CN109593865A - The analysis of marine coral Bacterial community, gene excavating method and equipment - Google Patents
The analysis of marine coral Bacterial community, gene excavating method and equipment Download PDFInfo
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Abstract
The embodiment of the invention provides a kind of analysis of marine coral Bacterial community, gene excavating method and equipment.Wherein, it clusters to obtain OTU table the described method includes: carrying out OTU to the 16S rRNA of marine coral flora sample, reject OTU unevenly distributed, marine coral flora sample is analyzed using QIIME2 analysis process, the classification results of marine coral flora are obtained, and obtain the composed structure and abundance of marine coral flora；The analysis of Core/Pan species is carried out to sorted marine coral flora, obtain the function that the bacterium in marine coral flora plays during forming marine coral homobium, and construct marine coral and bacterium relational network and marine coral development tree, the correlation between marine coral core bacterium and flora abundance is obtained, the flora gene with core ecological functions is excavated.The analysis of marine coral Bacterial community, gene excavating method and equipment provided in an embodiment of the present invention facilitate the diversity and distribution situation of studying marine coral flora species and gene comprehensively.
Description
Technical field
The present embodiments relate to marine coral flora microbe research technical field more particularly to a kind of marine coral bacterium
Group structure analysis, gene excavating method and equipment.
Background technique
Coral homobium is a kind of generally existing mode that coral and bacterial community combine, but its composition can be with the external world
The variation of environment and constantly change, the variation in ocean in different geographical locations or time scale may all drive specifically
Flora quickly breeds or gradually withers away, so that host be helped to settle down in new biology and abiotic system.Therefore, may be used
To infer the variation tendency of environment and the adaptation process of host according to the variation of coral flora.In coral reef ecologic system
In, certain specific bacteriums and its group may be crucial in living body functional and dynamics of ecosystem, these are thin
Close connection and interaction mechanism between bacterium are not yet found, and specific bacterial symbiont is in entire coral reef ecologic system
Done in go out contribution be not mined out yet.In order to excavate the specific bacteria for assisting host to play certain basic functions, in addition to
It probes into except the composition of different coral species symbiosis floras, it will also be in conjunction with geographical, time and spatial stability and dynamic changeability
The fungal component group that different coral ecological environments are in analyze identical coral species forms, and this requires us not only to consider coral
Chemistry, physics and the biology fluctuating factor (such as PH, temperature, depth, nutrient content) of coral surrounding seawater, also by coral
Some biological differences (between such as species or in species space resource contention, health status etc.) of coral itself are taken into account, this
A little factors can all lead to the variability of coral flora.
On the other hand, due to mankind's activities such as Global climate change, seawater eutrophication, acidification, overfishing and divings
Coral quantity is resulted in constantly to decline.In face of worsening environment, coral reef infection coral pandemic reached it is preceding not
Some speed results in the coral-bacterial symbiont for originally being difficult to classify by extraneous natural environment influence and becomes more complicated.
Since coral microbial population is huge, tradition is separately cultured the coral microorganism that technical research obtains classifying annotated to be had very much
Limit so that understand bacterial community in terms of the functional importance of coral bacteria paragenesis relationship and exist substantive knowledge blank and
Challenge.Therefore, finding one kind can be to avoid can be only applied to the drawbacks of can cultivating group's component, and probing into influences Bacterial community and function
The central factor of energy finds out molecule to the mechanism to interact between cell or even population inside, and excavating has important ecology
The microorganism of the ecological significance of meaning facilitates the diversity and distribution situation of studying marine coral flora species and gene comprehensively
Method, just become industry extensive concern the problem of.
Summary of the invention
In view of the above-mentioned problems existing in the prior art, the embodiment of the invention provides a kind of marine coral Bacterial communities point
Analysis, gene excavating method and equipment.
In a first aspect, the embodiment provides a kind of analysis of marine coral Bacterial community, gene excavating method, packet
It includes: obtaining the 16S rRNA of marine coral flora sample, OTU is carried out to the 16S rRNA and clusters to obtain OTU table, described in rejecting
OTU unevenly distributed in OTU table, using QIIME2 analysis process to the marine coral bacterium after rejecting OTU unevenly distributed
Group's sample is analyzed, and the classification results of marine coral flora are obtained, and according to the classification results, obtains marine coral flora
Composed structure and abundance；The analysis of Core/Pan species is carried out to sorted marine coral flora, is obtained in marine coral flora
The function that is played during forming marine coral homobium of bacterium, and construct marine coral and bacterium relational network and ocean
Coral development tree, obtains the correlation between marine coral core bacterium and flora abundance, in conjunction in the marine coral flora
The function that is played during forming marine coral homobium of bacterium, excavate the flora gene with core ecological functions.
