Have you ever wished to sequence SPECIFIC bacteria but NOT the vast background in #microbiome? Today, we introduce *mEnrich-seq*: #methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. 4yr project led by @clannabel7! biorxiv.org/content/10.110…🧵1/10 
#Metagenomic sequencing throughput is largely consumed by abundant microbes while those with relatively lower abundance cannot be sequenced in a cost-effective manner, due to the highly skewed abundance distribution of diverse bacteria and host DNA. 2/10
Although several methods have been developed (pls see Introduction in preprint) to exclude host DNA and/or the highly abundant microbes, there are still key challenges in achieving high enrichment efficiency and differentiating between bacterial taxa w/ very similar genomes. 3/10
Bacterial DNA methylation naturally differentiates self vs. non-self DNA (Restriction-Modification systems), and has been exploited as epigenetic barcodes for methylation binning in our previous work by @bowerlauwer nature.com/articles/nbt.4… & @_Alan_T nature.com/articles/s4159… 4/10
However, methylation binning is only applicable as a post-hoc analysis, *AFTER* @PacBio or @nanopore sequencing. Is it possible to make use of bacterial DNA methylation to enrich bacterial taxa of interest *BEFORE* sequencing? YES! Building on the >4,000 bacterial methylomes 5/10
mapped to date or de novo methylation discovery from a pilot sequencing run, we can rationally choose methylation-sensitive restriction enzymes (REs), individually or in combination, to deplete most background (microbial & host) DNA while enriching bacterial taxa of interest 6/10
This core idea is integrated with library preparation in a way that only non-digested DNA libraries are sequenced. We performed in-depth evaluations of #mEnrich-seq and demonstrated its use in several applications to enrich (up to 117-fold) gDNA of pathogenic or beneficial 7/10
bacteria from urine & fecal samples, including species that are hard to culture (e.g. #Akkermansia) or of low abundance. We also assessed the broad applicability of #mEnrich-seq: 3130 (68%) of the 4601 strains w/ mapped methylomes to date can be targeted, representing 55% of 8/10
the species examined in this analysis. #mEnrich-seq provides researchers w/ a versatile approach to selectively sequence diverse taxa of interest from microbiome, *tailor* sequencing strategy to best serve their goals. It is compatible with @nanopore, @PacBio, @illumina, etc 9/10
4yr proj led by FANTASTIC PostDoc @clannabel7! Great help from @kong_yimeng @fanyu48696214 @Fannimi2001 @_Alan_T @MagdalenaKsi Andy Mead, Tonny Koo, Melissa Gitman @SinaiGenetics @IcahnInstitute & @XuesongRutgers! Also thanks to @jeremiahfaith1 @valdi001 @lauren282012 ! 10/10
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