CN107451425A - A kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies - Google Patents

A kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies Download PDF

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Publication number
CN107451425A
CN107451425A CN201710720330.1A CN201710720330A CN107451425A CN 107451425 A CN107451425 A CN 107451425A CN 201710720330 A CN201710720330 A CN 201710720330A CN 107451425 A CN107451425 A CN 107451425A
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gene
function
bacterium
rrna
microorganism
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薛正晟
寇文伯
郭桐舟
姜丽荣
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SHANGHAI PERSONAL BIOTECHNOLOGY CO Ltd
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SHANGHAI PERSONAL BIOTECHNOLOGY CO Ltd
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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

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Abstract

A kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies disclosed by the invention, it is by the way that existing 16S rRNA gene sequencing data and microorganism reference gene group database known to metabolic function are compared, so as to realize the prediction to bacterium and ancient bacterium metabolic function；It is comprised the following steps that：(1) first infer that the gene function of their common ancestor is composed according to the 16S rRNA full length gene sequences of micrometer biological genome；(2) to other gene function spectrums for not surveying species are inferred in Greengenes databases, the Gene correlation spectrum of the ancient full pedigree in bacterium and bacterium domain is built；(3) obtained flora composition " mapping " will be sequenced into database, bacterial metabolism function is predicted.The present invention is by the way that existing 16SrRNA gene sequencing data and microorganism reference gene group database known to metabolic function are compared, so as to realize the prediction to bacterium and ancient bacterium metabolic function.

Description

A kind of bacterial metabolism function prediction analysis based on microorganism rRNA gene sequencing technologies Method
Technical field
The present invention relates to technical field of biological, more particularly to a kind of bacterium based on microorganism rRNA gene sequencing technologies Group's metabolic function prediction analysis method.
Background technology
The focal point of microorganism rRNA gene sequencing technologies is the Nomenclature Composition and Structure of Complexes of flora.But for microbial ecology For research, that most pays close attention to is undoubtedly flora possessed metabolic function., now can root with the development of data analysis technique According to known microbial genome data, to the sequencing data (typical such as the sequencing result of 16S rRNA genes) of flora composition The prediction of bacterial metabolism function is carried out, so as to which " identity " and their " function " of species is mapped.According to bacterial metabolism Function prediction result, on the one hand can one peep flora function spectrum general picture, play bacterial diversity composition spectrum sequencing it is cost-effective Advantage；Another aspect can also help to instruct the experimental design of follow-up grand genome De novo shotgun sequencings, more reasonably screen Sample for follow-up study.
The content of the invention
The technical problems to be solved by the invention are to provide a kind of flora based on microorganism rRNA gene sequencing technologies Metabolic function prediction analysis method.
The technical problems to be solved by the invention can be achieved through the following technical solutions：
A kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies, it is by by now Some 16S rRNA gene sequencing data compare with microorganism reference gene group database known to metabolic function, so as to realize Prediction to bacterium and ancient bacterium metabolic function；Comprise the following steps that：
(1) first infer their common ancestor's according to the 16S rRNA full length gene sequences of micrometer biological genome Gene function is composed；
(2) other gene function spectrums for not surveying species in Greengenes databases are inferred, builds ancient bacterium and thin The Gene correlation spectrum of the full pedigree in bacterium domain；
(3) obtained flora composition " mapping " will be sequenced into database, bacterial metabolism function is predicted.
In a preferred embodiment of the invention, the step (3) is realized especially by the following manner：
(3.1) the 16S rRNA gene orders obtained to sequencing, carry out " closed " with reference to OTU divisions (Closed- Reference OTU picking), by being compared with Greengenes databases, each sequencing sequence of searching " refers to sequence Row nearest-neighbors ", and be classified as referring to OTU；
(3.2) according to the rRNA gene copy numbers of " reference sequences nearest-neighbors ", school is carried out to the OTU abundance matrix of acquisition Just；
(3.3) the gene function modal data such as KEGG/EggNOG according to corresponding to " reference sequences nearest-neighbors ", conversion prediction The overall metabolic function of flora.
As a result of technical scheme as above, the present invention is by by existing 16S rRNA gene sequencing data and metabolism Microorganism reference gene group database compares known to function, so as to realize the prediction to bacterium and ancient bacterium metabolic function.This The difference of different plant species 16S rRNA gene copy numbers is also contemplated during the prediction of invention, and to the species in initial data Abundance data is corrected, and makes prediction result more accurately and reliably.
Embodiment
A kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies, it is by by now Some 16S rRNA gene sequencing data compare with microorganism reference gene group database known to metabolic function, so as to realize Prediction to bacterium and ancient bacterium metabolic function；Comprise the following steps that：
(1) first infer their common ancestor's according to the 16S rRNA full length gene sequences of micrometer biological genome Gene function is composed；
(2) other gene function spectrums for not surveying species in Greengenes databases are inferred, builds ancient bacterium and thin The Gene correlation spectrum of the full pedigree in bacterium domain；
(3) obtained flora composition " mapping " will be sequenced into database, bacterial metabolism function is predicted.
Above-mentioned steps (3) are realized especially by the following manner：
(3.1) the 16S rRNA gene orders obtained to sequencing, carry out " closed " with reference to OTU divisions (Closed- Reference OTU picking), by being compared with Greengenes databases, each sequencing sequence of searching " refers to sequence Row nearest-neighbors ", and be classified as referring to OTU；
(3.2) according to the rRNA gene copy numbers of " reference sequences nearest-neighbors ", school is carried out to the OTU abundance matrix of acquisition Just；
(3.3) the gene function modal data such as KEGG/EggNOG according to corresponding to " reference sequences nearest-neighbors ", conversion prediction The overall metabolic function of flora.