Further, the 16S rRNA for obtaining marine coral flora sample, comprising: obtain to come from ncbi database
From the 16S rRNA of the marine coral flora sample of ten disparity items.
Further, described that 16S rRNA progress OTU is clustered to obtain OTU table, comprising: to use Parallel-
16S rRNA is clustered into 6,6183 OTU according to 97% similitude by META3 analysis method, with Greengenes reference data
Library, which compares, carries out primary filtration, by Bacteria identification to door, guiding principle, mesh, section and belongs in taxology level, obtains the OTU table.
Further, described to reject OTU unevenly distributed in the OTU table, comprising: to be picked out using R software described
The OTU unevenly distributed occurred during Parallel-META3 analysis method.
Further, the marine coral flora after the OTU unevenly distributed to rejecting using QIIME2 analysis process
Sample is analyzed, and the classification results of marine coral flora are obtained, comprising: calls the type in QIIME2
Marine coral flora sample format is turned to qza or qzv format by EMPSingleEndSequences order, and production includes ocean
The csv sample file format inventory of coral flora sample names, the absolute path of sequence and sequence direction, using " qiime
The marine coral flora sample of formatting is carried out preliminary mistake according to mass fraction by quality-filter q-score " order
Filter；P-trim-left is removed by edge low mass region using p-trunc-len, and generates Feature table；By the Feature
Table and Greengenes reference database, Silva integrated database and Unite comparison data library are compared, and call QIIME2
In qiime feature-classifier classify-sklearn order carry out species taxonomy, obtain marine coral bacterium
The classification results of group.
Further, described according to the classification results, obtain the composed structure and abundance of marine coral flora, comprising:
According to the classification results, hypervariable region is removed, using qiime phylogeny midpoint-root order by qiime
The unrooted chadogram that phylogeny fasttree order obtains has been converted into root chadogram, and using minimum data amount as taking out again
Sample depth, primary axis analysis geographical location, the ecological position of sampling, marine coral based on Unweighted Unifrac are good for
The influence of health situation and marine coral species to marine coral flora composed structure, obtain marine coral flora composed structure and
Abundance.
Further, the building marine coral and bacterium relational network, comprising: according to the bacterial system of any two section
The Pearson correlation of type, using Cytoscape software building marine coral and bacterium relational network.
Second aspect, the embodiment provides a kind of analysis of marine coral Bacterial community, gene excavating device, packets
It includes:
The composed structure and abundance of marine coral flora obtain module, for obtaining the 16S of marine coral flora sample
RRNA carries out OTU to the 16S rRNA and clusters to obtain OTU table, reject OTU unevenly distributed in the OTU table, uses
QIIME2 analysis process analyzes the marine coral flora sample after rejecting OTU unevenly distributed, obtains marine coral
The classification results of flora obtain the composed structure and abundance of marine coral flora according to the classification results；
The flora gene excavating module of core ecological functions, for carrying out Core/Pan to sorted marine coral flora
Species analysis obtains the function that the bacterium in marine coral flora plays during forming marine coral homobium, and constructs
Marine coral and the development of bacterium relational network and marine coral are set, and the phase between marine coral core bacterium and flora abundance is obtained
Guan Xing excavates tool in conjunction with the function that the bacterium in the marine coral flora plays during forming marine coral homobium
There is the flora gene of core ecological functions.
The third aspect, the embodiment provides a kind of electronic equipment, comprising:
At least one processor；And
At least one processor being connect with processor communication, in which:
Memory is stored with the program instruction that can be executed by processor, and the instruction of processor caller is able to carry out first party
The analysis of marine coral Bacterial community provided by any possible implementation, gene in the various possible implementations in face
Method for digging.
Fourth aspect, the embodiment provides a kind of non-transient computer readable storage medium, non-transient calculating
Machine readable storage medium storing program for executing stores computer instruction, and computer instruction makes the various possible realization sides of computer execution first aspect
The analysis of marine coral Bacterial community provided by any possible implementation, gene excavating method in formula.
The analysis of marine coral Bacterial community, gene excavating method and equipment provided in an embodiment of the present invention, pass through ocean coral
The 16S rRNA of coral flora sample obtains corresponding OTU table, is analyzed using QIIME2 analysis process marine coral sample,
And the analysis of Core/Pan species is carried out to sorted marine coral flora, it can be to avoid can be only applied in the prior art can
The drawbacks of cultivating group's component facilitates the diversity and distribution situation of studying marine coral flora species and gene comprehensively.
