Why I Bake With Organic Flour (and Why It Matters More Than You Think)

If you’ve ever wondered why I’m so committed to organic ingredients, especially organic flour, this is the deep dive.

This isn’t about perfection or fear. It’s about choosing ingredients that align with how living systems work: soil ecosystems, microbial ecosystems, and our bodies. Bread is simple food, but the story behind the grain is anything but simple.

The short version

I use organic flour because organic agriculture prohibits most synthetic pesticides and herbicides, and in particular it does not allow the use of glyphosate-based herbicides on organic crops. (USDA) That matters because modern grain production is often paired with chemical weed control, and glyphosate is the most widely used herbicide in the world. Glyphosate exposure debates tend to focus on cancer, but the topic is broader than that. One of the most biologically relevant questions is: what does a broad-use herbicide do to microbial life, in soil and in the gut?

Soil has a microbiome too (and it runs the whole show)

Soil is not “dirt.” It’s a living ecosystem filled with bacteria, fungi, protozoa, and other organisms that:

• cycle nutrients (helping plants access nitrogen, phosphorus, minerals)

• build soil structure

• support plant resilience and immune function

• influence nutrient density and crop quality

Healthy soil is a microbial city. When farming practices harm that living community, soil becomes more like lifeless substrate: it can still grow crops, but often with heavier reliance on external inputs.

Research comparing organic and conventional systems has repeatedly found that organic farming is associated with increased soil microbial abundance and activity, and distinct microbial communities connected to nutrient cycling. (OUP Academic)

This is one reason “organic” matters to me. I want grain grown in a way that supports living soil, not grain that succeeds in spite of soil biology being stressed.

Glyphosate: what it does, biologically

Glyphosate’s primary herbicidal action is inhibition of an enzyme called EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) in the shikimate pathway. That pathway is essential for producing aromatic amino acids in plants and is also present in many microorganisms. (PMC)

That detail matters because it helps explain why glyphosate is often described as having antimicrobial effects under certain conditions: it can inhibit organisms that rely on the same biochemical machinery. (That does not mean it’s a prescription antibiotic or that it affects every microbe equally. Biology is quite nuanced.)

Researchers have explored microbial sensitivity by analyzing EPSPS variants across species and assessing which organisms may be intrinsically more sensitive or resistant. (PMC)

What the science says about glyphosate and the gut microbiome

This is an active research area. The most honest summary is:

• There is evidence (especially from animal studies, mechanistic work, and reviews) that glyphosate exposure can alter gut microbial composition and metabolic outputs.

• The magnitude and human relevance of these changes depends on dose, formulation, exposure route, diet, and individual biology.

• Translating preclinical findings into real-world human outcomes is complex and still evolving.

A 2023 review focused specifically on glyphosate and gut microbiome impacts, summarizing a growing body of mechanistic and preclinical evidence. (PMC) A 2023 mouse study reported changes in gut microbiota composition, including reductions in certain commensal bacteria and changes in metabolic pathways like short-chain fatty acid (SCFA) biosynthesis. (PMC) A 2024 PRISMA-based systematic review concluded that glyphosate and its formulations can induce intestinal dysbiosis in preclinical models, including effects on bacterial metabolism and gut barrier-related features (for example, intestinal permeability and mucus-related parameters). (RSC Publishing)

Again: these findings do not prove “glyphosate ruins everyone’s gut.” But they do support a reasonable, science-based motivation to reduce exposure when you can, especially if gut health is a personal priority.

“But aren’t residues regulated?”

Yes. And it’s worth saying plainly: regulatory agencies do not fully agree on how to interpret glyphosate’s risk profile.

• The International Agency for Research on Cancer (IARC) classified glyphosate as “probably carcinogenic to humans” (Group 2A) in 2015. (IARC)

• The U.S. EPA concluded in its 2020 interim decision that glyphosate is “not likely to be carcinogenic to humans” and did not identify human health risks of concern when used according to label directions. (US EPA)

Separately, multiple reviews of residue monitoring data report that most detected glyphosate residues in foods are below regulatory limits. (ift.onlinelibrary.wiley.com)

So why choose organic anyway?

