A bacterium explained most ulcers, but most chronic illness has many roots

Key takeaways

• Doctors once blamed stomach ulcers on stress, until two Australian researchers showed in the 1980s that a bacterium causes most of them, work that won the 2005 Nobel Prize.
• Even that bacterium isn’t enough on its own: about half of all people carry it, and only 10% to 15% of them ever get an ulcer.
• Root-cause detective work pays off when a specific, testable cause exists, such as hidden bleeding behind low iron or a common medicine behind low vitamin B12.
• Most chronic diseases, including autoimmune conditions that affect more than 23.5 million Americans, come from genes and surroundings acting together, with no single root to dig up.
• Before you pay for a root-cause workup, ask whether the test is proven, whether the result would change what you do, and where the search stops if nothing turns up.

In 1982, a pathologist in Perth, Australia, named Robin Warren kept seeing something odd under his microscope. About half of the stomach biopsies he examined held small, curved bacteria, and inflammation always sat nearby¹.

A young doctor, Barry Marshall, joined him. It took Marshall several attempts, but he finally got the microbe to grow in a lab dish¹. To show it could cause disease, he swallowed a culture of it himself and developed gastritis, an inflamed stomach lining².

At the time, most doctors blamed peptic ulcers on stress and lifestyle¹. Acid-blocking drugs healed the sores, but they kept coming back¹. Now a brief round of antibiotics, taken with an acid-lowering drug, clears the infection and cures the ulcer disease. In 2005, Warren and Marshall shared the Nobel Prize for finding the bacterium, Helicobacter pylori¹.

It’s the most famous root-cause story in modern medicine. It also explains why “find the root cause” carries so much power in natural health. Sometimes the experts really are treating symptoms while a hidden cause waits to be found.

But the ulcer story has a twist that rarely gets told, and most chronic illness doesn’t work like an ulcer. This article explains when looking for one root pays off, and when it leads to endless testing, costly protocols and blame you don’t deserve.

Even the ulcer germ needed accomplices

H. pylori lives in the stomachs of about half of all people on Earth¹. Most people pick it up as young children, and it can stay for life, usually without causing symptoms¹.

Only about 10% to 15% of infected people ever develop an ulcer, according to the Nobel Assembly¹. So the bacterium is a powerful cause, yet it isn’t the whole story. Something about the person, or their circumstances, helps decide who gets sick.

The numbers cut the other way, too. The bacterium causes more than 90% of ulcers in the first part of the small intestine and up to 80% of stomach ulcers¹. That leaves a share of ulcers with other causes.

None of this takes anything away from Warren and Marshall. It shows how scientists think about cause. Even a breakthrough “root” usually works alongside other factors.

Scientists draw causes as pies, not roots

In 1976, the epidemiologist Kenneth Rothman offered a picture that is now the main way epidemiologists model cause³⁴. The CDC’s training course in epidemiology still teaches it³.

Picture a pie cut into slices. Each slice is one factor that raises risk, which epidemiologists call a “component cause.” A finished pie, with no slice missing, is a “sufficient cause”: it’s enough to produce the disease³.

One disease can be baked many ways, with different pies leading to it. If one ingredient turns up in all of them, it earns the label “necessary cause,” since no version of the disease forms without it³.

Lung cancer shows how this works. Smoking and asbestos can sit together in one pie³. But smoking is neither necessary nor sufficient, because some people who never smoked get lung cancer³. Radon and diesel exhaust are slices in other pies⁵.

HIV is necessary for AIDS, yet not sufficient by itself; going without antiviral treatment is another slice⁵. For coronary heart disease, risk may run highest in people with a family history who also smoke or drink⁵. Only some conditions, like cystic fibrosis, trace back to one genetic cause⁵.

The CDC course is frank about why this matters. The classic infection model, one germ meeting one host in one setting, falls short for heart disease and cancer, it says, because so many factors feed into them³.

Two researchers writing in the journal Environmental Health in 2006 noted that cancer and heart disease have only a few known necessary causes. They also pointed to the “causal web,” a widely used way of picturing many causes tangled together⁴.

This is the hopeful part. You don’t have to find every slice to prevent disease. Remove one slice, and that whole pie can’t be completed³. That’s why quitting smoking prevents many lung cancers even though smoking isn’t behind all of them.

When the search for one cause pays off

Root-cause thinking shines when a symptom has a specific, testable cause that can be fixed. Medicine is full of these.

Iron-deficiency anemia. Low iron is often a clue, not a final answer. MedlinePlus, the National Library of Medicine’s consumer site, puts blood loss at the top of its list of causes⁶. Sources include heavy periods, ulcers, cancers of the stomach or colon, and long-term use of aspirin or ibuprofen⁶. Poor absorption from celiac disease or Crohn disease can also drain iron⁶.

That’s why a doctor may order a colonoscopy or an upper endoscopy, a camera exam of the digestive tract, instead of just handing you iron pills⁶. The pills fix the number. The exam looks for the reason.

