Probiotics - Are They Really Necessary
Dr. Afsoun Khalili
Afsoun Khalili is a Naturopathic Doctor in Toronto and a graduate of the Canadian College of Naturopathic Medicine (CCNM) with a bachelor of science in biochemistry. While Dr. Khalili’s practice is eclectic, using all naturopathic modalities for treatment, patients can also benefit from her advanced training in Cosmetic/Facial rejuvenation acupuncture and anti-aging treatments.
In addition to co-owning a practice in the Toronto area, she is currently an associate professor and clinic faculty member at CCNM lecturing and teaching Advanced Clinical Nutrition as well as supervising 4th year clinical residents at the RSNC teaching clinic at CCNM.
Dr. Khalili is the creator and facilitator of a healthy lifestyle change and weight management program at the RSNC, called “Be Your Best Self” (BYBS) which has now been running successfully for over 15 years.
Dr. Khalili has been involved with the Corporate Wellness Program (CWP) at CCNM in the past. Additional topics which she currently treats and has written about and lectured on include obesity, stress and stress management-meditation, eating whole and healthfully, detoxification and food sensitivities, gastrointestinal disorders, sleep disorders, body image issues, diabetes, thyroid health and menopause among many others.
Afsoun Khalili: Trainer | Canadian College of Naturopathic Medicine
Whichever way you look at it, we have more bacteria than we have human cells. We are covered in bacteria inside and out, and this is really interesting and important because our gut is our second brain.
Summary
- Probiotics are live microorganisms found in fermented foods that have been linked to human health, longevity, and disease prevention for thousands of years. - Beyond digestive issues, healthy gut bacteria support the immune system and help regulate systemic conditions such as hypertension, diabetes, and obesity. - The gut-brain axis is a bidirectional communication system where gut microbiome health can directly impact mental health conditions like anxiety, depression, and autism. - Lifestyle factors, including regular low-intensity exercise, consistent sleep cycles, and stress reduction, are essential for fostering a diverse and healthy bacterial environment. - Because people respond differently to standard supplements, the future of probiotics involves personalized treatments tailored to an individual’s unique gut microbiota.
Article
Probiotics, Gut Health, And The Limits Of One-Size-Fits-All Wellness
At Biohacker Summit 2018 Toronto, Dr. Afsoun Khalili Made A Case Not For More Supplements, But For Smarter, More Personal Use Of Them
The modern probiotic has been sold as a small capsule with outsized promise: calmer digestion, stronger immunity, better mood, cleaner skin, steadier blood sugar. In health food shops and pharmacy aisles, it arrived as a quiet miracle of the wellness age, an easy answer to the chaos of modern living.
But in her presentation, *Probiotics - Are They Really Necessary*, at **Biohacker Summit 2018 Toronto** on **15 October 2018**, **Dr. Afsoun Khalili** offered a more nuanced, and ultimately more compelling, view. Yes, probiotics mattered, she argued. They were deeply entangled with human health, from inflammation to metabolism to mental wellbeing. But no, they should not be treated as universal cure-alls.
“**Probiotics should not be universally given as a one-size-fits-all supplement,**” Dr. Khalili said. “**The future of health lies in tailoring probiotics to an individual based on their own unique gut microbiota.**”
It was a decisive rebuttal to one of wellness culture’s favourite instincts: if something is good, more of it must be better for everyone.
The Invisible World That Shapes Human Health
Dr. Khalili, a Toronto-based naturopathic doctor, associate professor at the Canadian College of Naturopathic Medicine, and longtime lecturer in advanced clinical nutrition, began with a truth that still feels faintly astonishing. Human beings do not live alone in their own bodies. We are ecosystems.
She pointed to research suggesting the body contains roughly **39 trillion bacterial cells**, compared with about **30 trillion human cells**. The exact ratio has shifted as science refined its estimates, but the lesson remained the same. The human organism is not merely human. It is microbial too.
