26 results about "Phylogenetic profiling" patented technology

The invention discloses a lytic bacteriophage for preventing and controlling vibrio in an aquaculture environment. The bacteriophage vBValMR42H belongs to a muscle tail bacteriophage and is insensitive to chloroform, the capsid of the bacteriophage vBValMR42H is free of lipid substances, and the preservation number is GDMCC No: 67434-B1. The bacteriophage has the characteristics of high adsorption speed, short incubation period and high cracking amount, keeps high activity in a wide range of temperature (4-55 DEG C) and pH (2-11), and has strong environmental adaptability. Genome analysis shows that the bacteriophage does not contain virulence factors, antibiotic resistance genes and lyogen related genes, and is high in biological safety. Physical development analysis shows that the method can be divided into a new genus. The bacteriophage R42H has the advantages of high splitting efficiency, good environmental stability, strong specificity, gene safety and the like, and can be used as an ideal biological prevention and control agent for preventing and controlling vibrio alginolyticus diseases in aquaculture.

The invention discloses a PCR (Polymerase Chain Reaction) primer for amplifying a reverse transcription product of dengue virus, a PCR kit and a method for detecting the dengue virus, and belongs to the technical field of virus detection. Comprising an upstream primer DENV-F as shown in SEQ ID NO. 1 and a downstream primer DENV-R as shown in SEQ ID NO. 2. The dengue virus detection method based on the PCR amplification reaction, the three-generation sequencing and the phylogenetic analysis is established by utilizing the characteristics that the PCR reaction is efficient, rapid and accurate, the three-generation sequencing is rapid, the full-length sequencing of about 10,000 basic groups can be provided, one sequencing result represents one complete virus sequence, the phylogenetic analysis is accurate in strain analysis and the like. The kit plays a role in rapid and accurate detection of dengue viruses. The PCR primer used in the invention has high sensitivity, can reach 0.01 pg / reaction, has good specificity, and does not react with other sequences while amplifying the dengue virus.

The present invention relates to the field of biotechnology, and more particularly to a highly active S-sulfo-L-cysteine ​​synthetase mutant and its applications. The present invention screened and identified a preferred SSC03 enzyme through cluster analysis and phylogenetic analysis, and further engineered mutations thereof. The resulting SSC03-S256PΔCT achieved a 24-hour conversion rate of 56% and produced 84 mM of S-sulfo-L-cysteine, demonstrating its applicability to further purification process development.

One bacterial strain, designated HC1M1C21T, was isolated from human faeces and analyzed using phylogenetic, morphologic and biochemical approaches. Phylogenetic analyses based on 16S rRNA sequences and a set of 92 bacterial core genes indicated that this strain belongs to the Lachnospiraceae family and clusters near Pilosibacter fragilis (96.9% 16S rRNA sequence identity). HC1M1C21T has a DNA G+C content of 48.7 mol%. This strain is anaerobic, Gram- stain-positive, non-motile and non-spore-forming. HC1M1C21T cells appear as single rods or chained rods with tapered ends. Optimal growth was observed at 37°C, at pH between 5.5 and 6.5 and at salinity below 10 g / L. HC1M1C21T is a potent butyrate producer. The invention pertains to a new bacterial strain that produces butyrate and several independent factors with anti-inflammatory properties.

The invention discloses a marine shipping marinobacter SND-2 strain as well as a culture method and application of the marine shipping marinobacter SND-2 strain. According to the invention, a heterotrophic synchronous nitrification and denitrification functional strain SND-2 capable of efficiently degrading nitrogen concentration in a marine culture water body under an aerobic condition is separated from a prawn culture pond, and the strain is identified as Marinobacter nauticus according to colonial morphology and 16S rDNA gene sequencing analysis and phylogenetic analysis, the marine marinobacter SND-2 strain is preserved in the China Center for Type Culture Collection on October 15, 2024 (the preservation number is CCTCC NO: M 20242217). The marine marinobacter SND-2 strain belongs to heterotrophic ammonia oxidizing bacteria, has a heterotrophic nitrification-aerobic denitrification function, can efficiently degrade ammonia nitrogen, nitrite nitrogen, nitrate nitrogen and total nitrogen concentration in a marine culture water body under an aerobic condition, has no toxic effect on aquatic animals, and can be applied to ecological restoration of a seawater water environment.

