Culturing methods in combination with sequencing technology will help us discover and characterize bacteria.

The continuing development of sequencing technologies has shifted our understanding of the microbial world. Our knowledge, however, is still limited because we cannot isolate and culture the vast majority of microorganisms. Genomics-based sequencing tools have great advantages for profiling the composition of environmental microbial samples via taxonomic assignment, enabling new species discovery and highlighting the diversity of microbial communities. Yet precise taxonomic assignment is not easy. Computational tools have been developed to aid such metagenomics analysis for better assembly of sequence reads into functional and taxonomic compositions (Nat. Methods 16, 603–606, 2019).

Culturing methods and sequencing technology facilitate the culture of more species. Credit: Katherine Vicari/Springer Nature

Notably, sequencing-enabled taxonomic compositions heavily depend on the abundance of species in the microbiota, which likely favors dominant populations and thus limits our view of minority populations. Microbiologists have hence started to revisit culture-dependent methods for previously unculturable microorganisms.

Unknown parameters in growth conditions, such as a requirement for exotic nutrients or interspecies interaction, make culturing a real challenge. But culture-dependent methods beyond conventional techniques are emerging to counteract recalcitrance to cultivation. For example, microfluidics-enabled in-droplet cultivation offers a high-throughput approach to exploring pairwise interactions between signaling cells (Proc. Natl Acad. Sci. USA 114, 2550–2555, 2017).

Targeted culturing of bacteria with specific phenotypes has been developed for culturing a subset of intestinal bacteria (Nature 533, 543–546, 2016). Recently, a genome-informed approach was established to physically isolate microorganisms based on the expression of a membrane protein (Nat. Biotechnol. 37, 1314–1321, 2019).

Surely, sequencing technology will continue to grow and assist microbial profiling, as well as deciphering of the underlying metabolic pathways. Culture-dependent methods in return will afford a way to experimentally validate hypotheses generated from metagenomics studies. We envision microbial cultures and omics technologies serving as complementary tools to broaden our knowledge of bacterial communities.