Detailed description of the invention
In order to more clearly explain the embodiment of the invention or the technical proposal in the existing technology, to embodiment or will show below
There is attached drawing needed in technical description to be briefly described, it should be apparent that, the accompanying drawings in the following description is this hair
Bright some embodiments for those of ordinary skill in the art without creative efforts, can be with root
Other attached drawings are obtained according to these attached drawings.
Fig. 1 is marine coral Bacterial community provided in an embodiment of the present invention analysis, gene excavating method flow chart；
Fig. 2 is marine coral Bacterial community provided in an embodiment of the present invention analysis, gene excavating apparatus structure schematic diagram；
Fig. 3 is the entity structure schematic diagram of electronic equipment provided in an embodiment of the present invention.
Specific embodiment
In order to make the object, technical scheme and advantages of the embodiment of the invention clearer, below in conjunction with the embodiment of the present invention
In attached drawing, technical scheme in the embodiment of the invention is clearly and completely described, it is clear that described embodiment is
A part of the embodiment of the present invention, instead of all the embodiments.Based on the embodiments of the present invention, those of ordinary skill in the art
Every other embodiment obtained without making creative work, shall fall within the protection scope of the present invention.In addition,
Technical characteristic in each embodiment or single embodiment provided by the invention can mutual any combination, to form feasible skill
Art scheme, but must be based on can be realized by those of ordinary skill in the art, when the combination of technical solution occur it is mutual
Contradiction or when cannot achieve, it will be understood that the combination of this technical solution is not present, also not the present invention claims protection scope
Within.
The embodiment of the invention provides a kind of analyses of marine coral Bacterial community, gene excavating method, referring to Fig. 1, the party
Method includes:
101, the 16S rRNA for obtaining marine coral flora sample carries out OTU to the 16S rRNA and clusters to obtain OTU
Table rejects OTU unevenly distributed in the OTU table, after QIIME2 analysis process OTU unevenly distributed to rejecting
Marine coral flora sample is analyzed, and the classification results of marine coral flora are obtained, and according to the classification results, obtains ocean
The composed structure and abundance of coral flora；
102, the analysis of Core/Pan species is carried out to sorted marine coral flora, obtained thin in marine coral flora
The function that bacterium plays during forming marine coral homobium, and construct marine coral and bacterium relational network and marine coral
Development tree, obtains the correlation between marine coral core bacterium and flora abundance, in conjunction with thin in the marine coral flora
The function that bacterium plays during forming marine coral homobium excavates the flora gene with core ecological functions.
Marine coral Bacterial community provided in an embodiment of the present invention analysis, gene excavating method, pass through marine coral flora
The 16S rRNA of sample obtains corresponding OTU table, is analyzed using QIIME2 analysis process marine coral sample, and to point
Marine coral flora after class carries out the analysis of Core/Pan species, can be to avoid can be only applied to that group can be cultivated in the prior art
The drawbacks of falling component facilitates the diversity and distribution situation of studying marine coral flora species and gene comprehensively.
On the basis of the above embodiments, the analysis of marine coral Bacterial community, the gene digging provided in the embodiment of the present invention
Pick method, the 16S rRNA for obtaining marine coral flora sample, comprising: obtained from ncbi database and come from ten differences
The 16S rRNA of the marine coral flora sample of project.
On the basis of the above embodiments, the analysis of marine coral Bacterial community, the gene digging provided in the embodiment of the present invention
Pick method, it is described that 16S rRNA progress OTU is clustered to obtain OTU table, comprising: to use Parallel-META3 analysis method
16S rRNA is clustered into 6,6183 OTU according to 97% similitude, compares progress just with Greengenes reference database
Step filtering by Bacteria identification to door, guiding principle, mesh, section and belongs in taxology level, obtains the OTU table.
On the basis of the above embodiments, the analysis of marine coral Bacterial community, the gene digging provided in the embodiment of the present invention
Pick method, it is described to reject OTU unevenly distributed in the OTU table, comprising: the Parallel- is picked out using R software
The OTU unevenly distributed occurred during META3 analysis method.
On the basis of the above embodiments, the analysis of marine coral Bacterial community, the gene digging provided in the embodiment of the present invention
Pick method, it is described that the marine coral flora sample after rejecting OTU unevenly distributed is divided using QIIME2 analysis process
Analysis obtains the classification results of marine coral flora, comprising:
Call the type EMPSingleEndSequences order in QIIME2 by marine coral flora sample format
For qza or qzv format, production includes the csv sample of marine coral flora sample names, the absolute path of sequence and sequence direction
File format inventory is ordered using " qiime quality-filter q-score " by the marine coral flora sample of formatting
Primary filtration is carried out according to mass fraction；P-trim-left is removed by edge low mass region using p-trunc-len, and is generated
Feature table；
By the Feature table and Greengenes reference database, Silva integrated database and Unite comparison data
Library is compared, and the qiime feature-classifier classify-sklearn order in QIIME2 is called to carry out object
Kind classification, obtains the classification results of marine coral flora.Execute qiime metadata tabulate and qiime taxa
Barplot order visualizes classification results.