The invention discloses separation and application of a vibrio parahaemolyticus lytic bacteriophage vBVpaSR27Z (Vibrio parahaemolyticus lytic bacteriophage). The preservation number of the bacteriophage vBVpaSR27Z is GDMCC No: 67438-B1 (GDMCC No: 1). The bacteriophage is separated from an environmental sample by adopting a double-layer plate method, the head of the bacteriophage is in a regular icosahedron shape (84 nm * 71 nm), the tail length of the bacteriophage is about 141 nm, the incubation period of the bacteriophage is only 20 min, the lysis speed is high, and the activity of the bacteriophage is stable within the pH range of 5-10 and the temperature range of 4-37 DEG C; the genome of the vibrio bacteriophage is double-stranded DNA without known drug resistance and toxicity genes, phylogenetic analysis shows that the vibrio bacteriophage has low homology with known vibrio bacteriophages, and the vibrio bacteriophage belongs to a novel genetic resource. The vBVpaSR27Z can rapidly inhibit the growth of strains such as vibrio parahaemolyticus, is suitable for green prevention and control of diseases such as vibrio parahaemolyticus in aquaculture, and can be used as an active component of a biological antibacterial preparation.

The invention discloses a pseudomonas stutzeri SND-1 strain as well as a culture method and application thereof. According to the invention, a broad-salt synchronous nitrification and denitrification functional strain SND-1 capable of efficiently degrading nitrogen concentration in an aquaculture water body is separated from a prawn aquaculture pond, and the strain is identified as Stutzeria stutzeri according to colonial morphology and 16S rDNA gene sequencing analysis and phylogenetic analysis, the pseudomonas stutzeri SND-1 strain is preserved in the China Center for Type Culture Collection (the preservation number is CCTCC NO: M 20242216) on October 15, 2024, and the pseudomonas stutzeri SND-1 strain is preserved in the China Center for Type Culture Collection (CCTCC). The pseudomonas stutzeri SND-1 strain belongs to heterotrophic ammonia oxidizing bacteria, has a heterotrophic nitrification-aerobic denitrification function, can efficiently degrade ammonia nitrogen, nitrite nitrogen, nitrate nitrogen and total nitrogen in fresh water, seawater and aerobic environments, has no toxic effect on aquatic animals, and can be applied to ecological restoration of fresh water or seawater water environments.

The invention relates to the technical field of biological information, and relates to a method and a system for predicting the metabolic capability of uncultured microorganism individuals, and the method comprises the following steps: obtaining a metagenome sequence of a to-be-analyzed object; extracting an uncultured microorganism assembly genome from the metagenome sequence; performing phylogenetic analysis on the uncultured microorganism assembled genome to obtain an analysis result; establishing a metabolic network model according to the analysis result; and performing individual metabolic capability prediction on the uncultured microorganism assembled genome by using the metabolic network model to obtain a prediction result. According to the method, the individual metabolic capability of the uncultured microorganisms can be predicted.

The invention discloses a chlamydia psittaci cgMLST molecular typing method, and belongs to the field of microbial molecular typing and tracing. According to the invention, an operation technology for carrying out molecular typing on chlamydia psittaci by using a core genome multi-site sequence typing system (cgMLST) is established for the first time. The chlamydia psittaci cgMLST system is established through the processes of collecting chlamydia psittaci genomes in a disclosed genome database, obtaining core genomes through quality control screening and generic genome analysis, screening core genes suitable for typing under multiple screening conditions and the like. And comparing with a phylogenetic analysis result based on core genome SNP difference to confirm the resolution and reliability of the typing system. According to the typing technology, the core genome of the chlamydia psittaci is determined for the first time, and the typing technology can be used for molecular typing and epidemiological monitoring of the chlamydia psittaci.

The invention belongs to the technical field of biological medicines, and provides an S protein ancestor sequence AS mRNA of a porcine acute diarrhea syndrome coronavirus, the ancestor sequence of an SADS-CoV Spike protein is constructed through phylogenetic analysis, and the sequence aims at the existing virus and also aims at the evolution pedigree of the virus; the sequence design is used for converting target defense aiming at a single pathogen into active intervention on a virus evolution trajectory; and the prepared AS mRNA vaccine has important significance on feeding safety of animals and prevention and control of zoonosis diseases.

