# Microbial pigments & bio-dyes

Chromophores and conjugation, why substantivity and reactive groups separate a dye from a pigment, vat chemistry and bio-indigo, and the mycotoxin risk in some fungal pigment pathways.

Being coloured is easy. Being a dye means staying on the fibre — and that is a bonding problem, not a colour problem.

Source: https://en.bioecon.ru/docs/biochem-industrial/specialty-fine-chem/biodyes-microbial-pigments/
Updated: 2026-08-25



Microorganisms make a wide range of coloured compounds — carotenoids, the red prodiginines of *Serratia*, violacein, fungal azaphilones from *Monascus*, melanins, the blue indigoidine. Producing them by fermentation is well demonstrated. Turning them into textile dyes is a separate problem, and it is where the field's difficulty lies.

## Why a molecule is coloured

Colour comes from a **chromophore**: a system of alternating single and double bonds, whose delocalised electrons can be excited by visible light. The longer the conjugated system, the lower the energy needed and the longer the wavelength absorbed — which is why short conjugation gives yellows and extended conjugation gives reds and blues. Auxochromes, substituent groups such as amino or hydroxyl, shift the absorption further and often provide the chemistry by which the dye attaches to something.

That is the whole of the colour question, and microbial pigments answer it well.

## Dye and pigment are not synonyms

A **pigment** is insoluble and sits on a surface, held by a binder. A **dye** dissolves, penetrates the fibre and stays there after washing. Staying there is called **substantivity**, and it is a property of the interaction between dye and fibre, not of the dye alone.

Different fibres demand different chemistry. Cellulose — cotton, viscose — is hydroxyl-rich and mildly anionic in water; it is dyed with anionic direct dyes that bind by hydrogen bonding and van der Waals forces, or, for real wash-fastness, with **reactive dyes** that form a covalent bond to the fibre hydroxyl. Wool and silk are proteins with ionisable groups and take acid dyes by ionic interaction. Polyester is non-polar and crystalline with no bonding sites at all, and is dyed with disperse dyes forced into the fibre at high temperature.

**This is the constraint on microbial pigments.** They evolved as metabolites, not as textile dyes, so most have no reactive group and little affinity for cellulose. They wash out. The available answers are all borrowed from natural-dye practice or from synthetic chemistry: mordanting with metal salts to bridge dye and fibre, chemically derivatising the pigment with a reactive anchor, or restricting use to protein fibres where ionic binding does the work. Each adds cost or reintroduces the chemistry that was being avoided.

## Indigo is the instructive case

Indigo is insoluble and has no affinity for cotton in that state. It is applied by **vat dyeing**: reduce it to the soluble, yellow-green leuco form, let that penetrate the fibre, then re-oxidise it in air so the insoluble blue re-forms *inside* the fibre and is trapped mechanically rather than bonded chemically.

Biology can supply the molecule — indole hydroxylated to indoxyl by an oxygenase, then dimerising spontaneously in air. But the dyeing step still needs reduction, conventionally with sodium dithionite, which is the main environmental burden of denim dyeing. Routes that produce the soluble precursor **indican** and release indoxyl enzymatically at the fibre address the actual problem, whereas producing indigo biologically and then vatting it conventionally does not.

## One safety point specific to fungal pigments

Some fungal pigment pathways are related to, or co-expressed with, mycotoxin pathways in the same or neighbouring species — *Monascus* pigments and citrinin being the documented example. Strain selection and toxin screening are part of qualifying a fungal colorant, not a formality, and this applies whether the product is destined for textiles or for food.