Wherein, the more common chimera that carries out after 16S rRNA gene high-flux sequence of the Greengenes database is gone
The reference data library removed.The Silva database is the reference database most often selected after current rRNA gene high-flux sequence
One of.The Unite database is commonly used for carrying out fungi after ITS sequence high-flux sequence the comparison data of classification annotation
Library.
On the basis of the above embodiments, the analysis of marine coral Bacterial community, the gene digging provided in the embodiment of the present invention
Pick method, it is described according to the classification results, obtain the composed structure and abundance of marine coral flora, comprising: according to described point
Class is as a result, hypervariable region is removed, using qiime phylogeny midpoint-root order by qiime phylogeny
The unrooted chadogram that fasttree order obtains has been converted into root chadogram, and using minimum data amount as double sampling depth, base
In Unweighted Unifrac primary axis analysis geographical location, sample ecological position, marine coral health status and
Influence of the marine coral species to marine coral flora composed structure obtains the composed structure and abundance of marine coral flora.
On the basis of the above embodiments, the analysis of marine coral Bacterial community, the gene digging provided in the embodiment of the present invention
Pick method, the building marine coral and bacterium relational network, comprising: according to the bacterial system type of any two section
Pearson correlation, using Cytoscape software building marine coral and bacterium relational network.
It is below that the technology of foregoing individual embodiments of the present invention is special for the presentation being more clear Spirit Essence of the invention
Sign carries out selection combination, a comprehensive embodiment is provided, to be further elaborated to Spirit Essence of the invention.It needs to illustrate
, which is only to help to more fully understand technological essence of the invention, does not represent the present invention and is limited in the reality
Within the scope for applying the technical solution of example.
By taking the coral species of 10 disparity items in ncbi database and Seawater Samples as an example:
1) 528 samples from 10 disparity items are had collected from ncbi database first (comprising 13 differences
Coral species and some regions Seawater Samples, 12 areas can be divided into according to geographical location) 16S rRNA data such as
The essential information of all samples of table 1.
Table 1
2) 16S rRNA sequence is clustered into 6,6183 OTU according to 97% similitude, with Greengenes reference number
It compares, by Bacteria identification to door, guiding principle, mesh, section, belongs in taxology level, and by various floras in each categorization levels according to library
Relative abundance visualizes (44 horizontal species of different mesh).
3) OTU unevenly distributed in all samples of above-mentioned analysis is picked out first with R software, and called
In QIIME2 -- type EMPSingleEndSequences order (will select remaining sample), and standard data format is
Qza qzv format, while making the csv sample arranged including absolute path, sequence direction three where sample ID, sequence
Product file format inventory；Secondly, using qiime quality-filter q-score order by standardized data according to matter
It measures score and primary filtration is carried out to sequence, then, -- p-trunc-len will -- p-trim-left is used to remove edge low mass region
Sequence be cut into certain length segment generate Feature table；Later, the hypervariable region in Feature table is removed, qiime is utilized
Qiime phylogeny fasttree order is obtained unrooted chadogram and is converted by phylogeny midpoint-root order
Rooted tree, and using minimum data amount as double sampling depth, the primary axis analysis based on Unweighted Unifrac is all
Sample geographical location and species and are sampled into ecological positional factor combination of two at geographical location, while disease coral will be contained
The data (be shown in Table 2 pairs of coral symbiosis floras and carry out control variable analysis) of two projects of sample are picked out and are individually analyzed,
To determine structure of the health status to marine coral flora of diverse geographic location, species, the ecological position of sampling and coral itself
With the influence of composition, and the conversion and distribution situation of coral species under each factor are analyzed.
Table 2 (★ indicates variable)
4) by Feature list file and Greengenes the reference database of archaeal 16S rRNA gene (bacterium),
Silva (integrated database of 16S rRNA and 18S rRNA gene order) and Unite are (to true after ITS sequence high-flux sequence
Bacterium carries out the comparison data library of classification annotation) database is compared, call the qiime feature- in QIIME2
Classifier classify-sklearn order carries out species taxonomy according to annotation information, obtains species taxonomy file, executes
Qiime metadata tabulate and qiime taxa barplot order visualizes classification results.