The invention relates to the technical field of biological control, in particular to a method for screening high-toxicity locust pathogenic strains based on carbon and nitrogen metabolism and application of the high-toxicity locust pathogenic strains based on carbon and nitrogen metabolism. And a strain with high toxicity to migratory locust is screened out. ITS (ribosome DNA spacer) sequences of fungi are amplified through ITS1 and ITS4 primers, sequence comparison and phylogenetic analysis are carried out through MEGA 7.0 software, and it is ensured that the strain is metarhizium ledebusii; the method can be used for systematically screening high-toxicity metarhizium ledebusii strains, can be used for biological control of pests, and provides a scientific basis for development of efficient and sustainable pest control strategies.

The purpose is to provide a novel bacteriophage having a wider range of bacterial strains that serve as hosts for infection than conventional bacteriophages and having bacteriolytic activity against Escherichia coli, including drug-resistant E. coli. The present inventors have discovered a novel bacteriophage having a broad antibacterial spectrum against E. coli, including drug-resistant E. coli. The phage was named ΦWec 277 phage and deposited with the Patent Microorganism Depositary (NPMD) of the National Institute of Technology and Evaluation (NITE) (accession number: NITE P-04067). It was discovered that E. coli can be effectively eliminated by using this bacteriophage, and the present invention was completed. Furthermore, genomic analysis of the ΦWec 277 phage was performed to clarify the full-length sequence. This ΦWec 277 phage was identified as a bacteriophage belonging to the Caudoviricetes Straboviridae as a result of phylogenetic analysis.

This invention concerns a method for identification, differentiation, and phylogenetic mapping of natural Indonesian rabies virus strains based on molecular analysis. This method includes the stages of extracting rabies virus RNA from biological samples, reverse transcription of RNA into cDNA, amplification of a nucleoprotein gene fragment with a length of 1047 base pairs and a glycoprotein gene fragment with a length of 1053 base pairs using polymerase chain reaction techniques, visualization of the amplification results, nucleotide sequencing, and homology and phylogenetic analysis. The use of two gene targets with specific fragment lengths allows for accurate identification of rabies viruses, differentiation between isolates based on geographic regions, and mapping of kinship relationships and the origins of rabies viruses in Indonesia.This method can be applied in molecular diagnostic activities, epidemiological surveillance, and tracing the spread of the rabies virus, and provides increased accuracy and efficiency compared to previous identification methods that only use one gene target.

The invention discloses a biological data management and phylogenetic analysis process method, and relates to the technical field of biological data management. The invention relates to biological data management, which comprises the following steps of data acquisition and input, data storage and organization, data detection and query, data analysis and visualization and report generation and sharing. The invention discloses a phylogenetic analysis process method for biological data management. The method comprises the following steps of sample preparation and culture, data acquisition, data management, phylogenetic analysis and result display and report generation. According to the invention, the monitoring mechanism is arranged to monitor the two culture dishes in turn and collect data, and then through the culture mechanism and the adding mechanism, medicaments can be automatically added into the culture dishes, so that the cell culture effect can be greatly improved, the success of experiments and the acquisition of research results are promoted, and the trouble of manual operation is avoided.

The invention relates to the field of biological identification, and particularly discloses a method for identifying sambucus williamsii seedlings based on DNA barcodes, the DNA barcodes comprise ITS2 barcodes, universal primer sequences are SF2: 5 '-ATGCGATACTTGGTGTGAAT-3' and S3R: 5 '-GACGCTTCTCAGACTACAAT-3', the ITS2 barcodes are used for specifically amplifying ITS2 fragments, and the universal primer sequences are used for specifically amplifying the ITS2 fragments. The identification method comprises the following steps: extracting DNA of a sample, carrying out PCR amplification by using the primer, sequencing the product, comparing the obtained sequence with a database, and carrying out phylogenetic analysis, so as to determine the species. The method has the advantages of rapidness, accuracy and good repeatability, solves the problem that the flower-free and fruit-free period of elderberry is difficult to identify, and can be widely applied to the fields of elderberry seedling authenticity detection, Chinese herbal medicine source tracing, variety right protection, germplasm resource management and the like.

