14 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.

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 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 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.

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.

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.

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 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.