Because “below legal limits” is not the same as “aligned with how I want my food produced,” and it’s not the same as “irrelevant to sensitive biological systems in every context.” If a chemical is designed to interfere with plant biochemistry and can affect microbial biology under some conditions, I’d rather not make it a background ingredient in a staple food if I can help it.

Organic flour: what it does and doesn’t guarantee

Organic certification means farmers must follow organic rules, which are built around allowing natural substances while prohibiting most synthetic ones, with specific exceptions. (USDA) That includes not permitting synthetic herbicides like glyphosate in organic production.

However, it’s also true that residues can sometimes appear in organic foods due to environmental contamination (drift, shared infrastructure, legacy soil contamination, etc.). Organic is not magic. It’s a set of practices and standards that meaningfully reduce certain exposures and support different farming systems.

Why organic matters even beyond glyphosate

Even if you never said the word “glyphosate” again, organic still matters for a few big reasons:

1) Soil ecology and long-term fertility Organic systems often support greater microbial abundance and activity, which is foundational for nutrient cycling and resilient agriculture. (PLOS)

2) Reduced synthetic pesticide residues A large systematic review comparing organic versus conventional foods reported that organic foods tend to have lower pesticide residues and other certain contaminants (though the details vary by region, crop, and study design). (PMC)

3) Values and transparency Organic certification is not perfect, but it’s one of the clearer, regulated signals available to consumers about how a food was produced.

The sourdough factor: fermentation changes the bread itself

Even the best flour is just the beginning. The way bread is made matters too.

Sourdough is a fermentation ecosystem (wild yeast + lactic acid bacteria). That fermentation produces organic acids and enzymes that can change the nutritional profile of the finished loaf. Reviews and systematic reviews have documented that sourdough fermentation can:

• reduce phytic acid (phytate), which can improve mineral bioaccessibility

• increase mineral bioavailability under certain conditions

• lower glycemic response compared with some conventional breads (depending on formulation and process)

• influence fiber characteristics relevant to gut physiology

A systematic review on the nutritional benefits of sourdough notes evidence for improved nutrient bioaccessibility and potential glycemic effects, while also being cautious about how these translate clinically. (PMC)A major review of sourdough fermentation literature also highlights increased mineral bioavailability, reduced anti-nutritional factors, and lower glycemic index as consistent findings across many studies. (ScienceDirect)

This is one reason I love sourdough: it’s not just “bread that tastes better.” It’s a biological process that can make grain more compatible with human digestion for many people.

Putting it all together: why this is my standard

My commitment to organic flour and organic ingredients is not about being trendy or “clean.” It’s about choosing:

• farming systems that support microbial life in the soil (PLOS)

• ingredients produced without synthetic herbicides like glyphosate (USDA)

• a fermentation process that improves flavor and can improve nutritional characteristics of bread (PMC)

I see bread as a bridge between ecosystems: soil, seed, culture, and body. Organic flour is one way to keep that bridge built from sturdier materials.

If you ever want to talk about flour sourcing, grain varieties, fermentation, or why a loaf tastes the way it does, I love those conversations. Bread is humble, but it’s also quietly profound.

Sources (selected)

• USDA Organic standards overview and National List framework (USDA)

• Glyphosate mechanism via EPSPS inhibition (structural/biochemical work) (PMC)

• Soil microbiome benefits in organic systems (meta-analysis; soil quality and microbial activity) (PLOS)

• Gut microbiome and glyphosate (review, systematic review, and preclinical study) (PMC)

• Regulatory positions: IARC 2015 classification and EPA 2020 interim decision (IARC)

• Sourdough nutrition reviews/systematic review (PMC)