This invention proposes an ancestral 7β-hydroxysteroid dehydrogenase and its application. The amino acid sequence of the ancestral 7β-hydroxysteroid dehydrogenase is shown in SEQ ID NO.2. This invention obtains an ancestral 7β-hydroxysteroid dehydrogenase with significantly improved stability by reconstructing the ancestral enzyme sequence. This method is based on the theory that ancestral enzymes have higher stability in early evolutionary stages. Through homology alignment and phylogenetic analysis of the amino acid sequences of modern enzymes 7β-HSDH-T189V & V207M, ancestral enzyme sequences at several key evolutionary nodes were identified and synthesized. After activity screening and stability evaluation, ancestral enzyme No. 81 was finally obtained. Experimental results show that the residual enzyme activity of this ancestral enzyme after incubation at 55℃ for 60 minutes increased from 14% of the original enzyme to over 80%, significantly improving the enzyme's thermostability and providing important support for its application in the industrial production of ursodeoxycholic acid.

This invention discloses a lytic bacteriophage for controlling Vibrio alginolyticus in aquaculture environments. The bacteriophage, vB_ValM_R42H, belongs to the myotail bacteriophage family, is insensitive to chloroform, has a lipid-free capsid, and its preservation number is GDMCC No:67434-B1. This bacteriophage exhibits rapid adsorption, short latency, and high lysis rate, and maintains high activity over a wide temperature range (4℃~55℃) and pH range (2~11), demonstrating strong environmental adaptability. Genomic analysis shows that this bacteriophage does not contain virulence factors, antibiotic resistance genes, or lysogen-related genes, indicating high biosafety. Phylogenetic analysis indicates that it can be classified into a new genus. Due to its high lysis efficiency, good environmental stability, strong specificity, and genetic safety, the bacteriophage R42H of this invention can serve as an ideal biocontrol agent for controlling Vibrio alginolyticus disease in aquaculture.

This invention discloses a DNA barcode sequence and its applications, belonging to the field of microbial identification technology. This invention provides a method for identifying *Tomato Canker* pathogens. Clavibacter michiganensis A novel DNA barcode sequence with high specificity for identification. Phylogenetic analysis showed that in the phylogenetic tree constructed based on the DNA barcode sequence described in this invention, all tested species formed independent monophyletic groups with high support. Further sequence alignment analysis showed that the amplified sequences of each species all possessed their unique SNP sites. These results confirm that the DNA barcode provided by this invention can accurately distinguish *Tomato Canker* pathogens. Clavibacter michiganensis It can also effectively identify Clavibacter The other species within the genus demonstrate its strong species-level resolution.

The present invention relates to a method for conducting phylogenetic analysis of cells. The method of the present invention includes steps of: (1) comparing, for a plurality of single cells derived from the same individual, the RNA sequence data of the transcriptome of each single cell with the corresponding genome sequence data, and then screening for a site where the RNA sequence differs from the genome sequence; (2) screening the sites identified by screening in step (1) for a site where three or more single nucleotide polymorphisms are detected, as a site of somatic mutation; and (3) generating a cell lineage tree based on the nucleotide sequence information of the site of somatic mutation obtained in step (2).

The invention discloses a traceability analysis and multi-habitat homology evaluation method for antibiotic drug-resistant genes in an environmental sample, which is used for cross-habitat transmission and potential source identification of the drug-resistant genes. Comprising the following steps: 1) establishing a multivariate abundance matrix of antibiotic drug-resistant genes in environmental samples, constructing a drug-resistant gene traceability model by utilizing a machine learning algorithm, and accurately predicting potential contribution proportions of different habitats to a target habitat resistance group; and 2) aiming at the identified source habitat, reconstructing a bacterial genome through a genome assembly and binning technology, identifying homologous drug-resistant genes of the source-sink habitat by utilizing multi-sequence alignment and phylogenetic analysis, constructing a multi-medium transmission map of the drug-resistant genes and a transmission network between bacterial hosts, and clarifying connectivity and a transmission mechanism between habitats. According to the method, machine learning traceability and gene homology analysis are integrated, so that systematic evaluation of drug-resistant gene cross-habitat transmission is realized, and technical support is provided for pollution source identification and risk prevention and control of bacterial drug resistance.

To infer transmission links using within-host variation, Applicants first developed a statistical model of minor variant frequencies, which Applicants fit to a dataset of 134,682 SARS- CoV-2 genomes from Massachusetts, USA. Applicants then combined this model with a stochastic epidemic process to develop a hierarchical Bayesian statistical model of viral outbreaks. After validating the approach on both synthetic and real outbreak datasets, Applicants applied the tool to 5,692 outbreak clusters among the 134,682 Massachusetts genomes. Applicants found that informative sub-consensus variants are relatively rare in outbreaks, but that when they do occur, they significantly help resolve transmission networks. Applicants methods and results demonstrate the utility of within-host variation for transmission inference of SARS-CoV-2 and other pathogens, stressing the importance of pathogen sequencing in epidemiology and public health.

