49 results about "Microbial genome" patented technology

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 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 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 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.

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.

The invention relates to the field of medicinal chemistry, and relates to a small molecule peptide for inhibiting growth of staphylococcus, and an analogue and application thereof. The method comprises the following steps: finding a rhodococcus genome from an NCBI (National Center of Biotechnology Information) microbial genome database, and predicting a non-ribosome peptide structure synthesized by a non-ribosome peptide synthetase (NRPS) sequence through software such as AntiSMASH and Prism; the method comprises the following steps: classifying all NRPS biosynthetic gene clusters (BGCs) through Bigscape to obtain a gene cluster family (GCFs); the method comprises the following steps: predicting the selectivity of a GCFs substrate and screening a polypeptide with antibacterial potential through Phammapper; a small molecule peptide (compound I) is obtained through chemical synthesis, and the small molecule peptide is found to have an inhibition effect on staphylococcus epidermidis and staphylococcus pseudointermedius; afterwards, alanine is used for replacing glutamine to increase hydrophobicity of glutamine (compound II), the antibacterial effect of the compound II is obviously enhanced, and the compound II has the potential of developing novel antibacterial drugs and biopesticides.

The invention relates to the technical field of biological genome information processing, in particular to a ship ballast water pathogenic microorganism genome information analysis method. Comprising the following steps: acquiring an original water sample in a ship ballast water tank, analyzing the original water sample through a high-throughput genome sequencing technology to generate original genome data, and preprocessing the original genome data to obtain preprocessed genome data; and performing genome comparative analysis and risk assessment on the preprocessed genome data and a database of known pathogenic microorganism gene information by using a self-adaptive genome comparative risk assessment algorithm based on a deep convolutional neural network, and judging the risk level of the pathogenic microorganisms to obtain an assessment result. The technical problems that the accuracy and timeliness of identifying pathogenic microorganisms in ship ballast water are insufficient, and the self-adaptability is poor are solved.

The invention provides a data processing method and device for dynamically monitoring microbial genomes in a global range and a storage medium. The method comprises the following steps: acquiring a reference genome sequence, and constructing an evolutionary tree database of sketches of the reference genome; obtaining a sequence of a sample genome submitted by a user, and calculating to obtain an evolutionary tree location of the sample genome; based on the distance between the sketch of the sample genome and the sketch of the reference genome and the evolutionary tree database of the sketch of the reference genome, calculating evolutionary tree localization of the sample genome by using an evolutionary tree localization algorithm; obtaining whether the evolutionary tree positioning in the adjacent time and geographic area has more submission amount compared with other evolutionary tree positioning; and outputting the information of the submission amount. According to the method, the data transmission and operation speed can be increased, the consumption of calculation resources is reduced, the data processing efficiency is improved, the user data security is protected, and whether the corresponding strain has an outbreak trend or not is judged.

This invention relates to a reagent combination, extraction kit, and extraction method for extracting microbial genomic DNA from soil, belonging to the field of biotechnology. The reagent combination for extracting microbial genomic DNA from soil of this invention includes individually packaged grinding beads I, grinding beads II, lysis buffer, inhibitor removal, binding buffer, magnetic beads, rinsing solution I, rinsing solution II, and elution buffer. In this invention, soil samples are ground and heated after adding grinding beads of two particle sizes and lysis buffer, which effectively lyses and releases nucleic acids from soil microorganisms. The inhibitor removal agent in this invention reduces the interaction between impurities in the sample and nucleic acids, and the flocculant in the inhibitor removal agent effectively settles impurities such as humic acid in the soil. The binding buffer in this invention promotes the binding of nucleic acid molecules to magnetic beads. The two rinsing solutions in this invention effectively remove impurities such as proteins and some small molecule compounds during the extraction process.

The invention belongs to the technical field of genome comparison, and particularly relates to a genome comparative analysis system for multi-drug-resistant staphylococcus aureus, prophage and split phage. According to the present invention, the genome sequence analysis of the multi-drug-resistant staphylococcus aureus, the prophage and the split phage is integrated, the initial and dynamic change and mutation information is covered, the complete analysis chain is constructed, the gene data analysis in different time periods can clearly present the gene dynamic change process, and the analysis result is accurate. The invention discloses a response mechanism of a microbial genome to the influence of an external environment or bacteriophage, discloses the interaction between the bacteriophage and the multi-drug-resistant staphylococcus aureus, particularly the action in a drug-resistant gene transfer or anti-bacteriophage mechanism, can efficiently recognize important gene changes, and can be used for preparing the multi-drug-resistant staphylococcus aureus. And a powerful decision basis is provided for drug research and development and drug resistance mechanism research.

The present application relates to a kind of high concentration DMF waste water biological treatment method, belong to wastewater treatment technical field;Including: mixed strain screening, activation and scale-up culture are carried out;And join DMF waste water;In fermentation treatment, the growth of microorganism and the change situation of COD are monitored regularly, when microorganism growth is in logarithmic phase, extract microbial genomic DNA, high-throughput sequencing is carried out to microorganism in fermentation waste water, determine the proportion of final fermentation waste water and dominant genus;When mixed strain processing efficiency reduces in fermentation process, add certain genus according to genus proportion to make its proportion consistent, and add carbon source and growth factor;Compared with single bacteria degradation DMF, the mixed strain selected by the present application converts DMF in waste water into dimethylamine and methylamine by the process of mixed strain biological fermentation, and is finally converted into ammonia and carbon dioxide, and the biochemical property can be increased by 2-5 times, to reduce the load of subsequent conventional sludge system.

This invention discloses a metagenomics-based method and system for detecting resistance genes, belonging to the field of resistance gene detection. The method includes the following steps: constructing a microbial genome sequence based on metagenomic reads; performing species annotation and resistance gene identification based on the microbial genome sequence to obtain annotated resistance gene sequences; analyzing the evolutionary relationships of resistance genes in the annotated resistance gene sequences; and monitoring and providing early warning of dynamic changes in resistance gene expression based on the evolutionary relationships and annotation information of the resistance gene sequences. This invention achieves a complete analysis process from raw data to the distribution, evolution, and propagation patterns of resistance genes, providing strong data support for the tracing of resistance genes and risk assessment.