5) it finds even to say between two samples firstly, carrying out the analysis of Core/Pan species to sorted all species
The OTU quantity of pan coral microorganism does not all change significantly between all samples, and when considering each sample one by one, Core
Significant change can occur for the quantity of species OTU, therefore Core species OTU is probed into each coral society as the method for distinguishing sample
It potentially interacts between area；
Secondly, removing all Seawater Samples (obtaining 474 samples) to 6,6183 OTU's in entire coral group
Core bacterium carry out Taxonomic analysis, discovery be more than 50% corallite in contain only 66 kinds of bacterial system types, wherein belonging to
The Hah Endozoicomonas of Hahellaceae section and ocean spirillum mesh (Oceanospirillales) are all coral reefs
It is most common in system to belong to horizontal bacterial community.It is all made of it more than 90% sample, as a kind of aerobic-type marine bacteria, energy
Enough degradation organic compounds, are metabolized dimethyl thio propionate, are able to carry out photosynthetic algae to colonize in coral
Sulfur cycle provide precursor；Other be more than 80% corallite in all existing bacterial community include Rho
Rhodobacteraceae Group, Pel Pelagibacteraceae Group, Pse Pseudomonas and Pse
Pseudoalteromonas.In addition, analyzing the symbiotic bacteria group in all groupings, one shares the careful bacterium of 125 seed nucleus
Flora is although important but does not carry out taxology identification also, can not know specific species information, and some bacteria abundances compared with
It is low to be found.
Later, according to the Pearson correlation of the bacterial system type of any two section level in Cytoscape software structure
It builds coral-bacterium and occurs network (entirely occurring network altogether to be made of 97 nodes and 684 sides) altogether, wherein
Procabacteriaceae, Bartonellaceae, Dermabacteraceae, Sneathiellaceae and OM60 are that occur
The highest 5 kinds of bacterial system types of frequency, followed by Methylococcaceae (Methylococcaceae), Ulvophyceae,
Chitinophagaceae, Parvularculaceae and Saprospiraceae, and the higher overwhelming majority of the frequency of occurrences
Species always belong to the lower system type of abundance.
Then there are correlation, discoveries between phylogenetic tree construction analysis coral core bacterium and bacterial community richness
There are 50 system types in 80% or more sample, and 21 germlines in the 99 horizontal systematic bacteriologies of section detected
System type is present in 80% or more sample, and the bacterial community of these high abundances always existed of deducibility is in host's physiology accordingly
Play an important role (such as Hahellaceae and Rhodobacteraceae) in, while there is also some low-abundance systems
Type is accredited as generally existing coral symbiotic microorganism group, such as Piscirickettsiaceae, Moraxellaceae and
Halomonadaceae.Wherein, Moraxellaceae belongs to pseudomonad guiding principle, and Gammaproteobacteria section is distributed in
Various natural habitats play an important role in various ecologies and clinical process；Halomonadaceae is considered as coral
" resident ", i.e., all there is this kind of flora in most of coral, some functional enzymes can be generated to decompose two in coral tissue
Methylpropanethioate and acrylate.Also have other compared with high abundance there may be the bacterial system types of function assessment meaning, but
It is to only occur under specific geographical conditions (such as Synechococcus section (Synechococcaceae), screw rod Cordycepps
(Helicobacteraceae) and wart germ section (Verrucomicrobiacea)), show the symbiotic bacteria group of individual corals
Only occur in specific geographical location, illustrates that coral microorganism and host colony have certain relevance again.
Finally, analyzing the bacterial community relative abundance between different coral types and seawater, 15 kinds of coral species packets are found
Containing the biggish symbiotic bacteria group of these correlations, some of abundance are higher and the micropopulation that is present in most of corals
Can tend to there are in some specific coral symbiosis floras (such as Rhodobacteraceae, Rhodospirillaceae and
Flavobacteriaceae).Some coral species are mainly several by Acropora cervicomis and A.hyacinthus etc.
Section's composition, and the relative abundance of Vibrionaceae obviously increases in Eunicella.Verrucosay coral species.This
Outside, Pelagibacteraceae exists in most of Seawater Samples.
The optimized integration of each embodiment of the present invention is the processing that sequencing is carried out by the equipment with processor function
It realizes.Therefore engineering in practice, can be by the technical solution of each embodiment of the present invention and its function package at various moulds
Block.Based on this reality, on the basis of the various embodiments described above, the embodiment provides a kind of marine coral bacterium
Group structure analysis, gene excavating device, the device be used for execute in above method embodiment marine coral Bacterial community analysis,
Gene excavating method.Referring to fig. 2, which includes:
The composed structure and abundance of marine coral flora obtain module 201, for obtaining the 16S of marine coral flora sample
RRNA carries out OTU to the 16S rRNA and clusters to obtain OTU table, reject OTU unevenly distributed in the OTU table, uses
QIIME2 analysis process analyzes the marine coral flora sample after rejecting OTU unevenly distributed, obtains marine coral
The classification results of flora obtain the composed structure and abundance of marine coral flora according to the classification results；
The flora gene excavating module 202 of core ecological functions, for carrying out Core/ to sorted marine coral flora
The analysis of Pan species obtains the function that the bacterium in marine coral flora plays during forming marine coral homobium, and structure
It builds marine coral and bacterium relational network and marine coral development is set, obtain between marine coral core bacterium and flora abundance
Correlation is excavated in conjunction with the function that the bacterium in the marine coral flora plays during forming marine coral homobium
Flora gene with core ecological functions.
