How Soil Bacteria Shapes Coffee Flavours

A recent study in Scientific Reports (June 3, 2025) reveals a fascinating link between bacterial communities in coffee farms and the unique flavours of specialty Arabica coffee.

Researchers sampled 22 Arabica coffee farms in Cundinamarca, Colombia:

- Half were sun-grown coffee

- Half was shade-grown coffee 

They collected 320 soil samples and 320 cherry samples, categorising farms by whether they consistently produced a sought-after "brown-sugar" flavour profile

Using DNA sequencing, they identified which bacterial strains were present in soils and cherries, and searched for patterns linked to flavour and farming methods.

What did they discover?

1. Different Worlds Underfoot vs On-Fruit

Only about 3% of bacterial species were shared between soil and coffee cherries. Soil hosted a more diverse microbiome, while the fruit carried fewer—but distinct—bacterial types. This highlights how plant and soil ecosystems nurture their own unique bacterial communities.

2. Flavour Meets Farm Management

Shade farms producing the "brown-sugar" flavor had unique, identifiable bacterial communities in both soil and fruit.

Some bacterial strains were strongly and consistently associated with high-quality flavor—but these differed between sun- and shade-grown farms. It means “microbial terroir”, or bacteria influenced by environment, may help define coffee taste.

3. Star Bacteria Linked to Flavour

In shade, flavourful farms, bacteria like Acidothermus, Chujaibacter, and Sphingomonas were more abundant. On the cherries themselves, Pantoea stood out in "flavored" shade farms. These strains could be key partners in crafting distinctive coffee flavour.

Why is this important?

Microbial insights might help develop eco-friendly biofertilisers that enhance quality, encouraging shade-coffee farming which benefits ecosystems.

Flavour consistency & innovation: Understanding which microbes deliver great flavour opens doors to precision farming and artisanal profiling.

Shade farms are biodiversity hotspots, so linking their microbiomes to desirable flavours is a win–win for nature and coffee!

References

Kutos, S., Bennett, R., Santos, D. et al. Soil and cherry bacterial communities predict flavor on coffee farms. Sci Rep 15, 19387 (2025)