That microbial world begins shaping us at birth, when a baby passing through the birth canal first encounters maternal bacteria. It is then influenced by diet, environment, stress, movement, sleep, medication, and the increasingly sterile habits of modern life. Fermented foods, once a staple of preservation, have become less central in everyday diets. Sanitised surfaces, chlorinated water, processed foods, and chemical exposures have altered the bacterial inheritance that earlier generations absorbed more naturally.
If this sounds esoteric, Dr. Khalili insisted its effects were anything but. The microbiome, she said, was implicated not only in digestive health but also in **immune regulation, inflammation, blood pressure, diabetes, obesity, and the gut-brain axis**.
“**Approximately eighty percent of our immune system is located in the gut,**” she said. “**If you are dealing with chronic inflammation, addressing your gut health is one of the most important things you can do for your body.**”
Ancient Foods, Modern Science
The language of the microbiome may be contemporary, but the instinct behind it is ancient. Dr. Khalili traced the history of probiotics back thousands of years, long before capsules and branded blends. Fermented dairy, sour milk, and cultured foods had long been linked to digestive resilience and longevity.
She cited the work of **Élie Metchnikoff**, the early 20th-century scientist who observed that Bulgarians consuming fermented dairy products appeared healthier and longer-lived. She also invoked Persian folklore that credited Abraham’s longevity to sour milk, and Roman uses of fermented dairy in digestive care.
What science has done, in effect, is give molecular detail to a very old intuition: the bacteria humans consume and host can alter the quality of their lives.
Beyond Digestion, Into Immunity, Skin, And Metabolism
The strongest public association with probiotics remains digestive relief, and Dr. Khalili did not dismiss that. Evidence, she noted, supported the use of probiotics in conditions including **ulcerative colitis**, **antibiotic-associated diarrhea**, **acute diarrhea**, **pouchitis**, and some cases of **irritable bowel syndrome**.
But she was careful to resist simplification. In **Crohn’s disease**, especially in active phases, probiotics could sometimes aggravate symptoms. In IBS, they could help many people, but not all. Even in gastrointestinal medicine, the story was not straightforward.
Elsewhere, the evidence was striking. Certain probiotic strains had shown promise in **atopic dermatitis in children**, while broader microbial support appeared relevant to **acne**, **immune resilience**, and even the prevention of common infections. Some studies linked probiotics to improved **lipid profiles**, reduced **insulin resistance**, and lower **blood pressure**, though often only after sustained use and at relatively high doses.
And then there was obesity, a condition often treated as a simple arithmetic failure of calories and will. Dr. Khalili described a more intricate picture in which altered gut flora, poor lifestyle, and chronic low-grade inflammation could gradually push the body toward weight gain and metabolic dysfunction.
The Gut-Brain Axis And The Emotional Cost Of Dysbiosis
Perhaps the most arresting part of Dr. Khalili’s presentation concerned the **bidirectional relationship between the gut and the brain**. The phrase “second brain” can sound like a wellness cliché, but the science behind gut-brain signalling has become increasingly difficult to ignore.
The microbiome communicates with the central nervous system through neural, endocrine, immune, and humoral pathways. In practical terms, that means what happens in the gut can shape mood, cognition, and behaviour, while stress and emotional states can alter gut physiology in return.
Dr. Khalili highlighted emerging work in **psychobiotics**, a field examining how probiotic interventions may influence mental health conditions such as **anxiety**, **depression**, and even behavioural symptoms associated with **autism**. She also discussed the role of stress in aggravating inflammatory bowel disease, IBS, reflux, ulcers, and changes in motility.
Stress, she suggested, does not simply make symptoms feel worse. It can alter the biological conditions that produce them.
Sleep, Exercise, And The Rhythm Of Bacteria
If the probiotic industry has taught consumers to think in terms of products, Dr. Khalili repeatedly returned attention to habits.
