Do you know anything about the degradation products? For instance if they are acidic you will need to lower the pH before running the extraction procedure. You can also change the organic solvent. 

Thank you for your suggestion Omar. I don't have exact idea about the products however, I'll try with your suggestion.

Textile dyes vary widely in terms of structure and solubility as the fibres and methods by which they are applied are different in character.  Depending upon these qualities and the nature of the biological degradation, they could produce breakdown products that will not be extracted readily by ethyl acetate from an aqueous medium.  For example, let's assume that you are using the most common water-soluble structural type, i.e. drawn from the sulphonated azo class (a chemical type very typical of acid, direct or reactive dyes), and the degradation process is reductive.  If so, then it is possible that the fragments you are generating will be highly hydrophilic, consisting of sulpho- and/or amine-substituted aromatics that partion very strongly towards water in an aqueous/ethyl acetate system.  In such case, you could try adding salt to lower solubility in the aqueous phase or manipulating pH as Omar suggests, but even then, extraction may be inefficient and also miss particularly hydrophilic species.  Consequently, other techniques might be needed for which you get inspiration from the enormous number of papers out there describing studies into dye degradation products:  some authors are fortunate enough to have access to HPLC-MS for example which enables to identify some of the breakdown products.

Thank you for your great explanation Andy.

As you are working on textile dyes, only ethyl acetate extraction is enough to find out the fate of metabolism. In your case dye might be mineralized to very simpler compounds. To get fate of metabolism go for partial degradation and extract.

As I have experienced, dye degradation products have different chemical and physical properties than the parent dye molecule. In case of azo dyes I was able to detect some monocyclic aromatic amines and naphthalene based compounds in my decolorized broth.

Ethyl acetate extraction is a good method to extract such compounds, though you can also try using diethyl ether as an extracting solvent, since it has less polarity index than ethyl acetate and also has low solubility in water. Generally, azo dyes (or textile dyes) have high polarity due to addition of the sulfo group. It can be expected that dye degradation products does not have a sulfo group as it has been often reported that desulfonation is a common phenomenon (in case of microbial degradation, I am not sure about other physico-chemical degradation processes). So, you can expect that the degradation products might have less polarity than the parent compound.

Also, as others have suggested you can also try to vary the pH of the medium for the better extraction. As in my case microbial growth alters the pH of the media therefore, for some compounds it is advisable to alter the pH before performing extraction procedures.

If you are working at higher concentration and on a single dye (rather than textile effluent sample) you can try to speculate the degradation products and read about their properties. You can also perform a TLC before extraction or after extraction to see any difference in the composition of the medium, you can see some new spots on the TLC plate and can compare the polarity of the degradation products and the dye (start with a solvent system with low polarity and then subsequently increase the polarity). TLC worked for me, though you can only detect major reaction products but it advisable to always preform such preliminary experiments before moving to HPLC. Also, you can perform a UV-Vis scan of the decolorized broth, it can help to identify the such degradation products (however, the salts and other components in the decolorized medium can cause mixing of peaks so it is a crude way of detection).

Finally, if you are working on bio-degradation, it is possible that the dye is mineralized so you are not able to detect any thing after extraction.

Feel free to ask if you have any queries.