Phylogeny, culturing, and metagenomics of the human gut microbiota

•Metagenomics has revolutionised research into human intestinal microbes.•Limitations of metagenomics mean that culturing and phylogeny remain relevant.•Phylogeny and culture will be crucial for the development of new microbial therapeutics.•A combination of culturing and metagenomics is needed to gain new insights into functionality.

The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.