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Ulandelelwano lweMetagenomic -NGS
I-metagenome yingqokelela yezinto ezipheleleyo zemfuza yoluntu oluxubileyo lwezinto eziphilayo, ezifana neemetagenome zendalo kunye nezomntu. Iqulethe iigenome zeentsholongwane ezinokulinywa kunye nezingenakulinywa. Ukulandelelana kwe-metagenomic ye-Shotgun nge-NGS kwenza kube lula ukufunda ezi ndawo zintsonkothileyo ze-genomic ezifakwe kwiisampuli zendalo ngokubonelela ngaphezu kokubhala i-taxonomic, okunika nokuqonda okubanzi malunga nokwahluka kweentlobo, i-dynamics yobuninzi, kunye nezakhiwo ezintsonkothileyo zabantu. Ngaphaya kwezifundo ze-taxonomic, i-shotgun metagenomics ikwabonelela ngembono esebenzayo ye-genomics, evumela ukuphononongwa kwee-genes ezifakwe kwi-encoded kunye neendima zazo ezichazayo kwiinkqubo zendalo. Okokugqibela, ukusekwa kothungelwano lolwalamano phakathi kwezinto zemfuza kunye nezinto zendalo kunceda ekuqondeni ngokupheleleyo ukusebenzisana okuntsonkothileyo phakathi kweendawo ezintsonkothileyo kunye nemvelaphi yazo yendalo. Ukuqukumbela, ulandelelwano lwe-metagenomic lumi njengesixhobo esibalulekileyo sokutyhila ubunzima be-genomic beendawo ezahlukeneyo ezintsonkothileyo, ukukhanyisa ubudlelwane obunemiba emininzi phakathi kwe-genetics kunye ne-ecology ngaphakathi kwezi ndawo zintsonkothileyo zendalo.
Amaqonga: Illumina NovaSeq kunye ne-DNBSEQ-T7
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Ukulandelelana kweMetagenomic-TGS
I-metagenome yingqokelela yezinto zemfuza zoluntu oluxubileyo lwezinto eziphilayo, ezifana neemetagenome zendalo kunye nezomntu. Iqulethe iigenome zeentsholongwane ezinokulinywa kunye nezingenakulinywa. Ukulandelelana kwe-metagenomic kwenza ukuba kufundwe ezi ndawo zintsonkothileyo ze-genomic ezifakwe kwiisampuli zendalo ngokubonelela ngeprofayili engaphezulu kwe-taxonomic. Ikwabonelela ngombono osebenzayo we-genomics ngokuhlola ii-genes ezifakwe kwi-encoded kunye neendima zazo ezibekayo kwiinkqubo zendalo. Ngelixa iindlela zendabuko ze-shotgun kunye ne-Illumina sequencing zisetyenziswe kakhulu kwizifundo ze-metagenomic, ukufika kwe-Nanopore kunye ne-PacBio sequencing efunde ixesha elide kuyitshintshile intsimi. Itekhnoloji ye-Nanopore kunye ne-PacBio iphucula uhlalutyo lwe-bioinformatic olusezantsi, ngakumbi ukuhlanganiswa kwe-metagenome, ukuqinisekisa ukuhlanganiswa okuqhubekayo. Iingxelo zibonisa ukuba i-metagenomics esekelwe kwi-Nanopore kunye ne-PacBio ziphumelele ukuvelisa ii-genome zebhaktheriya ezipheleleyo nezivaliweyo ezivela kwii-microbiomes ezintsonkothileyo (Moss, EL, et al., Nature Biotech, 2020). Ukudibanisa iiNanopore reads kunye neeIllumina reads kubonelela ngendlela enobuchule yokulungisa iimpazamo, ukunciphisa ukuchaneka okuphantsi kweNanopore. Olu dibaniselwano oluhambelanayo lusebenzisa amandla eqonga ngalinye lokulandelelana, lubonelela ngesisombululo esomeleleyo sokoyisa imida enokubakho kunye nokuphucula ukuchaneka kunye nokuthembeka kohlalutyo lwe-metagenomic.
Iqonga: I-Nanopore PromethION 48, i-Illumia kunye ne-PacBio Revio
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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.
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16S/18S/ITS Amplicon Sequencing-NGS
Ukulandelelana kwe-Amplicon ngetekhnoloji ye-Illumina, ejolise ngokukodwa kwiimpawu zemfuza ze-16S, 18S, kunye ne-ITS, yindlela enamandla yokutyhila i-phylogeny, i-taxonomy, kunye nobuninzi beentlobo zezilwanyana kuluntu lweentsholongwane. Le ndlela ibandakanya ukulandelelanisa iindawo eziguquguqukayo kakhulu zeempawu zemfuza zokugcinwa kwendlu. Ekuqaleni yaziswa njengeminwe ye-molecular yiUWoeses nabanyeNgo-1977, le ndlela itshintshe indlela yokuhlalutya ii-microbiome ngokuvumela uhlalutyo olungenazo izinto ezizimeleyo. Ngokulandelana kwe-16S (iibhaktheriya), i-18S (ifungi), kunye ne-Internal Transcribed Spacer (ITS, ifungi), abaphandi banokuchonga kungekuphela nje iintlobo ezininzi kodwa kunye nezo zinqabileyo nezingaziwayo. Njengoko yamkelwe ngokubanzi njengesixhobo esibalulekileyo, ukulandelana kwe-amplicon kuye kwaba luncedo ekuqondeni ukwakheka kwee-microbial ezahlukeneyo kwiindawo ezahlukeneyo, kubandakanya umlomo womntu, amathumbu, indle, nangaphaya.
