What's the difference between shotgun metagenomic sequencing and culture-based methods?

They're two very different approaches, and they answer different questions.
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Shotgun metagenomic sequencing reads all the DNA in a sample. That means we can identify microbes down to species — and sometimes strain — level, and see their functional genes and pathways. It tells us both who's there and what they can do. It detects bacteria, fungi, protists, and Archaea, and can even discover entirely new species.
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Culture-based methods grow live organisms in nutrient media. They're useful for confirming specific organisms with known growth requirements — pathogens, Bifidobacterium, Lactobacillus — and for testing antimicrobial susceptibility. But culture only captures a small subset of the microbiome. Current research suggests we only know the culture conditions for about 63% of gut microbes, and testing even that portion would require hundreds of different cultures.
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In short, culture is great for targeted questions like pathogen detection. Shotgun metagenomics gives you the community-wide view — diversity and function in one test.