Designing fecal microbiota transplant trials that account for differences in donor stool efficacy

by Scott Olesen Microbes appear to be involved in a complicated interaction with their human hosts, protecting us from some diseases and possibly helping to cause others. Gut microbiota are suspected to be involved in inflammatory bowel disease, a condition where the human body’s immune system attacks its own digestive system. Inflammatory bowel disease, or […]

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Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

Analyses of metagenomic datasets that are sequenced to a depth of billions or trillions of bases can uncover hundreds of microbial genomes, but naive assembly of these data is computationally intensive, requiring hundreds of gigabytes to terabytes of RAM. We present latent strain analysis (LSA), a scalable, de novo pre-assembly method that separates reads into […]

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ConStrains identifies microbial strains in metagenomic datasets

An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly […]

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