Ukulandelana kwe-Metagenomic-TGS
I-metagenome iqoqo lezinto zofuzo zomphakathi oxubile wezinto eziphilayo, njenge-metagenome yezemvelo neyabantu. Iqukethe ama-genome ezinto ezincane ezitshalwa kanye nezingalinywa. Ukulandelana kwe-metagenomic kwenza ucwaningo lwalezi zindawo eziyinkimbinkimbi ze-genomic ezifakwe kumasampula emvelo ngokunikeza okungaphezu kokulandelela i-taxonomic. Iphinde inikeze umbono osebenzayo we-genomics ngokuhlola izakhi zofuzo ezifakiwe kanye nezindima zazo ezibeka engcupheni yezemvelo. Ngenkathi izindlela zendabuko ze-shotgun nge-Illumina sequencing zisetshenziswe kabanzi ezifundweni ze-metagenomic, ukufika kokulandelana kwe-Nanopore ne-PacBio okufundwa isikhathi eside kushintshe insimu. Ubuchwepheshe be-Nanopore ne-PacBio buthuthukisa ukuhlaziywa kwe-bioinformatic okuphansi, ikakhulukazi ukuhlanganiswa kwe-metagenome, ukuqinisekisa ukuhlanganiswa okuqhubekayo. Imibiko ikhombisa ukuthi ama-metagenomics asekelwe ku-Nanopore kanye ne-PacBio akhiqize ngempumelelo ama-genome aphelele futhi avaliwe avela kuma-microbiomes ayinkimbinkimbi (Moss, EL, et al., Nature Biotech, 2020). Ukuhlanganisa ukufundwa kwe-Nanopore nokufundwa kwe-Illumina kunikeza indlela ehlakaniphile yokulungisa amaphutha, kunciphisa ukunemba okuphansi kwe-Nanopore. Le nhlanganisela yokusebenzisana isebenzisa amandla epulatifomu ngayinye yokulandelana, inikeza ikhambi eliqinile lokunqoba imikhawulo engaba khona kanye nokuthuthukisa ukunemba nokuthembeka kokuhlaziywa kwe-metagenomic.
Ipulatifomu: I-Nanopore PromethION 48, i-Illumia kanye ne-PacBio Revio
Izici Zesevisi
● Ukulandelana kokufunda isikhathi eside ku-Nanopore P48 (umtapo wezincwadi we-10Kb); i-PacBio Revio (umtapo wezincwadi we-8Kb)
● Ukulungiswa kwamaphutha: ukulandelana kwezithombe ku-Illumina NovaSeq (umtapo wolwazi we-PE150)
Izinzuzo Zesevisi
●Ukuhlanganiswa kweMetagenome esezingeni eliphezulu:Ngama-contig ambalwa anokuqhubeka okuphezulu.
●Ukunemba Okuphakeme:Ukuhlonza izinhlobo kanye nokubikezela izakhi zofuzo ezisebenzayo.
●Ukuhlanganiswa Okuthuthukisiwe: Ukwenza kube lula ukuhlukaniswa kwezakhi zofuzo zamagciwane kanye nokuhlaziywa kwe-metagenome eqhathaniswayo.
●Ukuhlaziywa Okuphelele Kwe-Bioinformatics:Ukuhlaziywa kwethu akugxili nje kuphela ekwahlukaneni kwe-taxonomic kodwa futhi nasekwahlukaneni kokusebenza komphakathi.
●Ulwazi Olubanzi: Ithimba lethu liletha ulwazi oluningi kuyo yonke iphrojekthi, ngomlando wokuvala ngempumelelo amaphrojekthi amaningi e-metagenomics emikhakheni eyahlukene yocwaningo kanye nokucubungula amasampula angaphezu kuka-200,000, ithimba lethu liletha ulwazi oluningi kuyo yonke iphrojekthi.
Imininingwane Yesevisi
| Ipulatifomu yokulandelana | Isu Lokulandelana | Kunconywa idatha |
| I-Illumina NovaSeq | I-PE150 | 6 Gb |
| I-Nanopore P48 | 10 kb | 6 / 10 Gb |
| I-PacBio Revio | 8 kb | 10 / 20 Gb |
Izidingo Zesampula
| Ukugxila (ng/µL) | Inani eliphelele (µg) | Ivolumu (µL) | |
| Umtapo Wezincwadi we-Illumina PE150 | ≥1 | ≥0.03 | ≥20 |
| Umtapo wezincwadi we-Nanopore 10 kb | ≥40 | ≥2 | ≥20 |
| Umtapo wolwazi we-PacBio ongu-8 kb | ≥50 | 10 µg/iseli | ≥20 |
Ukugeleza Komsebenzi Wesevisi
Ukulethwa kwesampula
Ukwakhiwa komtapo wolwazi
Ukulandelana
Ukuhlaziywa kwedatha
Izinsizakalo zangemuva kokuthengisa
Kufaka phakathi ukuhlaziywa okulandelayo:
● Ukulawula Ikhwalithi Yedatha Ngokulandelana
● Ukuhlanganiswa kwe-Metagenome kanye nokubikezela i-Gene
● Isichasiselo Sezakhi Zofuzo
● Ukuhlaziywa Kokuhlukahluka Kwe-Taxonomic Alpha
● Ukuhlaziywa Kokusebenza Komphakathi: Umsebenzi Wezinto Eziphilayo, Ukwakheka Kwezinto Eziphilayo, Ukumelana Nemithi Elwa Namagciwane
● Ukuhlaziywa kokubili kokwehlukahlukana kokusebenza kanye nokwe-taxonomic:
Ukuhlaziywa Kokuhlukahluka kwe-Beta
Ukuhlaziywa Kwamaqembu Ahlukene
Ukuhlaziywa Kobudlelwano: phakathi kwezici zemvelo kanye nokwakheka kanye nokuhlukahluka kwe-OUT
Ukusatshalaliswa kwesethi yezakhi zofuzo ezingadingeki:
Isichasiselo se-gene: Indlela ye-KEGG
Isichasiselo se-Gene: iqandaNOG
Isichasiselo se-Gene: Ama-carbohydrate aqinile
Inethiwekhi yokuhlobana kwezinhlobo:
Hlola intuthuko eyenziwe yisevisi yokulandelana kwe-metagenomics ye-BMKGene nge-Nanopore + Illumina ngale ncwadi evelele:
UJin, H. et al. (2023) 'Iqoqo le-genome elisezingeni eliphezulu le-microbiome yamathumbu omuntu yamaMongolia angaphakathi', i-Nature Microbiology 2023 8:1, 8(1), amakhasi 150–161. doi: 10.1038/s41564-022-01270-1.
