The Microbiome and Detoxification

May 20th, 2022 | Posted in Info

No article on health these days is complete without reference to the effects of the microbiome. Detoxification is no exception. The human gut is home to a broad spectrum of microorganisms. The bacteria and other microorganisms that colonise the gastrointestinal tract are called the gut microbiota or the microbiome. The gut microbiome plays a profound role in metabolic processes, energy production, immune function, cognitive development and homeostasis. The microbiome influences many organs and body systems beyond the gut, including the brain via the gut-brain axis. The gut microbiota may be altered by factors such as antibiotics, diet and environmental toxins such as pesticides. The micro-organisms in our guts play a key role in breaking down or inactivating toxic chemicals and enabling their elimination from the body. Different bacteria break down different toxins which is why having a diverse range of gut organisms is so beneficial for health. Here are some of the ways the organisms in our guts have been found to help with detoxification:

Bisphenol A (BPA) – a constituent of some plastics and epoxy resins, widely applied to food packaging, receipts, money, dental composites and canned food liners. BPA is a known endocrine disruptor. It’s also hard to avoid. The good news is that some probiotic species have been shown to aid the degradation and removal of BPA. The beneficial organisms include Bifidobacterium Breve, Lactobacillus casei, Lactococcus lactis, Bacillus subtilis, Lactobacillus plantarum, Enterococcus faecalis, and Saccharomyces cerevisiae. These may all reduce the adverse effects of BPH on human and animal health (1,2).

Pesticides – Organophosphates (OPs) are toxic compounds used in agriculture and industry. Consumption of these compounds affects the central nervous system contributing to developmental abnormalities, endocrine disruption, neurodegeneration, neuro-inflammation and cancer. Research suggests that certain lactic acid bacteria reduce OP toxicity as they use the carbon and phosphorous in OPs as food. Kimchi has been found to contain some of the organisms that break down OPs including Lactobacillus brevis, Lactobacillus plantarum and Lactobacillus sakei (3,4,5).

Heavy Metals –  cadmium, lead, arsenic and aluminium, have toxic effects on humans, animals and plants. They are widespread in the environment existing in soil, water, and air. Lactobacillus bacteria may reduce heavy metal toxicity by binding and sequestering heavy metals to their cell surfaces and removing them via the bowel (6,7).

Food Preservatives – nitrite is added to meat products to help retain colour and prevent decay. It is known that excessive intake can be carcinogenic. The probiotic L. fermentum RC4 has been shown to degrade nitrite (8). The fermented food kimchi may also contain a strain of bacteria that is capable of breaking down sodium nitrate (9,10).

Perchlorate – an ingredient in jet fuel and fireworks that contaminates the environment and our food.  Perchlorate is so pervasive that it is commonly found in breast milk and urine. It is a known endocrine disruptor that blocks the iodine receptor in the thyroid, resulting in hypothyroidism and neurological dysfunction. Bifidobacterium Bifidum is capable of degrading perchlorate. This may explain why breast fed infants have lower levels of perchlorate than formula fed babies due to the bacteria in breast milk’s ability to degrade perchlorate (11).

Heterocylic Amines (HCA) – these are formed when meat is cooked at high temperatures. They are mutagenic (damaging to DNA). Some Lactobacillus strains significantly reduce the toxicity of theses compounds (12,13).

One of the key sources of beneficial organisms is the soil in which our food is grown. Eating organic food is one of the best ways of ensuring that the food you eat is rich in beneficial organisms and low in toxins.

See also blog posts on Daily Habits for Detoxification and Daily Detoxing – Dietary Tips.


1. Kenji Oishi et al. Effect of probiotics, Bifidobacterium breve and Lactobacillus casei, on bisphenol A exposure in rats. Biosci Biotechnol Biochem. 2008 Jun;72(6):1409-15.

2. Kyrila G et al. Bisphenol A removal and degradation pathways in microorganisms with probiotic properties. J Hazard Mater. 2021 Jul 5;413:125363.

3. Roman P et al. Microbiota and organophosphates. Neurotoxicology. 2019 Dec;75:200-208.

4. Shah Md Asraful Islam et al. Organophosphorus hydrolase (OpdB) of Lactobacillus brevis WCP902 from kimchi is able to degrade organophosphorus pesticides. J Agric Food Chem. 2010 May 12;58(9):5380-6.

5. Kye Man Cho et al. Biodegradation of chlorpyrifos by lactic acid bacteria during kimchi fermentation. J Agric Food Chem. 2009 Mar 11;57(5):1882-9.

6. Monachese M et al. Bioremediation and tolerance of humans to heavy metals through microbial processes: a potential role for probiotics? Appl Environ Microbiol. 2012 Sep ;78(18):6397-404.

7. Abdel-Megeed RM. Probiotics: a Promising Generation of Heavy Metal Detoxification. Biol Trace Elem Res. 2021 Jun;199(6):2406-2413.

8. Zeng X et al. Potential mechanism of nitrite degradation by Lactobacillus fermentum RC4 based on proteomic analysis. J Proteomics. 2019 Mar 1;194:70-78.

9. Chang-Kyung Oh et al. The depletion of sodium nitrite by lactic acid bacteria isolated from kimchi. J Med Food. 2004;7(1):38-44.

10. Nowak A et al. Probiotic lactic acid bacteria detoxify N-nitrosodimethylamine. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2014 Jul 10. Epub 2014 Jul 10.

11. Shelor CP et al. Breastfed infants metabolize perchlorate. Environ Sci Technol. 2012 May 1 ;46(9):5151-9. Epub 2012 Apr 20.

12. Nowak A et al. Ability of probiotic Lactobacillus casei DN 114001 to bind or/and metabolise heterocyclic aromatic amines in vitro. Eur J Nutr. 2009 Oct ;48(7):419-27. Epub 2009 May 16.

13. Khosravi-Darani K et al. Detoxification of Heterocyclic Aromatic Amines by Probiotic to Inhibit Medical Hazards. Mini Rev Med Chem. 2019;19(15):1196-1203.