Vitamin B12 deficiency. About 2% to 3% of U.S. adults are low in B12, according to a 2025 review in American Family Physician⁷. It can cause fatigue, brain fog, depression and nerve problems⁷. The root is often a medicine. In one trial, 19.1% of people taking the diabetes drug metformin had low or borderline B12, compared with 9.5% on a placebo⁷. Acid-reducing pills called proton pump inhibitors also raise the odds⁷.

When no clear cause turns up, the review advises checking for a stomach-lining condition called atrophic gastritis, including a test for H. pylori⁷. The ulcer germ shows up again. And the fix is often simple: for most patients, B12 pills by mouth work as well as shots, though shots are advised for severe deficiency⁷.

Sleep apnea. Snoring, gasping during sleep and sleepiness are signs of this condition, in which breathing stops and starts through the night⁸. The National Heart, Lung, and Blood Institute notes that untreated sleep apnea keeps sleep from being restful and can harm many parts of the body⁸. For someone who is always tired, a sleep study can find a cause no supplement would reach.

Notice what these wins share. Each has a proven test, a clear biological link and a treatment that works once the cause is found. If you’ve been exhausted for weeks, ask a clinician to check for common, treatable causes like these before you buy a protocol.

Many chronic illnesses have no single root to find

Autoimmune diseases are a good test case. In these conditions, the immune system attacks the body’s own tissues. The National Institute of Environmental Health Sciences (NIEHS) counts more than 80 of them, affecting more than 23.5 million Americans, more often women⁹.

The agency says their causes remain largely unknown⁹. The growing consensus is that genes and surroundings interact⁹. Researchers have tied certain exposures to certain diseases: crystalline silica to several, solvents to systemic sclerosis, smoking to two forms of rheumatoid arthritis, and gluten to celiac disease⁹.

Lupus shows how tangled this gets. It has no diagnostic test and no cure, according to a 2024 NIEHS report on research by Lindsey Criswell¹⁰. Genes on chromosome 6 raise risk, but genes don’t fully explain who gets sick¹⁰.

Evidence on environmental triggers is limited and sometimes anecdotal¹⁰. Most lupus drug trials have failed, partly because scientists still don’t fully understand the disease¹⁰.

So when a program promises to find “the” root cause of lupus or rheumatoid arthritis, ask how it knows something the field’s leading researchers don’t.

Heart disease works the same way, with many risk factors adding up. Our article on prevention and treatment shows how they combine.

What research shows about functional medicine

“Root cause” is the core promise of functional medicine, a model that aims to address underlying causes and imbalances across body systems¹¹. Cleveland Clinic runs a Center for Functional Medicine¹². In 2019, its researchers published an early look at patient outcomes in JAMA Network Open¹¹¹².

The team, led by Michelle Beidelschies, compared 1,595 patients at the functional medicine center with 5,657 patients at a Cleveland Clinic family practice¹¹. They used PROMIS, a health questionnaire validated by the National Institutes of Health¹².

The two groups started out different. The primary care patients had higher incomes, more diabetes and high blood pressure, and better starting scores on the questionnaire¹². To make the comparison fairer, the researchers matched 398 pairs of similar patients¹¹.

At six months, the functional medicine patients’ physical health score rose 1.59 points, versus 0.33 points in primary care¹¹. About 31% improved by 5 points or more, a change the researchers treat as meaningful, compared with 22%¹¹¹².

At 12 months, the gap was no longer statistically significant, and only 220 matched pairs had data by then¹¹. The study looked back at existing records rather than assigning people to one kind of care, and the authors said forward-looking studies are needed¹¹.

There’s another wrinkle. New patients at the center met a dietitian and a health coach, as well as a clinician, in a first visit lasting about 60 to 75 minutes¹². The researchers named several possible explanations for the results: the care model, the kind of patients who seek it out, and patients’ commitment to it or belief in it¹².

That makes it hard to say what helped. Long visits, food coaching and a supportive team are valuable in their own right. The study can’t tell us whether “finding the root cause” was the active ingredient.

Where the root-cause hunt goes wrong

The search for a single root can drift in three costly directions.

More tests, less meaning. If one panel finds nothing, the next may test hormones, then the gut, then food reactions. Each extra test adds cost and another chance of a false alarm. Our articles on unnecessary tests and on out-of-range results explain why a flagged number often means nothing.

Tests that measure the wrong thing. IgG food panels are a common root-cause tool. They report antibodies to roughly 90 to 100 foods¹³. The American Academy of Allergy, Asthma & Immunology says IgG is likely a normal response to eating a food, and higher levels of one type may even signal tolerance¹³. The academy and its Canadian counterpart recommend against using these tests to diagnose food allergy or intolerance¹³. Acting on them can mean cutting healthy foods for no reason.

Blame. If every illness has one hidden root you should have found, then staying sick looks like your failure. The pie model says otherwise. Many slices, including your genes and exposures you never chose, sit outside your control. Our article on personal control explores how taking charge can tip into self-blame.

Natural-health values point to a better use of root-cause thinking. Looking upstream at sleep, food, movement, stress and surroundings is good prevention, and it can remove slices from many pies at once. Cleveland Clinic’s own description of its model centers on those same lifestyle factors¹².

