23 results about "Microbial Genomes" 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 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 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 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 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 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 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 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.

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.

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.

This invention discloses a probiotic screening method based on neural networks and metagenomic data, relating to the field of probiotic screening. It involves obtaining metagenomic sequencing data from NCBI, preprocessing the data, and dividing the processed sequence data into training, validation, and test sets. A deep learning model is constructed based on a Transformer architecture combined with a HyenaOperator hybrid mechanism to capture the internal dependencies of sequence fragments at different distances, performing pooling to obtain better sequence features. These features are then input into a multilayer perceptron (MLP) base model for dimensionality reduction, and the predicted probabilities are output using a softmax function. A voting mechanism is used to summarize and determine the predicted results of the sequence fragments. This invention employs the aforementioned probiotic screening method based on neural networks and metagenomic data, enabling efficient and accurate screening of potential probiotics in large-scale microbial genome data.

The invention relates to direct cloning of a biosynthetic gene cluster, in particular to a direct cloning method and application of an ultra-large biosynthetic gene cluster, a microbial genome is extracted from a low-melting-point agarose gel block through combination, and the ultra-large gene cluster can be rapidly cloned in a targeted manner by utilizing the specific cutting characteristic of CRISPR / Cas and a saccharomyces cerevisiae TAR technology. According to the method, mechanical shearing can be avoided by extracting and treating the genome in the thallus embedding block, and the operation is simple, so that the integrity of an ultra-large target gene cluster can be maintained to the maximum extent, and particularly, the probability that rearrangement is extremely easy to occur in a yeast body due to excessive overlapped fragments can be reduced for (ultra)-large PKS / NRPS gene clusters. CRISPR / Cas mediated cleavage can occur at any DNA site, and a target gene cluster can be released in a most accurate and fastest manner, so that targeted cloning is not limited by restriction enzyme cleavage sites any more. The high efficiency of the TAR technology enables the target cloning of (ultra) large gene clusters to be simple and feasible.

The invention discloses an information encryption method and system based on strain genome coding and identification. The method comprises the following steps: extracting target gene sequence features from a strain genome database, including conservative marker gene sequences, necessary functional gene sequences and genome variation site distribution, and generating a strain specific key matrix; after to-be-encrypted information is converted into binary codes, a dynamic mapping rule is established according to the strain specificity key matrix, the binary codes are converted into quaternary pseudo-gene sequences, and strain identity identification codes are embedded into the quaternary pseudo-gene sequences; a hierarchical coding mechanism is adopted to allocate different security levels according to strain system development levels, and multi-level key management and authority control are achieved; inserting a strain specific marker sequence and an integrity check code into the pseudo-gene sequence to generate a final biological ciphertext; according to the method, high-security quantum resistant encryption is realized by utilizing natural diversity and randomness of microbial genomes.

The invention relates to the field of agricultural microbial technology and synthetic biology, in particular to a preparation method of a coffee continuous cropping stress-resistant microbial agent designed based on a DepSeek genome, microbial genomes are analyzed and optimized through a DeepSeek R1 large model, coffee continuous cropping stress-resistant functional genes and regulatory elements are designed, and then, the coffee continuous cropping stress-resistant microbial agent is prepared. The preparation method comprises the following steps: carrying out genome modification on four strains, namely bacillus subtilis COFFEE-B1, pseudomonas lipolytica COFFEE-P2, bacillus licheniformis COFF EE-B3 and trichoderma sp. COFFEE-T4, carrying out optimized fermentation culture on the modified strains to achieve an optimal growth state, finally, mixing according to a specific weight ratio (B125%, P2%, B3 25%, T4 10% and 20% of a carrier and an auxiliary material), drying, screening and packaging to obtain a finished product. And preparing the microbial agent for continuous cropping of coffee.

The invention belongs to the technical field of biological information, and particularly relates to a compost N2O emission path identification and environmental risk quantification method based on multiple omics. The method comprises the following steps: extracting and sequencing total DNA (Deoxyribonucleic Acid) and total RNA (Ribonucleic Acid) of a collected compost sample; by analyzing metagenome data, reconstructing an N2O-generated microbial genome and performing function annotation on the N2O-generated microbial genome; according to a functional gene set annotated by a genome, dividing four generation ways of nitrification, nitrifying bacteria denitrification, heterotrophic denitrification and reduction of dissimilatory nitrate into ammonium; and analyzing gene expression dynamics in the genome by combining with a metatranscriptome and carrying out risk quantification. Compared with targeted gene detection technologies such as PCR (polymerase chain reaction) and the like, the method has the advantages that the generation way and the emission potential of N2O in a composting system are accurately recognized by fusing the metagenome and the metatranscriptome, the limitation of a traditional method on the gene coverage degree is broken through, and the method has important application value on accurate management and control of organic solid waste engineering greenhouse gases.

The invention discloses a gene editing system CRISPR-Cas12p (Clustered Regularly Interspaced Short Palindromic Repeats) and application According to the method, on the basis of microbial genome and metagenome data, a Prodital gene prediction tool, a Pfam database, HMMER software and the like are utilized for preliminary screening, CRISPR-Cas12p protein of a CRISPR-Cas12p protein family is obtained, and a gene editing system CRISPR-Cas12p is constructed. PAM preference and interference function identification shows that the editing system has PAM preference of 5 '-TTC-3', target cutting can be effectively realized by respectively utilizing a long transcript and a double-RNA hybrid chain transcript, and target genes can be edited in prokaryotic and eukaryotic cells. The CRISPR-Cas12p gene editing system obtained by the invention has miniaturized protein components, is beneficial to delivery, can realize gene editing in prokaryotic and eukaryotic cells, and has a wide application prospect.

The application provides a formula flora construction method and device, electronic equipment and storage medium, and belongs to the field of bioinformatics, and comprises the following steps: converting a phylogenetic tree constructed by a microbial genome sequence into a weight matrix; inputting a central logarithmic ratio transformed original abundance matrix into an iterative random forest model; correcting the original feature importance to smooth feature importance by using the weight matrix to update the feature sampling weight in the next round; and extracting high-order ecological interaction rules based on the decision path when the model converges to output a candidate core flora, and then determining a target formula flora. The application breaks the independence assumption of traditional abundance data by introducing phylogenetic relationships to smooth correct features, effectively overcomes the sparsity of high-dimensional sequencing data and false positive interference, accurately captures and retains the real interspecies synergistic relationship driven by evolution, and thus guarantees the efficient and stable colonization and precise targeted metabolic regulation of the formula flora in the host microenvironment.

The application provides a method for batch detection of viruses in single-cell microbial genomes. The method realizes high-throughput, batch and automatic analysis by constructing a comprehensive reference index, an independent reference index and combining a two-stage detection strategy, can simultaneously detect whether all viruses / plasmids in the database exist in the sample in one run, and automatically completes the correlation analysis with all strains, greatly improving the detection efficiency.