Marine coral Bacterial community provided in an embodiment of the present invention analysis, gene excavating device, using marine coral flora
Composed structure and abundance obtain the flora gene excavating modules of module and core ecological functions, pass through marine coral flora sample
16S rRNA obtain corresponding OTU table, marine coral sample is analyzed using QIIME2 analysis process, and to classification after
Marine coral flora carry out the analysis of Core/Pan species, can be to avoid can be only applied to that group's group can be cultivated in the prior art
Facilitate the diversity and distribution situation of studying marine coral flora species and gene comprehensively the drawbacks of dividing.
The method of the embodiment of the present invention is to rely on electronic equipment to realize, therefore it is necessary to do one to relevant electronic equipment
Lower introduction.Based on this purpose, the embodiment provides a kind of electronic equipment, as shown in figure 3, the electronic equipment includes:
At least one processor (processor) 301, communication interface (Communications Interface) 304, at least one deposits
Reservoir (memory) 302 and communication bus 303, wherein at least one processor 301, communication interface 304, at least one storage
Device 302 completes mutual communication by communication bus 303.At least one processor 301 can call at least one processor
Logical order in 302, to execute following method: the 16S rRNA of marine coral flora sample is obtained, to the 16S rRNA
It carries out OTU to cluster to obtain OTU table, OTU unevenly distributed in the OTU table is rejected, using QIIME2 analysis process to rejecting
Marine coral flora sample after OTU unevenly distributed is analyzed, and the classification results of marine coral flora is obtained, according to institute
Classification results are stated, the composed structure and abundance of marine coral flora are obtained；Core/ is carried out to sorted marine coral flora
The analysis of Pan species obtains the function that the bacterium in marine coral flora plays during forming marine coral homobium, and structure
It builds marine coral and bacterium relational network and marine coral development is set, obtain between marine coral core bacterium and flora abundance
Correlation is excavated in conjunction with the function that the bacterium in the marine coral flora plays during forming marine coral homobium
Flora gene with core ecological functions.
In addition, the logical order in above-mentioned at least one processor 302 can be real by way of SFU software functional unit
Now and when sold or used as an independent product, it can store in a computer readable storage medium.Based in this way
Understanding, the technical solution of the present invention substantially portion of the part that contributes to existing technology or the technical solution in other words
Dividing can be embodied in the form of software products, which is stored in a storage medium, including several
Instruction is used so that a computer equipment (can be personal computer, server or the network equipment etc.) executes the present invention
The all or part of the steps of each embodiment the method.For example, the 16SrRNA of marine coral flora sample is obtained, it is right
The 16S rRNA carries out OTU and clusters to obtain OTU table, rejects OTU unevenly distributed in the OTU table, using QIIME2 points
Analysis process analyzes the marine coral flora sample after rejecting OTU unevenly distributed, obtains point of marine coral flora
Class obtains the composed structure and abundance of marine coral flora as a result, according to the classification results；To sorted marine coral bacterium
Group carries out the analysis of Core/Pan species, and the bacterium obtained in marine coral flora plays during forming marine coral homobium
Function, and construct marine coral and bacterium relational network and marine coral development is set, obtain marine coral core bacterium and bacterium
Correlation between group's abundance, plays during forming marine coral homobium in conjunction with the bacterium in the marine coral flora
Function, excavate have core ecological functions flora gene.And storage medium above-mentioned include: USB flash disk, it is mobile hard disk, read-only
Memory (ROM, Read-Only Memory), random access memory (RAM, Random Access Memory), magnetic disk or
The various media that can store program code such as person's CD.
The apparatus embodiments described above are merely exemplary, wherein described, unit can as illustrated by the separation member
It is physically separated with being or may not be, component shown as a unit may or may not be physics list
Member, it can it is in one place, or may be distributed over multiple network units.It can be selected according to the actual needs
In some or all of the modules achieve the purpose of the solution of this embodiment.Those of ordinary skill in the art are not paying creativeness
Labour in the case where, it can understand and implement.
