A set of microbial interaction network markers for screening disease-related bacterial flora and its application

An interactive network and marker technology, applied in the fields of bioinformatics and medical health, can solve problems such as the application limitations of microbial flora research, and achieve the effect of reliable technical support and rapid screening

Active Publication Date: 2021-12-17
KUNMING INST OF ZOOLOGY CHINESE ACAD OF SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Although network analysis has been widely used in computational biology and bioinformatics, such as gene network, protein network, metabolic network, etc., its application in the study of microbial flora is still relatively limited.

Method used

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  • A set of microbial interaction network markers for screening disease-related bacterial flora and its application
  • A set of microbial interaction network markers for screening disease-related bacterial flora and its application
  • A set of microbial interaction network markers for screening disease-related bacterial flora and its application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0019] Example 1: Comparing the number of special trios in the intestinal flora network of HIV positive and negative persons

[0020] The calculation process of the present invention is as accompanying drawing figure 1 shown

[0021] Data Sources:

[0022] In 2013, McHardy et al. published the microbial data of HIV-positive and negative individuals. The samples were collected from the intestinal mucosa of 20 HIV patients who had not received antiretroviral treatment and 20 healthy people. 16S rDNA fragments were amplified from the sample DNA using universal primers, sequenced using the Illumina HiSeq 2000 sequencing platform, and microbial operational taxonomic units (operational taxonomic units, OTUs) with 97% similarity were obtained through subsequent bioinformatics analysis, in which each An OTU represents a species, and the sequencing content of the OTU in each sample represents the species abundance of the OTU in the sample.

[0023] Construct the intestinal flora int...

Embodiment 2

[0030] Example 2: Comparing the number of special trios in the oral flora interaction network of smokers and non-smokers

[0031] The calculation process of the present invention is as accompanying drawing figure 1 shown

[0032] Data Sources:

[0033] Lazarevic et al published the oral saliva microbial data of smokers and non-smokers in 2010, and collected oral saliva samples of two non-smoking individuals and three smoking individuals at three time points within 29 days. The 16S rDNA fragment was amplified from the sample DNA using universal primers, and the sequence was sequenced on the Genome Sequencer FLX system, and the microbial operational taxonomic unit (OTU) with 97% similarity was obtained through subsequent bioinformatics analysis, in which each An OTU represents a species, and the sequencing content of the OTU in each sample represents the species abundance of the OTU in the sample.

[0034] Build an oral flora interaction network:

[0035] Based on the abundanc...

Embodiment 3

[0040] Example 3: Comparing the number of special trios in the skin flora interaction network of AD patients and healthy people

[0041] The calculation process of the present invention is as accompanying drawing figure 1 shown

[0042] Data Sources:

[0043] The skin microbiome data of AD patients and healthy people published by Kong et al. in 2012, samples were collected from the skin samples of 12 AD patients aged 2-15 years and 11 healthy people. 16SrDNA fragments were amplified from the sample DNA using universal primers. After sequencing, microbial operational taxonomic units (operational taxonomic unit, OTU) with 97% similarity were obtained through bioinformatics analysis. Each OTU represented a species, and each The sequence content of the OTU in a sample represents the species abundance of the OTU in the sample.

[0044] Build a skin flora interaction network:

[0045] Based on the abundance of OTUs, the Spearman correlation coefficient R between OTUs in the skin...

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Abstract

The invention discloses a set of flora interaction network markers capable of screening disease-related flora and uses thereof. The markers are composed of 15 special triangular interaction network motifs. The present invention takes the bacterial species composition of the flora and the relative abundance of each bacterial species as input, based on the flora interaction network and 15 special triangular interaction network motifs, the number of target markers obtained according to statistics and the relationship between the flora to be tested and The value ratio (RDHT) of the remaining target markers in the normal flora can be used to judge whether the flora to be tested is abnormal. The present invention has been verified by the microbial flora data of multiple groups of human body including intestinal tract, vagina, lung, oral cavity, semen and skin, and found that the number of special triangular interaction network motifs in the flora interaction network is higher than that of the experimental group / disease There are significant differences between the healthy control group and the healthy control group, and the invention can effectively and rapidly screen the healthy and diseased flora.

Description

technical field [0001] The invention relates to the fields of biological information technology and medical health, in particular to a set of bacterial flora interaction network markers capable of screening disease-related flora and a device for screening disease-related flora based on it. Background technique [0002] Human commensal bacteria are the normal flora of the human body, and a large number of microorganisms exist in the skin, oral cavity, intestinal tract, respiratory tract, and genitourinary tract. The human microbial flora is closely related to the health and disease of the host. At the same time, the health status of the human body also affects the composition and stability of the microbial flora. With the implementation of the Human Microbiome Project (HMP), more and more studies have shown that microbial flora is closely related to various human diseases, such as colon cancer, pulmonary fibrosis, periodontitis, mastitis, bacterial The occurrence and develop...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/689A61B5/00
CPCA61B5/00
Inventor 马占山
Owner KUNMING INST OF ZOOLOGY CHINESE ACAD OF SCI
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