Ngena kwi-BMKCloud

Iimveliso

16S/18S/ITS Amplicon Sequencing-PacBio

I-16S kunye ne-18S rRNA genes, kunye nommandla we-Internal Transcribed Spacer (ITS), zisebenza njengeempawu zeminwe ze-molecular ezibalulekileyo ngenxa yokudibanisa kwazo iindawo ezigcinwe kakhulu neziguquguqukayo kakhulu, nto leyo ezenza zibe zizixhobo ezibalulekileyo zokuchonga izinto eziphilayo ze-prokaryotic kunye ne-eukaryotic. Ukwandiswa kunye nokulandelelana kwezi ndawo kunika indlela engenako ukwahlulwa yophando lokwakheka kweentsholongwane kunye nokwahluka kwazo kwiindawo ezahlukeneyo ze-ecosystem. Ngelixa ulandelelwano lwe-Illumina luhlala lujolise kwiindawo ezimfutshane eziguquguqukayo kakhulu ezifana ne-V3-V4 ye-16S kunye ne-ITS1, kuye kwabonakaliswa ukuba i-superior taxonomic annotation inokufezekiswa ngokulandelelanisa ubude obupheleleyo be-16S, 18S, kunye ne-ITS. Le ndlela ibanzi ikhokelela kwiipesenti eziphezulu zolandelelwano oluchanekileyo, olufikelela kwinqanaba lesisombululo esiya kuchongwa kweentlobo. Iqonga lokulandelelanisa le-Single-Molecule Real-Time (SMRT) le-PacBio liphuma phambili ngokubonelela ngokufunda okude okuchanekileyo kakhulu (i-HiFi) okugubungela ii-amplicons ezipheleleyo, okulinganisa ukuchaneka kokulandelelanisa kwe-Illumina. Olu buchule luvumela abaphandi ukuba bafumane inzuzo engenakuthelekiswa nanto - umbono ocacileyo wendawo yemfuza. Ukugubungela okwandisiweyo kuphakamisa kakhulu isisombululo kwiinkcazo zeentlobo, ngakumbi kwiindawo zebhaktheriya okanye zefungus, okuvumela ukuqonda okunzulu kobunzima beentlobo zentsholongwane.

Qhagamshelana nathi

Iinkcukacha zeNkonzo

I-Bioinformatics

Iziphumo zeDemo

Iimpapasho ezibalaseleyo

Iimpawu zeNkonzo

● Iqonga lokulandelelanisa: I-PacBio Revio

● Imo yokulandelelanisa: CCS (iHiFi ifundeka)

● Ukwandiswa kwendawo ekujoliswe kuyo kulandele ukudityaniswa kwee-amplicons ngaxeshanye ngaphambi kokulungiswa kwethala leencwadi le-HiFi SMRT bell

Iingenelo zeNkonzo

●Isisombululo esiphezulu se-taxonomic: Tulandelelwano lwe-han short-amplicon,okuvumela amazinga aphezulu okuhlela i-OTU kwinqanaba leentlobo zezilwanyana.

●Ubizo olusisiseko oluchanekileyo kakhulu: Ulandelelwano lwendlela yePacBio CCS (iHiFi ifundeka).

●Akukho kuhlukaniswa: Ukuchongwa ngokukhawuleza kokwakheka kweentsholongwane kwiisampuli zokusingqongileyo.

●Isebenza ngokubanzi: Izifundo ezahlukeneyo zoluntu ngeentsholongwane.

●Uhlalutyo olupheleleyo lwe-bioinformatics: Iphakheji yamva nje ye-QIIME2 (ulwazi oluchanekileyo malunga ne-microbial ecology) enohlalutyo olwahlukeneyo ngokwedathabheyisi, isichazi-magama, i-OTU/ASV.

●Ubuchule Obubanzi: Ngamawaka eeprojekthi zokulandelelana kwe-amplicon ezenziwa minyaka le, i-BMKGENE izisa amava angaphezulu kweshumi leminyaka, iqela lohlalutyo elinobuchule obuphezulu, umxholo opheleleyo, kunye nenkxaso ebalaseleyo emva kokuthengisa.

