Kev Tshawb Fawb Txog Metagenomic-TGS
Ib qho metagenome yog ib qho kev sib sau ua ke ntawm cov khoom siv caj ces ntawm cov zej zog sib xyaw ntawm cov kab mob, xws li ib puag ncig thiab tib neeg metagenomes. Nws muaj cov genomes ntawm ob qho tib si cultivatable thiab uncultivatable microorganisms. Metagenomic sequencing ua rau kev kawm txog cov toj roob hauv pes genomic complex no embedded hauv cov qauv ecological los ntawm kev muab ntau dua li taxonomic profiling. Nws kuj muab ib qho kev xav genomics ua haujlwm los ntawm kev tshawb nrhiav cov noob encoded thiab lawv lub luag haujlwm putative hauv cov txheej txheem ib puag ncig. Thaum cov txheej txheem shotgun ib txwm muaj nrog Illumina sequencing tau siv dav hauv kev tshawb fawb metagenomic, qhov tshwm sim ntawm Nanopore thiab PacBio ntev-nyeem sequencing tau hloov pauv thaj chaw. Nanopore thiab PacBio thev naus laus zis txhim kho kev tshuaj xyuas bioinformatic downstream, tshwj xeeb tshaj yog metagenome sib dhos, ua kom ntseeg tau tias muaj kev sib dhos txuas ntxiv. Cov ntawv qhia qhia tias Nanopore-based thiab PacBio-based metagenomics tau ua tiav tsim cov genomes kab mob tiav thiab kaw los ntawm cov microbiomes nyuaj (Moss, EL, et al., Nature Biotech, 2020). Kev sib xyaw Nanopore nyeem nrog Illumina nyeem muab txoj hauv kev zoo rau kev kho qhov yuam kev, txo qhov tseeb qis ntawm Nanopore. Qhov kev sib xyaw ua ke no siv lub zog ntawm txhua lub platform sequencing, muab kev daws teeb meem zoo los kov yeej cov kev txwv thiab txhim kho qhov tseeb thiab kev ntseeg tau ntawm kev tshuaj xyuas metagenomic.
Platform: Nanopore PromethION 48, Illumia thiab PacBio Revio
Cov yam ntxwv ntawm kev pabcuam
● Kev nyeem ntev sequencing ntawm Nanopore P48 (10Kb tsev qiv ntawv); PacBio Revio (8Kb tsev qiv ntawv)
● Kev kho qhov yuam kev: kev txheeb xyuas kab ke ntawm Illumina NovaSeq (PE150 lub tsev qiv ntawv)
Cov Kev Pabcuam Zoo
●Kev Sib Dhos Metagenome Zoo:Nrog tsawg dua contigs uas muaj kev sib txuas ntxiv dua.
●Kev Raug Siab Dua:Kev txheeb xyuas cov hom tsiaj thiab kev kwv yees cov noob caj noob ces ua haujlwm.
●Kev Sib Dhos Zoo DuaPab txhawb kev cais cov kab mob bacterial genome thiab kev sib piv metagenome.
●Kev Tshuaj Xyuas Txog Bioinformatics Uas Muaj Kev Paub Tag Nrho:Peb qhov kev tshuaj xyuas tsis yog tsuas yog tsom mus rau qhov sib txawv ntawm cov tsiaj txhu xwb tab sis kuj tseem tsom mus rau qhov sib txawv ntawm kev ua haujlwm ntawm lub zej zog.
●Kev Paub Ntau YamPeb pab neeg muaj kev paub dhau los ntau yam rau txhua qhov project, nrog rau cov ntaub ntawv pov thawj ntawm kev ua tiav ntau qhov project metagenomics hauv ntau qhov chaw tshawb fawb thiab ua tiav ntau dua 200,000 cov qauv, peb pab neeg muaj kev paub dhau los ntau yam rau txhua qhov project.
Cov Lus Qhia Txog Kev Pabcuam
| Lub platform txheeb xyuas cov ntaub ntawv | Txoj Kev Npaj Txog Sequencing | Cov ntaub ntawv pom zoo |
| Illumina NovaSeq | PE150 | 6 Gb |
| Nanopore P48 | 10 kb | 6 / 10 Gb |
| PacBio Revio | 8 kb | 10 / 20 Gb |
Cov Qauv Yuav Tsum Tau Ua
| Kev Ntsuas (ng/µL) | Tag nrho cov nqi (µg) | Ntim (µL) | |
| Illumina PE150 Tsev Qiv Ntawv | ≥1 | ≥0.03 | ≥20 |
| Nanopore 10 kb tsev qiv ntawv | ≥40 | ≥2 | ≥20 |
| PacBio 8 kb tsev qiv ntawv | ≥50 | 10 µg/cell | ≥20 |
Kev Ua Haujlwm Pabcuam
Kev xa khoom qauv
Kev tsim kho tsev qiv ntawv
Kev txheeb xyuas kab ke
Kev tshuaj xyuas cov ntaub ntawv
Cov kev pab cuam tom qab muag
Muaj xws li cov kev tshuaj xyuas hauv qab no:
● Kev Tswj Xyuas Zoo ntawm Cov Ntaub Ntawv Sequencing
● Kev Sib Sau Ua Ke ntawm Metagenome thiab Kev Kwv Yees Gene
● Cov Lus Qhia Txog Gene
● Kev Tshawb Fawb Txog Kev Sib Txawv ntawm Alpha Taxonomic
● Kev Tshawb Fawb Txog Lub Zej Zog: Kev Ua Haujlwm ntawm Lub Cev, Kev Hloov Pauv, Kev Tiv Thaiv Tshuaj Tua Kab Mob
● Kev Tshawb Fawb Txog Ob Qhov Kev Ua Haujlwm thiab Kev Sib Txawv ntawm Cov Txheej Txheem:
Kev Tshawb Fawb Txog Kev Sib Txawv ntawm Beta
Kev Tshawb Fawb Txog Pawg Neeg
Kev Tshawb Fawb Txog Kev Sib Raug Zoo: ntawm cov yam ntxwv ib puag ncig thiab OUT cov khoom sib xyaw thiab ntau haiv neeg
Kev faib tawm ntawm cov noob caj noob ces uas tsis rov ua dua:
Kev piav qhia txog noob caj noob ces: KEGG txoj kev
Cov lus piav qhia txog noob caj noob ces: eggNOG
Kev piav qhia txog noob caj noob ces: CAZY carbohydrates
Kev sib raug zoo ntawm cov tsiaj txhu:
Tshawb nrhiav kev nce qib uas tau pab txhawb los ntawm BMKGene qhov kev pabcuam metagenomics sequencing nrog Nanopore + Illumina nrog cov ntawv tshaj tawm tshwj xeeb no:
Jin, H. et al. (2023) 'Ib phau ntawv qhia txog cov noob caj noob ces zoo ntawm cov kab mob hauv plab ntawm cov neeg Inner Mongolians', Nature Microbiology 2023 8:1, 8(1), nplooj ntawv 150–161. doi: 10.1038/s41564-022-01270-1.
