Gastrointestinal Health Marker Guide

Faecal pH

What this marker measures

A faecal pH test measures stool acidity or alkalinity. Stool pH is influenced by microbial fermentation, short-chain fatty acid production, diet, and gut transit^1–3. Low pH may suggest increased carbohydrate fermentation or malabsorption, while higher pH may reflect altered fermentation patterns or slower transit.

Clinical associations*

Consider this marker when your patient presents with:

Altered gut transit

Diarrhoea, rapid transit, constipation, or slow transit where fermentation patterns may be relevant. Studies suggest high pH may be associated with a slower gut transit time, while low pH may be associated with a faster gut transit time.

Dietary fermentation context

Low fibre intake, restricted diet, or altered SCFA-producing capacity. SCFA production and growth of beneficial bacteria tend to lower intestinal and faecal pH.

Carbohydrate malabsorption

Bloating, gas, diarrhoea, or suspected lactose/fructose malabsorption, particularly with low faecal pH. Acidic stool can support suspicion of carbohydrate malabsorption in the right clinical context.

*In addition to the assay’s intended use, all clinical associations have been reviewed by the Microba science team to ensure clinical validity supported by Microba’s cited literature.

Interpreting the result

OUT OF RANGE LOW

Below the literature-derived lower threshold of 5.7

May reflect increased carbohydrate fermentation, carbohydrate malabsorption such as lactose intolerance, lactulose use, or faster transit/diarrhoeal states. Lower pH may be associated with higher faecal fermentation acids, including SCFAs, but does not directly measure SCFA absorption.

WITHIN RANGE

Within the literature-derived reference range of 5.7 – 7.3.

Faecal pH is within the literature-derived reference range of 5.7 – 7.3. This suggests stool acidity is not abnormal in isolation. Interpret alongside symptoms, stool form, transit time, diet, and microbiome markers.

OUT OF RANGE HIGH

Above the literature-derived upper threshold of 7.3.

May reflect altered fermentation patterns, lower carbohydrate fermentation, greater protein fermentation, slower transit, constipation, or methane-associated patterns. Interpret alongside stool frequency, Bristol stool type, methane-producing potential, diet, and symptoms.

^negative result does not exclude intermittent or low-level bleeding. If bleeding is clinically suspected, further investigation is recommended regardless of this result.

Treatment guidance

Approach depends on whether pH is low or high.

Dietary strategies

High-dose resistant starch supplementation may reduce faecal pH^4,5. GRADE D

Increasing dietary fibre may reduce faecal pH^6–9. NHigh-fibre, vegan (but not vegetarian) diets may be associated with lower faecal pH^10–12. GRADE D

Out-of-range lactoferrin requires referral to a medical practitioner if cause is unknown, persistent or red-flag symptoms are present. GRADE D

Tips for discussing out-of-range results

Your faecal pH result gives us indirect insight into gut fermentation patterns and stool habits. Gut microbes produce acids, including short-chain fatty acids, that influence pH. Targeted dietary changes, such as adjusting fibre and resistant starch based on your symptoms and tolerance, may help support healthier fermentation patterns.”

Evidence grading for patient management insights

The letter grades shown next to each patient management insight show the quality of the research behind it. Every insight provided has been through a rigorous review of the scientific literature and graded using the NHMRC Levels of Evidence, so you can see exactly how strong the evidence is before applying it in practice.

Faecal pH_ Reference sourcesSource references for all clinical associations, interpretation definitions, and patient management insights on this card.

1. Brinck, J. E. et al. Intestinal pH: a major driver of human gut microbiota composition and metabolism. Nat Rev Gastroenterol Hepatol 22, 639–656 (2025).
2. Procházková, N. et al. Gut physiology and environment explain variations in human gut microbiome composition and metabolism. Nat Microbiol 9, 3210–3225 (2024).
3. LaBouyer, M. et al. Higher total faecal short-chain fatty acid concentrations correlate with increasing proportions of butyrate and decreasing proportions of branched-chain fatty acids across multiple human studies. Gut Microbiome 3, e2 (2022).
4. Shen, D. et al. Positive effects of resistant starch supplementation on bowel function in healthy adults: a systematic review and meta-analysis of randomized controlled trials. International Journal of Food Sciences and Nutrition 68, 149–157 (2017).
5. Noakes, M., Clifton, P., Nestel, P., Le Leu, R. & McIntosh, G. Effect of high-amylose starch and oat bran on metabolic variables and bowel function in subjects with hypertriglyceridemia. The American Journal of Clinical Nutrition 64, 944–951 (1996).
6. Haack, V. S., Chesters, J. G., Vollendorf, N. W., Story, J. A. & Marlett, J. A. Increasing amounts of dietary fiber provided by foods normalizes physiologic response of the large bowel without altering calcium balance or fecal steroid excretion123. The American Journal of Clinical Nutrition 68, 615–622 (1998).
7. Lampe, J. W., Slavin, J. L., Melcher, E. A. & Potter, J. D. Effects of cereal and vegetable fiber feeding on potential risk factors for colon cancer. Cancer Epidemiol Biomarkers Prev 1, 207–211 (1992).
8. Kashtan, H. et al. Manipulation of fecal pH by dietary means. Preventive Medicine 19, 607–613 (1990).
9. Hillman, L., Peters, S., Fisher, A. & Pomare, E. W. Differing effects of pectin, cellulose and lignin on stool pH, transit time and weight. British Journal of Nutrition 50, 189–195 (1983).
10. Trefflich, I., Dietrich, S., Braune, A., Abraham, K. & Weikert, C. Short- and Branched-Chain Fatty Acids as Fecal Markers for Microbiota Activity in Vegans and Omnivores. Nutrients13, 1808 (2021).
11. Zimmer, J. et al. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur J Clin Nutr 66, 53–60 (2012).12. van Dokkum, W., de Boer, B. C., van Faassen, A., Pikaar, N. A. & Hermus, R. J. Diet, faecal pH and colorectal cancer. Br J Cancer 48, 109–110 (1983).