These microorganisms improve nutrient availability by breaking down organic matter, fixing nitrogen, and solubilizing phosphorus, all of which increase the nutritional content of crops (Singh et al., 2025). Beneficial microbes like mycorrhizal fungi and plant growth-promoting rhizobacteria enhance root development and nutrient uptake, leading to more robust and nutritionally rich produce (Yadav et al., 2021).
But modern agricultural practices — heavy tilling, chemical fertilizers, and pesticides — have disrupted this microbial network, depleting soil biodiversity and fertility (Hartmann & Six, 2022).
When soil microbiomes are healthy, the crops they grow tend to be more
nutrient-dense. Organic farming and sustainable practices — which protect
microbial life — are associated with higher levels of vitamins, antioxidants,
and micronutrients in plants (Bertola
et al., 2021). For example, the use of compost and reduced chemical inputs not only
fosters microbial diversity but also improves soil organic matter and crop
quality (Marín-Guirao
et al., 2019).
The human gut microbiome, which helps digest food, regulate the immune
system, and produce essential compounds, is shaped in part by the foods we eat.
Diverse, fiber-rich, and minimally processed foods feed beneficial gut
bacteria. When those foods come from microbially rich soils, they may carry
more diverse microbial “passengers” — and potentially prebiotic compounds —
that support gut health (Blum et
al., 2019).
Evidence shows that our gut microbiome diversity has dramatically
decreased over time, in part due to industrialized diets and reduced contact
with soil microbes. This microbial loss has been linked to an increase in
lifestyle-related diseases like obesity, diabetes, and allergies (Lyamin
et al., 2024).
Special note - as a professional horticulturist with over 25 years of experience, I have developed several commercial products with compost as a core component. Here’s what you need to know: Compost is terribly inconsistent from a nutrient standpoint. Microbially, it’s awesome! But, essential plant nutrition needs to be consistent for the healthiest plants. The classic source is manure, but if you live in the city like me, you probably don't have farm animals either.
For best results, be sure to supplement your compost with organic fertilizers and soil food that have guaranteed amounts of N, P, K, and other essential elements. I only use organic inputs in my garden and there are several options available for purchase.
Conduct a soil test to determine how much to apply - either to your compost pile, or directly to your garden/soil.
This is especially important if you’re relying on compost to provide the bulk of your plant nutrients.
