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Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

by Zhu, Pengfei , Tzehau, Lam , Zhang, Rongchao , Niu, Qianya , Xu, Jian , Zhou, Lisha , Zhao, Helen , Lv, Jia , Liu, Jiquan , Jing, Gongchao , Bao, Zhenmin , Wang, Xiuping , Sun, Zheng , Zhang, Meng , Wang, Shi , Huang, Shi

in Accuracy / Animal Genetics and Genomics / Archaea / Bacteria / Bias / Biodegradation / Bioinformatics / Biomass / Biomedical and Life Sciences / cost effectiveness / Deoxyribonucleic acid / DNA / DNA sequencing / Enzymes / Evolutionary Biology / Fungi / genome / Genomes / Human Genetics / Life Sciences / metagenomics / Method / microbial biomass / Microbial Genetics and Genomics / microbiome / Microbiomes / Nucleotide sequence / Plant Genetics and Genomics / Species / Taxonomy

2022

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Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

2022

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Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

2022

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Journal Article

Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

Zhu, Pengfei,

Tzehau, Lam,

Zhang, Rongchao,

Niu, Qianya,

Xu, Jian,

Zhou, Lisha,

Zhao, Helen,

Lv, Jia,

Liu, Jiquan,

Jing, Gongchao,

Bao, Zhenmin,

Wang, Xiuping,

Sun, Zheng,

Zhang, Meng,

Wang, Shi,

Huang, Shi

2022

Overview

Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective strategy which only sequences ~ 1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles. 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with merely 1 pg of total DNA, high host DNA contamination, or severely fragmented DNA from degraded samples. Tests of 2bRAD-M on various stool, skin, environmental, and clinical FFPE samples suggest a successful reconstruction of comprehensive, high-resolution microbial profiles.

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Accuracy

/ Animal Genetics and Genomics

/ Archaea

/ Bacteria

/ Bias

/ Biodegradation

/ Bioinformatics