That instinct deserves respect. It just doesn’t require believing that one master cause explains everything.

Root-cause question or sales pitch? A side-by-side

The left column describes careful detective work. The right describes a pitch that borrows its language.

A good root-cause question	A root-cause sales pitch
“What could explain this specific finding, like low iron?”	“All your symptoms come from one hidden problem.”
Uses tests with proven accuracy for the question asked	Uses big panels or tests experts reject, like IgG food panels
Starts with common and dangerous causes	Starts with exotic causes your doctor “missed”
Has a plan if the test is normal	Treats a normal result as a reason for more tests
Leads to a treatment tested in people	Leads to a protocol sold by whoever ran the test
Accepts that some causes stay unknown	Promises an answer every time
Works alongside your current care	Asks you to stop proven treatment while you search

Five questions before you pay for a root-cause workup

1. What specific cause are we looking for, and which test checks it?
2. Has this test been shown to give accurate results for that cause?
3. If the result is abnormal, what will we do differently?
4. If it’s normal, where does the search stop?
5. Is the person ordering the test also selling the treatment?

What the evidence says

Claim	Evidence level	Basis
H. pylori causes most peptic ulcers, and clearing it cures them	Strong evidence	Nobel-winning research; antibiotics plus acid reducers now cure the disease1
Most chronic diseases have several interacting causes	Strong evidence	Standard epidemiology models and NIEHS research on autoimmune disease349
Looking for the cause of low iron or low B12 finds treatable problems	Strong evidence	Known causes include bleeding, poor absorption and common medicines67
A functional medicine model improves quality of life more than usual care	Promising but early	One look-back study; a benefit at 6 months that faded to no significant difference at 1211
One hidden root cause explains most autoimmune disease	Not enough evidence	NIEHS says causes remain largely unknown910
IgG food panels reveal the cause of symptoms	Evidence says no, or unsafe	Allergy experts say IgG reflects normal exposure and recommend against the tests13

Questions readers ask

The bottom line

Root-cause thinking won a Nobel Prize, and it still uncovers hidden bleeding, low B12 and sleep apnea every day. It works best when there’s a specific cause, a test that can find it and a treatment that fixes it.

Most chronic illness grows from several causes working together. That isn’t a dead end. It means you can lower your risk by changing the slices you control, without paying for an endless hunt or blaming yourself for the ones you can’t.

Related reading

• Simple health answers feel true, so how do you tell which ones are?
• Taking charge of your health helps, until it turns into blame
• When extra medical tests do more harm than good
• Why being out of range often means nothing at all
• Most heart attacks are preventable, and that doesn’t make treatment the enemy

Sources

1. Nobel Assembly at Karolinska Institutet. “The Nobel Prize in Physiology or Medicine 2005: Press Release.” Nobel Prize Outreach, October 3, 2005. nobelprize.org
2. Watts G. “Nobel Prize Is Awarded to Doctors Who Discovered H pylori.” BMJ, 2005 (PubMed Central copy). pmc.ncbi.nlm.nih.gov
3. Centers for Disease Control and Prevention. “Principles of Epidemiology in Public Health Practice, Lesson 1, Section 8: Concepts of Disease Occurrence.” CDC (archived). archive.cdc.gov
4. Vineis P, Kriebel D. “Causal Models in Epidemiology: Past Inheritance and Genetic Future.” Environmental Health, 2006. link.springer.com
5. Martenies S. “Causal Thinking in Epidemiology.” In Principles of Epidemiology: A Primer. Illinois Open Publishing Network, 2026. iopn.library.illinois.edu
6. MedlinePlus, National Library of Medicine. “Iron Deficiency Anemia.” Reviewed April 2025. medlineplus.gov
7. Patel H, McGuirk R. “Vitamin B12 Deficiency: Common Questions and Answers.” American Family Physician, 2025. aafp.org
8. National Heart, Lung, and Blood Institute. “Sleep Apnea: Signs, Symptoms, and Complications.” NIH (syndicated by HHS), updated 2026. akaprod-digitalmedia.hhs.gov
9. National Institute of Environmental Health Sciences. “Autoimmune Diseases.” NIH. niehs.nih.gov
10. Yewell J. “Lupus Arises From Complex Interplay of Genetic and Environmental Factors.” Environmental Factor, National Institute of Environmental Health Sciences, July 2024.
11. Beidelschies M, et al. “Association of the Functional Medicine Model of Care With Patient-Reported Health-Related Quality-of-Life Outcomes.” JAMA Network Open, 2019. pubmed.ncbi.nlm.nih.gov
12. Cleveland Clinic. “Cleveland Clinic Study Finds Functional Medicine Model Is Associated With Improvements in Health-Related Quality of Life.” Cleveland Clinic Newsroom, October 25, 2019. newsroom.clevelandclinic.org
13. American Academy of Allergy, Asthma & Immunology. “The Myth of IgG Food Panel Testing.” AAAAI, updated 2026. aaaai.org