Low-dose, regular physical activity, she said, helped support healthier bacterial growth and increased production of **butyrate**, a short-chain fatty acid associated with anti-inflammatory benefits. Sedentary living, by contrast, appeared to harm the microbial landscape.
“**Physical activity performed at a low dose on a regular basis helps support the growth of good bacteria in the gut,**” she said. “**Exercise can be used as an effective therapy for conditions related to an unbalanced microbiome.**”
She also underscored a less familiar idea: **gut bacteria have circadian rhythms**.
“**Our gut bacteria have a circadian rhythm just like our cells,**” Dr. Khalili said. “**Maintaining this rhythm is essential because disturbances in our internal clock can lead to glucose intolerance, metabolic issues, and even obesity.**”
This was not metaphor. Studies in mice and humans had suggested that disruptions such as **jet lag** and **shift work** could produce dysbiosis, with downstream effects on glucose regulation and weight. In a culture that treats sleep as expendable, it was a sharp reminder that the body’s smallest inhabitants keep time too.
Why Standard Probiotics Fail Some People
The most important challenge to probiotic orthodoxy came from research at the **Weizmann Institute**, which Dr. Khalili discussed in detail. In one study, healthy volunteers were given a multi-strain probiotic. Some participants showed successful colonization of the digestive tract. Others did not.
The researchers called them **“persisters”** and **“resistors.”**
For Dr. Khalili, this finding illuminated a clinical puzzle she had long seen in practice: why one patient with IBS improved dramatically on probiotics while another grew more bloated, uncomfortable, or unchanged. The answer may be that some digestive systems simply do not welcome standard commercial strains.
That insight alone destabilises the market logic of probiotic supplementation. A product can be biologically active, scientifically respectable, and still wrong for a given person.
In a second Weizmann study, participants received antibiotics and then followed different recovery strategies. Those given a microbiome intervention made from their **own stool-derived bacteria** recovered their native gut flora much faster than those given a standard probiotic or placebo.
The implication was profound. The future of microbial medicine may lie less in generic supplementation and more in **individualized microbial restoration**.
What Damages The Microbiome
Dr. Khalili described the microbiome not only as something to support, but as something modern life routinely depletes. Among the factors she listed were **excess sugar**, **smoking**, **alcohol overuse**, **poor sleep**, **physical inactivity**, and **chronic emotional stress**.
She also pointed to **glyphosate exposure**, **chlorination**, and **over-sanitation** as contributors to microbial damage, arguing that the problem is often not merely an overgrowth of harmful bacteria but a loss of beneficial ones. The distinction matters. Many chronic conditions may emerge not because bad microbes suddenly arrive, but because the protective ecosystem thins and leaves the body more vulnerable.
“**Health can be enhanced and senility delayed by manipulating the intestinal microbiome with host-friendly bacteria,**” she said. “**We have the power to influence our well-being by nurturing the microscopic life forms living within us.**”
Necessary, Yes. Universal, No.
By the end of the session, Dr. Khalili’s answer to her own title had become clear. **Probiotics were necessary**, in the broad sense that beneficial microbes are indispensable to human health. But the branded supplement on the shelf was not automatically necessary, nor automatically beneficial, for every person.
She urged caution against self-prescribing indiscriminately, noting in the question-and-answer session that probiotics could, in some cases, contribute to **small intestine bacterial overgrowth**. She recommended beginning with **fermented foods**, **whole foods**, and lifestyle measures that support microbial diversity, rather than assuming a high-dose supplement was the first or best intervention.
Her position was neither anti-probiotic nor anti-science. It was, rather, anti-simplification.
In the years since the microbiome became a cultural fascination, probiotics have often been marketed as the newest universal answer to very old problems. Dr. Afsoun Khalili’s presentation at Biohacker Summit 2018 Toronto suggested something more mature, and more interesting: that the future of gut health may depend not on swallowing more bacteria, but on understanding which bacteria belong to whom, and why.
In an era addicted to standardisation, that may be the most radical message of all.
Part of Biohacker Summit 2018 Toronto