Iinkcukacha zeNkonzo

Ithala leeNcwadi	Icebo Lokulandelelanisa	Idatha iyacetyiswa
I-Amplicon	Uhlaziyo lwePacBio	Iithegi ze-10/30/50 K (CCS)

Iimfuno zeSampuli

Uxinzelelo (ng/µL)	Isixa sisonke (µg)	Umthamo (µL)
≥5	≥0.3	≥20

Ukuhanjiswa kweSampuli okuCetyisiweyo

Faka iisampulu kwi-nitrogen engamanzi iiyure ezi-3-4 uze uzigcine kwi-nitrogen engamanzi okanye kwiidigri ezingama-80 ukuya kwixesha elide. Kufuneka ukuthunyelwa kwesampulu nge-dry-ice.

Ukuhamba komsebenzi wenkonzo

Ukuhanjiswa kwesampulu

Ukwakhiwa kweThala leeNcwadi

Ukulandelelana

Uhlalutyo lwedatha

Iinkonzo zasemva kokuthengisa

Ngaphambili: 16S/18S/ITS Amplicon Sequencing-NGS

Okulandelayo: Uvavanyo lweChromatin efikelelekayo kwiTransposase ene-High Throughput Sequencing (ATAC-seq)

Kubandakanya uhlalutyo olulandelayo:

● Ulawulo lomgangatho wedatha eluhlaza

●Ukudibanisa i-OTU/Ukususa ingxolo (ASV)

●Ingcaciso ye-OTU

●Uhlalutyo lokwahlukahluka kwe-Alpha: ii-indexes ezininzi, kuquka uShannon, uSimpson kunye ne-ACE.

●Uhlalutyo lokwahlukahluka kwe-Beta

●Uhlalutyo phakathi kwamaqela

●Uhlalutyo lolwalamano: phakathi kwezinto ezingqongileyo kunye nokwakheka kunye nokwahlukahluka kwe-OUT

●Uqikelelo lwe-16S olusebenzayo lwe-gene

I-Histogram yokusasazwa kwe-taxonomic

Umthi we-phylogenetic wokusasazwa koluntu

Uhlalutyo lokwahlukahluka kweAlpha: i-ACE

isalathisi

Uhlalutyo lokwahlukahluka kwe-Beta: PCoA

Uhlalutyo lwamaqela ahlukeneyo: i-ANOVA

Hlola inkqubela phambili eququzelelwe ziinkonzo ze-BMKGene zokulandelelanisa i-amplicon kunye nePacBio ngokusebenzisa ingqokelela yeempapasho ezikhethiweyo.

UGao, X. kunye noWang, H. (2023) 'Uhlalutyo oluQhathaniswayo lweeProfayili zeBhaktheriya yeRumen kunye neMisebenzi ngexesha lokuZiqhelanisa nePhenology eyahlukeneyo (iRegreen vs. Grassy) kwiMvu yeAlpine Merino eneZigaba ezimbini zoKhula kwiAlpine Meadow', Ukuvutshelwa, 9(1), iphe. 16. doi: 10.3390/FERMENTATION9010016/S1.

ULi, S. et al. (2023) 'Ukubamba izinto ezimnyama ze-microbial kumhlaba wasentlango kusetyenziswa i-metagenomics esekelwe kwi-culturomics kunye nohlalutyo oluphezulu', npj Biofilms kunye neMicrobiomes 2023 9:1, 9(1), iphe. 1–14. doi: 10.1038/s41522-023-00439-8.

UMu, L. et al. (2022) 'Iziphumo zetyuwa ye-fatty acid kwiimpawu zokubilisa, ukwahluka kwebhaktheriya kunye nokuzinza kwe-aerobic ye-silage exutyiweyo elungiselelwe i-alfalfa, i-rice straw kunye ne-wheat bran', iJenali yeSayensi yoKutya nezoLimo, 102(4), iphe. 1475–1487. doi: 10.1002/JSFA.11482.

UYang, J. et al. (2023) 'Intsebenziswano phakathi kwee-Biomarkers ze-Oxidative Stress kunye ne-Gut Microbiota kwi-Antioxidant Effects of Extracts ezivela kwi-Sonchus brachyotus DC. kwi-Oxazolone-Induced Intestinal Oxidative Stress kwi-Adult Zebrafish', ii-Antioxidants 2023, uMqulu. 12, Iphepha 192, 12(1), iphe. 192. doi: 10.3390/ANTIOX12010192.