The application discloses a method for constructing a basic population library of crop domestication breeding by using natural populations. The first aspect of the application provides a method for screening a library construction species of a basic population library of crop domestication breeding, which comprises the following steps: obtaining a target species of a crop; performing phylogenetic analysis on the target species according to genomic markers; clustering the target species according to a result of the phylogenetic analysis by using morphological characteristics to obtain a plurality of groups; obtaining species information of parents of a hybrid species of the crop, and screening a group containing the parents of the hybrid species from the plurality of groups; and screening the group according to reproductive ecological characteristics to obtain the library construction species. In this way, a suitable library construction species is screened, and an original population is quickly and effectively constructed, so that the time for resource collection and selection of mating experiments is greatly shortened, and the manpower, material resources and time required for construction of the basic population library are reduced.

The invention relates to the technical field of biology, in particular to a high-activity S-sulfo-L-cysteine synthetase mutant and application thereof. The optimized SSC03 enzyme is screened through clustering analysis and phylogenetic analysis, mutation design is further performed on the optimized SSC03 enzyme, the conversion rate of the finally obtained SSC03-S256P delta CT after 24-hour reaction is 56%, 84 mM of S-sulfo-L-cysteine is generated, and it is indicated that the SSC03-S256P delta CT can be used for further purification process development.

The invention relates to an agropyron cristatum variety identification method based on chloroplast genome high-throughput sequencing, and belongs to the technical field of plant taxonomy, and the method comprises the following steps: (a) sample collection and DNA extraction; (b) library construction and sequencing; (c) data processing and chloroplast genome assembly; (d) genome annotation and feature analysis; (e) comparison and phylogenetic analysis; (f) variation identification and analysis; (g) comprehensive judgment: performing species identification on the wheatgrass sample according to the phylogenetic tree topological structure, the PCA clustering result and whether the specific marker exists or not; according to the method, the chloroplast genome high-throughput sequencing technology is utilized, the wheatgrass is subjected to variety identification from the molecular level, the variety of the wheatgrass sample can be rapidly and accurately identified, the method is not interfered by morphological variation, hybridization and other factors, the limitation of a traditional identification method is effectively solved, and the identification accuracy is improved.

The invention relates to Klebsormidum sp. GXU-A8 and application of the Klebsormidum sp. GXU-A8, and belongs to the technical field of microalgae. The invention provides krill GXU-A8, the classification name of the krill GXU-A8 is Klebsormidium sp. GXU-A8, the krill GXU-A8 is preserved in the China Center for Type Culture Collection on June 16, 2025, the preservation address is Wuhan University, Wuhan, China, and the preservation number is CCTCC NO: M 20251401. According to the invention, an alga is obtained by screening and culturing, the alga is Kribosome and named as Kribosome GXU-A8 through assembling, annotation and phylogenetic analysis on ribosome, chloroplast and mitochondrial genes of the alga, and experiments prove that the alga has the capability of resisting acidic, alkaline and high-salt environments, and can be used for preparing the Kribosome GXU-A8. The potential of repairing degraded soil and promoting crop growth is also realized.

This application relates to the field of agricultural microbiology, and in particular to a phosphorus-solubilizing and growth-promoting bacterial strain adapted to cold and arid environments and its application. The strain was isolated from soil in cold regions and identified as *Pantoea agglomerans* by 16S rDNA gene sequencing and phylogenetic analysis. It can grow in LB medium at 12°C, form visible colonies in LB solid medium containing 1200 mM mannitol, and exhibits phosphorus-solubilizing ability in NBRIP liquid medium. The strain is classified as *Pantoea agglomerans* ZSP3, with accession number CCTCC NO: M 20252438, deposited on November 3, 2025, at the China Center for Type Culture Collection. This application demonstrates the stable survival of Pantoea agglomerans strain isolated from soil in high-altitude and cold regions under the dual stress of low temperature and drought. This not only solves the problem of low colonization rate of strains under the dual stress of low temperature and drought, but also effectively improves the biomass and stress resistance of forage grasses in high-altitude and cold and arid environments by integrating phosphorus solubilization function and growth promotion mechanism.