On the morning of February 5, 2019, the Shenzhen Huada team published the research results of the Human Intestinal Bacterial Genome Reference (CGR) in the natural biotechnology of the internationally renowned academic journals. The study provides more than 1,500 high-quality human intestinal bacterial genomes, providing a large number of new reference genomic data for gut microbiome research, and upgrading the functional analysis of gut microbiota to a new dimension, which is also the first time through large The technical means of scale cultivation yields such a large number of high quality bacterial genomic data. This human intestinal bacterial genome set and strain library, led by the metagenomics research team of Shenzhen Huada Life Science Research Institute, has important scientific research value for achieving accurate deciphering of the relationship between intestinal flora and disease. It provides valuable basic resources for the in-depth exploration of the function of human intestinal strains.
Anaerobic bacterial culture method: In the last month before sampling, collecting stool samples from 155 were not taking any medication healthy human donors. . The sample was immediately transferred to an anaerobic chamber (Bactron anaerobic chamber , Bactron IV-2, Shellab, USA) , homogenized in pre-reduced phosphate buffered saline (PBS) supplemented with 0.1% cysteine, and then diluted. Coated on agar plates containing different growth media (Supplementary Table 1). The plates were incubated for 2-3 days at 37 ° C under anaerobic conditions in an atmosphere of 90% N 2 , 5% CO 2 and 5% H 2 . Single colonies were picked and streaked onto new plates to obtain monoclonal. All strains were stored at -80 ° C in a suspension of glycerol (20%, v / v) containing 0.1% cysteine. The collection of 155 samples was approved by BGI's Bioethics and Biosafety Institutions Review Board, number: BGI-IRB17005-T1. All agreements are in accordance with the Helsinki Declaration and have the clear and informed consent of all participants. Bacteria in CGR (Cultivated Genomic Reference) are deposited in and available from E-BioBank (EBB) of the National Gene Bank of China.
Established human intestinal bacterial genome set in Huada for six years
In recent years, the study of intestinal flora has created a wave of enthusiasm, which has also driven the fiery development of the entire micro-ecological industry. In 2010, the human intestinal microbial reference gene set [1], which was led by Huada, opened a new direction for the study of intestinal flora. People began to explore the composition and function of human intestinal microbes from the genetic level. The study found that complex diseases such as metabolism, immunity, digestive system and nervous system are closely related to the intestinal flora, and confirmed the causal relationship between the microbial group and the occurrence and development of some diseases. With the continuous expansion and deepening of intestinal microbial research, it is increasingly important to study the interaction mechanism between high-quality reference genomes and living strains for diseases and intestinal flora. To further expand Enteric Bacilli and reference genomic library, 155 parts by researchers collected stool samples of healthy people, by (a Bactron anaerobic tank; Bactron IV-2 Shellab USA) operated cultured to obtain bacterial strains 6000 And selected more than 1,700 strains for genome-wide sequencing, and finally constructed 1520 high-quality gut bacterial genome sketches. Through the genus classification of species at the genomic level, a total of 338 Clusters (species group) were found, of which more than one-third were new species, covering the nine core genus of the Chinese [2]. At the same time, low abundance (< 1%) genus in 38 metagenomic analyses was found, enriching the diversity of existing gut microbial species and further broadening our understanding of gut microbes. In addition to providing a library of strains of human intestinal bacteria, genomic data has also been shown to improve the existing gut microbiome. Compared with the existing datasets, CGR has added a large amount of new data, which greatly enriches the existing reference genome data. For single-bacterial genomic and metagenomic analysis, the number of discoverable single nucleotide polymorphisms (SNPs) and new genes was significantly increased. At the functional level, the researchers analyzed the 9 types of KEGG basic functions of these strains and 7 types of beneficial and 2 types of potentially harmful related functional genes, systematically demonstrating the characteristics of these strains at the functional genomic level, and in-depth study of strain function. Comprehensive data support is provided for subsequent applications. In addition, the team also conducted a pan-genome analysis of 38 important intestinal bacteria, and found that the pan-genome of Bacteroides has a more open trend, and the actinomycete pan-genome is relatively closed. The functional pathways of these 38 kinds of bacteria were analyzed from the gene level. It was found that the butyric acid-producing pathway of beneficial bacteria such as E. faecalis and Escherichia coli existed in the core genome, indicating that the function of producing butyric acid was relatively conservative. Many other functions have also been found to have different distribution patterns in the core and non-core genomes. This also provides very important reference data for the screening and discovery of some potential probiotics. The large amount of strain resources and genomic data generated in the project are stored in the National Gene Bank Life Big Data Platform (CNGBdb), which provides global researchers with services such as group data storage, search, calculation, management, visualization, etc. For external sharing, researchers can apply for free.
