What are the differences between shotgun metagenomic sequencing and culture-based methods?

Shotgun metagenomic sequencing reads all the DNA in a sample. This allows identification of microbes down to the species — and sometimes strain — level, and shows their functional genes and pathways. It answers both “who is there?” and “what can they do?”. Shotgun sequencing also detects bacteria, fungi, protists, and Archaea, and can even discover new or previously unknown species, expanding our knowledge of the human microbiome.
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Culture-based methods:
- Grow live organisms in nutrient media.
- Useful for confirming specific organisms with known growth requirements (e.g., pathogens, Bifidobacterium spp, Lactobacillus spp).
- Can test antimicrobial susceptibility in those organisms.
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However, microbes grow under different conditions (e.g. nutrients, oxygen, pH). As a result, culture methods only capture a small subset of the microbiome. Current research suggests culture conditions are only known for about 63% of gut microbes (Pribyl et al 2025), and testing even this portion would require hundreds of different cultures.
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In short, culture-based methods are best for targeted questions like pathogen detection or antibiotic resistance. Shotgun metagenomics gives a broader, community-wide view, showing both the diversity of organisms and their potential functions.
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10.1038/s43705-021-00014-2