Toward a genetic tool development pipeline for host-associated bacteria

•Bacterial members of various microbiota are culturable but lack genetic tools.•Means to boost DNA delivery by mimicking the host's DNA methylation pattern.•Predictable gene expression by designing or screening promoter, RBS libraries.•Diverse CRISPR technologies for gene editing, repression, high-throughput screens.•Progress toward a pipeline for expediting genetic tool development.

Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host's health, behavior, and development, yet the causative mediators of host-microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host. This review discusses the current challenges to rendering culturable, non-model members of microbial communities genetically tractable - including overcoming barriers to DNA delivery, achieving predictable gene expression, and applying CRISPR-based tools - and details recent efforts to create generalized pipelines that simplify and expedite the tool-development process. We use the bacteria present in the human gastrointestinal tract as representative microbiota to illustrate some of the recent achievements and future opportunities for genetic tool development.