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Ukulandelelaniswa kwakhona kweGenome epheleleyo yeBhaktiriya kunye neFungal
Iiprojekthi zokulandelelanisa kwakhona i-genome epheleleyo yeebhaktiriya kunye neefungus zibaluleke kakhulu ekuphuculeni i-genomics yeebhaktiriya ngokwenza kube lula ukugqitywa kunye nokuthelekisa i-genomes yeebhaktiriya. Oku kwenza kube lula ubunjineli bokubila, ukuphucula iinkqubo zoshishino, kunye nokuhlola iindlela zesibini zemetabolism. Ngaphezu koko, ukulandelelanisa kwakhona i-fungus kunye neebhaktiriya kubalulekile ekuqondeni ukuziqhelanisa nokusingqongileyo, ukuphucula iintlobo, kunye nokuveza amandla okuvela kwezakhi zofuzo, kunye nefuthe elibanzi kumayeza, kwezolimo, nakwisayensi yokusingqongileyo.
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Ulandelelwano lwe-Prokaryotic RNA
Ukulandelelana kwe-RNA kunika amandla ukubhalwa ngokubanzi kwazo zonke ii-RNA transcripts ngaphakathi kweeseli phantsi kweemeko ezithile. Le teknoloji intsha isebenza njengesixhobo esinamandla, ityhila iiprofayili ezintsonkothileyo zokubonakaliswa kwezakhi zofuzo, izakhiwo zezakhi zofuzo, kunye neendlela zemolekyuli ezinxulumene neenkqubo ezahlukeneyo zebhayoloji. Yamkelwe ngokubanzi kuphando olusisiseko, ukuxilongwa kwezonyango, kunye nophuhliso lwamayeza, ukulandelelana kwe-RNA kunika ulwazi malunga nobunzima be-dynamics yeseli kunye nolawulo lwezakhi zofuzo. Ukucubungula kwethu isampulu ye-RNA ye-prokaryotic kulungiselelwe ii-transcriptomes ze-prokaryotic, ezibandakanya ukuncipha kwe-rRNA kunye nokulungiselela ilayibrari yesikhokelo.
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Ulandelelwano lweMetatranscriptome
Isebenzisa itekhnoloji yokulandelelanisa i-Illumina, inkonzo yokulandelelanisa i-metatranscriptome ye-BMKGENE ityhila ukubonakaliswa kwejini okuguquguqukayo koluhlu olwahlukeneyo lwee-microbes, oluquka ii-eukaryotes ukuya kwii-prokaryotes kunye neentsholongwane, ngaphakathi kwendalo efana nomhlaba, amanzi, ulwandle, indle, kunye namathumbu. Inkonzo yethu ebanzi inika abaphandi amandla okuphonononga kwiiprofayili ezipheleleyo zokubonakaliswa kwejini ezintsonkothileyo zeendawo ezincinci. Ngaphaya kohlalutyo lwe-taxonomic, inkonzo yethu yokulandelelanisa i-metatranscriptome inceda ukuphonononga ukutyebisa okusebenzayo, ikhanyisela iijini ezivezwe ngokwahlukeneyo kunye neendima zazo. Fumana ubutyebi bokuqonda kwezinto eziphilayo njengoko uhamba kwiindawo ezintsonkothileyo zokubonakaliswa kwejini, ukwahluka kwe-taxonomic, kunye nokusebenza ngaphakathi kwezi ndawo zahlukeneyo zokusingqongileyo.
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De novo Fungal Genome Assembly
I-BMKGENE inikezela ngezisombululo ezahlukeneyo ze-fungus genomes, ihlangabezana neemfuno ezahlukeneyo zophando kunye nokuphelela kwe-genome okunqwenelekayo. Ukusebenzisa i-short-read Illumina sequencing yodwa kuvumela ukuveliswa kwe-draft genome. I-short-reads kunye ne-long-read sequencing kusetyenziswa i-Nanopore okanye i-Pacbio zidityaniswe kwi-fungus genome ecociweyo ngakumbi ene-long contigs. Ngaphezu koko, ukudibanisa i-Hi-C sequencing kuphucula ngakumbi amandla, okuvumela ukufikelela kwi-gene epheleleyo ye-chromosome-level.
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De novo i-Bacterial Genome Assembly
Sinikezela ngenkonzo epheleleyo yokuhlanganisa i-genome yebhaktiriya, siqinisekisa izithuba ezi-0. Oku kunokwenzeka ngokuhlanganisa ubuchwepheshe bokulandelelana obufundwa ixesha elide, obufana neNanopore kunye nePacBio bokuhlanganisa kunye nokulandelelana okufundwayo okufutshane kunye ne-Illumina yokuqinisekisa indibano kunye nokulungiswa kweempazamo ze-ONT reads. Inkonzo yethu ibonelela ngomsebenzi opheleleyo we-bioinformatic ukusuka kwindibano, i-functional analysis, kunye nohlalutyo oluphambili lwe-bioinformatic, oluzalisekisa iinjongo zophando ezithile. Le nkonzo ivumela ukuphuhliswa kwe-genome echanekileyo yezifundo ezahlukeneyo ze-genetic kunye ne-genomic. Ukongeza, yenza isiseko sezicelo ezinje ngokulungiswa koxinzelelo, ubunjineli be-genetic, kunye nophuhliso lwetekhnoloji ye-microbial, ukuqinisekisa idatha ye-genomic ethembekileyo nengenazikhewu ebalulekileyo ekuphuculeni ukuqonda kwesayensi kunye nokuvelisa izinto ezintsha ze-biotechnology.
