Abstract:Despite extensive efforts to address it, the vastness of uncharacterized "dark matter" microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were … Show more
“…A hybrid genome assembly utilizing short and long reads was generated assembled using UniCycler version 0.4.8 using default parameters ( 28 ) (see Table S10 for sequencing coverage and statistics). The SPMP metagenomic library for short reads was constructed using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) and paired-end sequenced (2 × 151 bp reads) on an Illumina HiSeq4K platform as previously described ( 29 ).…”
Section: Methodsmentioning
confidence: 99%
“…Methanogen MAGs are derived from the Singapore Platinum Metagenomes Project (SPMP) ( 29 ). Methanogen MAGs are hybrid assemblies of Illumina and MinION data using OPERA-MS v0.9.0 ( 38 ).…”
Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents.
“…A hybrid genome assembly utilizing short and long reads was generated assembled using UniCycler version 0.4.8 using default parameters ( 28 ) (see Table S10 for sequencing coverage and statistics). The SPMP metagenomic library for short reads was constructed using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) and paired-end sequenced (2 × 151 bp reads) on an Illumina HiSeq4K platform as previously described ( 29 ).…”
Section: Methodsmentioning
confidence: 99%
“…Methanogen MAGs are derived from the Singapore Platinum Metagenomes Project (SPMP) ( 29 ). Methanogen MAGs are hybrid assemblies of Illumina and MinION data using OPERA-MS v0.9.0 ( 38 ).…”
Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents.
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