Quick answer: Microbial diversity is the variety and abundance of microbes in your gut, and higher diversity is generally linked with better health. Dysbiosis is an imbalance, with too many harmful microbes or too few beneficial ones. A low-fiber, high-sugar diet and antibiotics are common causes. Dysbiosis can lead to inflammation, increased gut permeability and poor nutrient absorption.
Key takeaways
Microbial diversity is the variety of microbes in the gut, and a more diverse community tends to be more resilient.
Dysbiosis is an imbalance, such as an overgrowth of harmful microbes, a loss of helpful ones or reduced diversity, often linked to diet, antibiotics and stress.
Dysbiosis can drive inflammation and gut permeability, and a wide variety of plants and fermented foods may help restore balance.
Microbial diversity
Diversity refers to the variety of microorganisms living in the gut, mainly the colon. A diverse community is more resilient. See what your gut bacteria do.
What is dysbiosis?
Dysbiosis is an imbalance of the gut microbiome: an overgrowth of harmful microbes, a loss of beneficial ones, or reduced diversity.
Causes of dysbiosis
Poor diet
Diets high in processed foods and sugar and low in fiber can starve beneficial bacteria and reduce microbial diversity.
Antibiotics
Antibiotics can be lifesaving, but they can also disrupt helpful bacteria, and changes can last for months.
Consequences of dysbiosis
Dysbiosis can drive inflammation, as harmful microbes release toxins that trigger immune responses, and increased permeability, since inflammatory signals can loosen tight junctions (see leaky gut overview). It can also lead to nutrient malabsorption, as digestion and vitamin production suffer.
Microbial diversity and healthy aging
The gut microbiome changes with age, and loss of diversity is linked with inflammation and frailty. Feeding a diverse microbiome is one of the simplest long-term health habits.
How to support diversity
Eat a wide variety of plants each week, include fermented foods if tolerated, and use antibiotics only when needed, supporting your gut afterward. Follow Phase 3 of the protocol (see Flora Fix).
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have ongoing bloating, gas, diarrhea or constipation, or food reactions that seem to be multiplying. The same is true if you have fatigue, skin flares or joint aches alongside gut symptoms, or if you want a personalized gut plan instead of guessing.
See a medical provider promptly for blood in your stool, black stools, unexplained weight loss, persistent vomiting, severe abdominal pain, fever, or trouble swallowing.
What the research shows
Low microbial diversity has been tied to metabolic health. A 2013 study by Le Chatelier and colleagues sequenced the gut microbes of 292 Danish adults and found that about 23% had low bacterial richness. That group had more body fat, more insulin resistance, less favorable cholesterol and more inflammation than people with high richness, and those with obesity in the low-richness group gained more weight over time. Because this was observational, it cannot show whether low diversity causes these problems or results from them.
Probiotics are not always the right step after antibiotics. In a 2018 study by Suez and colleagues that took gut tissue samples from people and mice after a course of antibiotics, a multi-strain probiotic colonized the human gut lining more readily, but it delayed the return of each person’s own native microbes compared with letting the gut recover on its own. A transplant of the person’s own stool, banked before the antibiotics, restored the original microbiome within days. The human groups were small and the probiotic was a single product, so this does not mean all probiotics are harmful, but it supports choosing them thoughtfully.
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Questions to bring to your clinician
These questions can help you get the most out of your next visit.
Do my symptoms or history suggest dysbiosis, and would testing help?
Could dysbiosis be part of what is behind my symptoms?
Which foods or habits might help rebalance my gut bacteria?
Would a stool test help us understand my gut balance?
Frequently asked questions
What is dysbiosis?
An imbalance in the gut microbiome.
What causes dysbiosis?
Low-fiber, high-sugar diets, antibiotics, stress and infections are common causes.
How do I increase gut diversity?
Eat a wide variety of fiber-rich plants and fermented foods.
Can antibiotics cause dysbiosis?
Yes, sometimes for months. Take them when needed and support your gut afterward.
Sources
- Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013. PMID: 23985870. https://pubmed.ncbi.nlm.nih.gov/23985870/
- Suez J, Zmora N, Zilberman-Schapira G, et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell 2018. PMID: 30193113. https://pubmed.ncbi.nlm.nih.gov/30193113/
- Sonnenburg ED, et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 2016. PMID: 26762459. https://pmc.ncbi.nlm.nih.gov/articles/PMC4850918/
- Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011. PMID: 20847294. https://pmc.ncbi.nlm.nih.gov/articles/PMC3063582/
- Capaldo CT, Nusrat A. Cytokine regulation of tight junctions. Biochim Biophys Acta 2009. PMID: 18952050. https://pmc.ncbi.nlm.nih.gov/articles/PMC2699410/
- Claesson MJ, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012. PMID: 22797518. https://pubmed.ncbi.nlm.nih.gov/22797518/
- MedlinePlus: Antibiotics
This article is for educational purposes only and is not medical advice. It does not replace an individual evaluation. Talk with your healthcare provider before starting supplements or changing medications, especially if you are pregnant, nursing, or managing a health condition.
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