Through the above description of the embodiments, those skilled in the art can be understood that each embodiment can
It realizes by means of software and necessary general hardware platform, naturally it is also possible to pass through hardware.Based on this understanding, on
Stating technical solution, substantially the part that contributes to existing technology can be embodied in the form of software products in other words, should
Computer software product may be stored in a computer readable storage medium, such as ROM/RAM, magnetic disk, CD, including several fingers
It enables and using so that a computer equipment (can be personal computer, server or the network equipment etc.) executes each implementation
Method described in certain parts of example or embodiment.
Finally, it should be noted that the above embodiments are merely illustrative of the technical solutions of the present invention, rather than its limitations；Although
Present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that: it still may be used
To modify the technical solutions described in the foregoing embodiments or equivalent replacement of some of the technical features；
And these are modified or replaceed, technical solution of various embodiments of the present invention that it does not separate the essence of the corresponding technical solution spirit and
Range.
Claims (10)
1. a kind of marine coral Bacterial community analysis, gene excavating method characterized by comprising
The 16S rRNA for obtaining marine coral flora sample carries out OTU to the 16S rRNA and clusters to obtain OTU table, rejects institute
OTU unevenly distributed in OTU table is stated, using QIIME2 analysis process to the marine coral after rejecting OTU unevenly distributed
Flora sample is analyzed, and the classification results of marine coral flora are obtained, and according to the classification results, obtains marine coral flora
Composed structure and abundance；
The analysis of Core/Pan species is carried out to sorted marine coral flora, the bacterium obtained in marine coral flora is being formed
The function of being played during marine coral homobium, and marine coral and bacterium relational network and marine coral development tree are constructed,
The correlation between marine coral core bacterium and flora abundance is obtained, is being formed in conjunction with the bacterium in the marine coral flora
The function of playing during marine coral homobium excavates the flora gene with core ecological functions.
2. marine coral Bacterial community analysis according to claim 1, gene excavating method, which is characterized in that described to obtain
Take the 16S rRNA of marine coral flora sample, comprising:
The 16S rRNA of the marine coral flora sample from ten disparity items is obtained from ncbi database.
3. marine coral Bacterial community analysis according to claim 1, gene excavating method, which is characterized in that described right
The 16S rRNA carries out OTU and clusters to obtain OTU table, comprising:
16S rRNA is clustered into according to 97% similitude by 6,6183 OTU using Parallel-META3 analysis method, with
Greengenes reference database, which compares, carries out primary filtration, by Bacteria identification to door, guiding principle, mesh, section and belongs in taxology level,
Obtain the OTU table.
4. marine coral Bacterial community analysis according to claim 2, gene excavating method, which is characterized in that described to pick
Except OTU unevenly distributed in the OTU table, comprising:
The OTU unevenly distributed occurred during the Parallel-META3 analysis method is picked out using R software.
5. marine coral Bacterial community analysis according to claim 1, gene excavating method, which is characterized in that described to adopt
The marine coral flora sample after rejecting OTU unevenly distributed is analyzed with QIIME2 analysis process, obtains ocean coral
The classification results of coral flora, comprising:
Call the type EMPSingleEndSequences order in QIIME2 that marine coral flora sample format is turned to qza
Or qzv format, production include the csv sample file of marine coral flora sample names, the absolute path of sequence and sequence direction
Format inventory, using " qiime quality-filterq-score " order by the marine coral flora sample of formatting according to
Mass fraction carries out primary filtration；P-trim-left is removed by edge low mass region using p-trunc-len, and is generated
Feature table；
By the Feature table and Greengenes reference database, Silva integrated database and Unite comparison data library into
Row compares, and the qiime feature-classifier classify-sklearn order in QIIME2 is called to carry out species point
Class obtains the classification results of marine coral flora.
6. marine coral Bacterial community analysis according to claim 1, gene excavating method, which is characterized in that described
According to the classification results, the composed structure and abundance of marine coral flora are obtained, comprising:
According to the classification results, hypervariable region is removed, it will using qiime phylogeny midpoint-root order
The unrooted chadogram that qiime phylogeny fasttree order obtains has been converted into root chadogram, and minimum data amount is made
For double sampling depth, primary axis analysis geographical location, sampling ecological position, ocean coral based on Unweighted Unifrac
Influence of the health status and marine coral species of coral to marine coral flora composed structure obtains the composition of marine coral flora
Structure and abundance.
7. marine coral Bacterial community analysis according to claim 3, gene excavating method, which is characterized in that the structure
Build marine coral and bacterium relational network, comprising:
According to the Pearson correlation of the bacterial system type of any two section, using Cytoscape software building marine coral with
Bacterium relational network.