The composition of human intestinal flora is greatly influenced by genetics and environment. The establishment of the gut bacterial genome dataset based on the Chinese population provides a powerful mechanism for the subsequent research and clinical application of microbial groups and complex diseases in the Chinese population. support. In particular, the diversified gut bacterial strains obtained in this study provide extremely valuable resources for the subsequent functional strain research and related scientific research transformation, and will further promote the development of related emerging industries based on human micro-ecological intervention.
Anaerobic bacterial culture method: In the last month before sampling, collecting stool samples from 155 were not taking any medication healthy human donors. . The sample was immediately transferred to an anaerobic chamber (Bactron anaerobic chamber , Bactron IV-2, Shellab, USA) , homogenized in pre-reduced phosphate buffered saline (PBS) supplemented with 0.1% cysteine, and then diluted. Coated on agar plates containing different growth media (Supplementary Table 1). The plates were incubated for 2-3 days at 37 ° C under anaerobic conditions in an atmosphere of 90% N 2 , 5% CO 2 and 5% H 2 . Single colonies were picked and streaked onto new plates to obtain monoclonal. All strains were stored at -80 ° C in a suspension of glycerol (20%, v / v) containing 0.1% cysteine. The collection of 155 samples was approved by BGI's Bioethics and Biosafety Institutions Review Board, number: BGI-IRB17005-T1. All agreements are in accordance with the Helsinki Declaration and have the clear and informed consent of all participants. Bacteria in CGR (Cultivated Genomic Reference) are deposited in and available from E-BioBank (EBB) of the National Gene Bank of China.
Established human intestinal bacterial genome set in Huada for six years
In recent years, the study of intestinal flora has created a wave of enthusiasm, which has also driven the fiery development of the entire micro-ecological industry. In 2010, the human intestinal microbial reference gene set [1], which was led by Huada, opened a new direction for the study of intestinal flora. People began to explore the composition and function of human intestinal microbes from the genetic level. The study found that complex diseases such as metabolism, immunity, digestive system and nervous system are closely related to the intestinal flora, and confirmed the causal relationship between the microbial group and the occurrence and development of some diseases. With the continuous expansion and deepening of intestinal microbial research, it is increasingly important to study the interaction mechanism between high-quality reference genomes and living strains for diseases and intestinal flora. To further expand Enteric Bacilli and reference genomic library, 155 parts by researchers collected stool samples of healthy people, by (a Bactron anaerobic tank; Bactron IV-2 Shellab USA) operated cultured to obtain bacterial strains 6000 And selected more than 1,700 strains for genome-wide sequencing, and finally constructed 1520 high-quality gut bacterial genome sketches. Through the genus classification of species at the genomic level, a total of 338 Clusters (species group) were found, of which more than one-third were new species, covering the nine core genus of the Chinese [2]. At the same time, low abundance (< 1%) genus in 38 metagenomic analyses was found, enriching the diversity of existing gut microbial species and further broadening our understanding of gut microbes. In addition to providing a library of strains of human intestinal bacteria, genomic data has also been shown to improve the existing gut microbiome. Compared with the existing datasets, CGR has added a large amount of new data, which greatly enriches the existing reference genome data. For single-bacterial genomic and metagenomic analysis, the number of discoverable single nucleotide polymorphisms (SNPs) and new genes was significantly increased. At the functional level, the researchers analyzed the 9 types of KEGG basic functions of these strains and 7 types of beneficial and 2 types of potentially harmful related functional genes, systematically demonstrating the characteristics of these strains at the functional genomic level, and in-depth study of strain function. Comprehensive data support is provided for subsequent applications. In addition, the team also conducted a pan-genome analysis of 38 important intestinal bacteria, and found that the pan-genome of Bacteroides has a more open trend, and the actinomycete pan-genome is relatively closed. The functional pathways of these 38 kinds of bacteria were analyzed from the gene level. It was found that the butyric acid-producing pathway of beneficial bacteria such as E. faecalis and Escherichia coli existed in the core genome, indicating that the function of producing butyric acid was relatively conservative. Many other functions have also been found to have different distribution patterns in the core and non-core genomes. This also provides very important reference data for the screening and discovery of some potential probiotics. The large amount of strain resources and genomic data generated in the project are stored in the National Gene Bank Life Big Data Platform (CNGBdb), which provides global researchers with services such as group data storage, search, calculation, management, visualization, etc. For external sharing, researchers can apply for free.
The composition of human intestinal flora is greatly influenced by genetics and environment. The establishment of the gut bacterial genome dataset based on the Chinese population provides a powerful mechanism for the subsequent research and clinical application of microbial groups and complex diseases in the Chinese population. support. In particular, the diversified gut bacterial strains obtained in this study provide extremely valuable resources for the subsequent functional strain research and related scientific research transformation, and will further promote the development of related emerging industries based on human micro-ecological intervention.
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