Claims (2)

1. a kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies, it is by will be existing 16S rRNA gene sequencing data compared with microorganism reference gene group database known to metabolic function, so as to realize pair Bacterium and the prediction of ancient bacterium metabolic function；Characterized in that, comprise the following steps that：
(1) the first 16S rRNA full length gene sequences according to micrometer biological genome, the gene of their common ancestor is inferred Function is composed；
(2) to other gene function spectrums for not surveying species are inferred in Greengenes databases, ancient bacterium and bacterium domain is built The Gene correlation spectrum of full pedigree；
(3) obtained flora composition " mapping " will be sequenced into database, bacterial metabolism function is predicted.
A kind of 2. bacterial metabolism function prediction analysis side based on microorganism rRNA gene sequencing technologies as claimed in claim 1 Method, it is characterised in that the step (3) is realized especially by the following manner：
(3.1) to sequencing obtain 16S rRNA gene orders, carry out it is " closed " with reference to OTU divide, by with Greengenes databases compare, and find " the reference sequences nearest-neighbors " of each sequencing sequence, and are classified as referring to OTU；
(3.2) according to the rRNA gene copy numbers of " reference sequences nearest-neighbors ", the OTU abundance matrix of acquisition is corrected；
(3.3) the gene function modal data such as KEGG/EggNOG according to corresponding to " reference sequences nearest-neighbors ", conversion prediction flora Overall metabolic function.
CN201710720330.1A 2017-08-21 2017-08-21 A kind of bacterial metabolism function prediction analysis method based on microorganism rRNA gene sequencing technologies Pending CN107451425A (en)

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112365932A (en) * 2020-10-19 2021-02-12 北京大学 Method for constructing bacterial community genome scale metabolic network
CN113403409A (en) * 2021-06-13 2021-09-17 中国疾病预防控制中心传染病预防控制所 Bacterial species level detection and analysis method based on bacterial 16S rRNA gene sequence

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
LDJ215323: "派森诺回馈新老用户助力国家自然科学基金撰写", 《HTTPS://MAX.BOOK118.COM/HTML/2017/0723/123844737.SHTM》 *
测序猫_PLTH1: "菌群代谢功能预测：宏基因组的一小步，多样性组成谱分析的一大步！", 《HTTPS://WWW.SOHU.COM/A/118675824_465237》 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112365932A (en) * 2020-10-19 2021-02-12 北京大学 Method for constructing bacterial community genome scale metabolic network
CN113403409A (en) * 2021-06-13 2021-09-17 中国疾病预防控制中心传染病预防控制所 Bacterial species level detection and analysis method based on bacterial 16S rRNA gene sequence

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