Culture collection screens | ADME | Identifies culturable active isolates | Front-ended effort for collection curation |
Ex vivo fecal incubations | ADME | Large genetic diversity sampled | Interstrain antagonism and culture bias |
Fecalase preparations | M | Culture independent | Requirement for cofactors may mask metabolism |
RNA-seq (microbial) | M | May identify single effectors/pathways | Induction may not occur for all effectors |
Comparative genomics | ADME | Yields information on evolution and distribution | Large number of isolates needed |
Functional genomics | M | Directly identifies genes | Choice of platform (host and vector) may influence expression/success |
Gene knockout library (microbial) | M | Systematically identifies candidate genes | Genetic tools not available for most gut bacteria |
Microbiota profiling | M | Identifies drug-responsive microbes | Drug may not be stimulatory or inhibitory to metabolizer |
Cell culture transport models | ADE | Well established and high throughput | Immunoregulation may not be represented |
Gnotobiotic models | ADE | Isolates in vivo effect of specific microbes | Differences in regulation/metabolism between host species |
Antibiotic knockdown models | ADE | Easier and cheaper than gnotobiotics | Knockdown incomplete/unstable; reproducibility |
RNA-seq (host) | ADE | Identifies pathways of modulation | Effects could be post-transcriptional |