Fig. 1

Strategies for detailed strain and molecular functional profiling of the microbiome in human population studies. a Culture-independent analysis methods can now identify members of the microbiome at the strain level using any of several related techniques. This is important in population studies as strains are often the functional units at which specific members of microbial communities can be causal in human health outcomes. b Among different approaches, reference-based methods can require less metagenomic sequence coverage (as little as ~ 1×), but are limited to identifying variation that is based on genes or single nucleotide variants (SNVs) related to available reference genomes. c Assembly-based methods can additionally resolve syntenic information across multiple markers at the cost of higher coverage (≥10×, Table 1). d , e Metatranscriptomic analysis, another emerging tool for characterizing microbiome function in human health, reveals over- or under-expression of microbial features with respect to their genomic content, both on d the population and e the individual level. ORF open reading frame