8. a kind of marine coral Bacterial community analysis, gene excavating device characterized by comprising
The composed structure and abundance of marine coral flora obtain module, for obtaining the 16S rRNA of marine coral flora sample,
OTU is carried out to the 16S rRNA to cluster to obtain OTU table, OTU unevenly distributed in the OTU table is rejected, using QIIME2
Analysis process analyzes the marine coral flora sample after rejecting OTU unevenly distributed, obtains marine coral flora
Classification results obtain the composed structure and abundance of marine coral flora according to the classification results；
The flora gene excavating module of core ecological functions, for carrying out Core/Pan species to sorted marine coral flora
Analysis obtains the function that the bacterium in marine coral flora plays during forming marine coral homobium, and constructs ocean
Coral and the development of bacterium relational network and marine coral are set, and are obtained related between marine coral core bacterium and flora abundance
Property, in conjunction with the function that the bacterium in the marine coral flora plays during forming marine coral homobium, excavation has
The flora gene of core ecological functions.
9. a kind of electronic equipment characterized by comprising
At least one processor, at least one processor, communication interface and bus；Wherein,
The processor, memory, communication interface complete mutual communication by the bus；
The memory is stored with the program instruction that can be executed by the processor, and the processor calls described program instruction,
To execute method as described in any one of claim 1 to 7.
10. a kind of non-transient computer readable storage medium, which is characterized in that the non-transient computer readable storage medium is deposited
Computer instruction is stored up, the computer instruction makes the computer execute the method as described in any one of claims 1 to 7.
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110444254A (en) * | 2019-07-08 | 2019-11-12 | 深圳先进技术研究院 | A kind of detection method, detection system and the terminal of flora marker |
| CN114093411A (en) * | 2021-11-29 | 2022-02-25 | 中国人民解放军总医院 | Method and equipment for analyzing evolutionary relationship and abundance information of microbial population based on sample |
Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104715165A (en) * | 2014-12-19 | 2015-06-17 | 中国石油天然气集团公司 | Petroleum pollution marine ecological environment evaluation method based on metagenome technology |
| CA3002110A1 (en) * | 2015-10-16 | 2017-04-20 | Genome Research Limited | Methods associated with a database that stores a plurality of reference genomes |
| WO2017096385A1 (en) * | 2015-12-04 | 2017-06-08 | Biome Makers Inc. | Microbiome based identification, monitoring and enhancement of fermentation processes and products |
| CN108486238A (en) * | 2018-04-10 | 2018-09-04 | 南京大学 | A kind of biological reinforced functional flora analytic method based on high-flux sequence |
-
2018
- 2018-10-25 CN CN201811252030.6A patent/CN109593865A/en active Pending
Patent Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104715165A (en) * | 2014-12-19 | 2015-06-17 | 中国石油天然气集团公司 | Petroleum pollution marine ecological environment evaluation method based on metagenome technology |
| CA3002110A1 (en) * | 2015-10-16 | 2017-04-20 | Genome Research Limited | Methods associated with a database that stores a plurality of reference genomes |
| WO2017096385A1 (en) * | 2015-12-04 | 2017-06-08 | Biome Makers Inc. | Microbiome based identification, monitoring and enhancement of fermentation processes and products |
| CN108486238A (en) * | 2018-04-10 | 2018-09-04 | 南京大学 | A kind of biological reinforced functional flora analytic method based on high-flux sequence |
Non-Patent Citations (4)
| Title |
|---|
| ENRIQUEZOZAYA-VALDES 等: "Acomprehensiveanalysisofthemicrobialcommunitiesofhealthyanddiseasedmarinemacroalgaeandthedetectionofknownandpotentialbacterialpthogens", 《FRONTIERSINMICROBIOLOGY》 * |
| MICHAEL HALL 等: "16S rRNA Gene Analysis with QIIME2", 《METHODS IN MOLECULAR BIOLOGY》 * |
| 张家超: "《肠道微生物组与人类健康》", 30 June 2017, 中国原子能出版社 * |
| 韩毛振 等: "中国南海和莫雷阿岛珊瑚礁共生的微生物菌群分析比较", 《2015中国遗传学会大会论文摘要汇编》 * |
Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110444254A (en) * | 2019-07-08 | 2019-11-12 | 深圳先进技术研究院 | A kind of detection method, detection system and the terminal of flora marker |
| CN110444254B (en) * | 2019-07-08 | 2021-10-19 | 深圳先进技术研究院 | Detection method, detection system and terminal for flora marker |
| CN114093411A (en) * | 2021-11-29 | 2022-02-25 | 中国人民解放军总医院 | Method and equipment for analyzing evolutionary relationship and abundance information of microbial population based on sample |
| CN114093411B (en) * | 2021-11-29 | 2022-08-09 | 中国人民解放军总医院 | Method and equipment for analyzing evolutionary relationship and abundance information of microbial population based on sample |
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