, through a bioinformatics method, endonuclease spCaslambda-2 is explored from an unknown microbial genome, and a crRNA sequence corresponding to the endonuclease spCaslambda-2 is identified. Compared with the known Caslambda enzyme, the spCaslambda-2 shows excellent cis and trans cleavage activity. The PAM sequence recognized by the enzyme is 5 '-YYR-3' (Y represents C or T, and R represents A or G), and can cover wider genome sites, so that the application potential of the Caslambda family in gene editing and detection is remarkably expanded.

The invention discloses an endonuclease Gs12a2-5 and a nucleic acid detection technology mediated by the endonuclease Gs12a2-5. A novel Cas endonuclease Gs12a2-5 and a related crRNA structure sequence are excavated from unknown microbial genomes of metagenomes through a bioinformatics technology, and compared with known SuCas12a2 endonuclease, the Gs12a2-5 endonuclease shows good trans-cleavage activity, is higher in sensitivity in nucleic acid detection, and can be applied to detection of various microorganisms. Therefore, a CRISPR-Gs12a2-5 system-mediated nucleic acid visual detection technology is developed, and the CRISPR-Gs12a2-5 system-mediated nucleic acid visual detection technology has the advantages of simplicity and convenience in operation, rapidness in detection, high sensitivity, strong specificity and the like, and has a wide application prospect in the field of nucleic acid detection.

The invention discloses a gene cluster cloning method and application thereof. The gene cluster cloning method comprises the following steps: performing restriction enzyme digestion on a target microbial genome to obtain a DNA fragment containing a target biosynthetic gene cluster; by utilizing a Gibson assembly method, connecting the upstream of the DNA fragment containing the target biosynthetic gene cluster with a p15Aorii-loxP-AmpR element containing pBE44 and a fragment aiming at a homologous arm of the upstream, and connecting the downstream of the DNA fragment containing the target biosynthetic gene cluster with a fragment containing a lacZ alpha-loxP-phage # imgabs0 # attP-traJ-ApmR element aiming at a homologous arm of the downstream and pBE45, so as to obtain a linear recombinant fragment formed by connecting three fragments; and electrically transferring the linear recombinant fragment into an escherichia coli host strain containing a Cre recombinase expression system, and cyclizing a large-fragment gene cluster in vivo by virtue of a Cre-loxP system, so as to obtain the annular recombinant plasmid. The method has the remarkable advantages of being easy and convenient to operate, high in cloning efficiency, high in universality and the like, and complex natural product gene clusters can be efficiently obtained.

The invention relates to the technical field of bioinformatics, in particular to a pathogenic microorganism genome, a construction method, a computer system and application. According to the method, a genome data quality control strategy in the pathogenic microorganism genome database creation process is innovated, ANI and AF double indexes are creatively adopted for classification error recognition, contig pollution sequence recognition and k-mer short sequence pollution recognition are combined for sequence pollution recognition and processing on genome data, the number of genomes is reserved to the maximum, and the number of the genomes is reduced to the maximum. According to the method, contig level sequence errors are accurately recognized, strain specific sequences are prevented from being mistakenly deleted, the diversity of species genomes is guaranteed, and the constructed database can improve the identification accuracy / sensitivity of pathogen infected species.