What a household shares: microbes between people, dogs and cats

People who live together swap bacteria constantly: through hands, kitchen, bathroom, kisses and the animal on the sofa. What studies on shared bacterial strains show, what is useful about it, which pathogens and resistant bacteria really do get passed on, and why shared bacteria are not proof of transmission.

How solid is the research? Promising

That people living together share considerably more bacterial strains than strangers do is shown consistently by several large metagenome studies, and the household transmission of individual pathogens and resistant bacteria is well documented too. Almost everything in between is open: whether shared bacteria settle for good, which way they travel, and whether any of it makes someone healthier or sicker. That the most easily transmissible gut species go along with poorer metabolic measures is a single cross-sectional finding from 2026.

Healthy state

For microbes, a household is a shared habitat. To measure who actually shares something with whom, comparing bacterial species is not enough: almost everyone carries the same common species. What matters is the strain, the specific variant of a species with its own genome. For an analysis of more than 9,700 stool and mouth samples, researchers therefore compared strains and found more than ten million instances in which two people carried the same strain. Among people living together, roughly one in eight gut strains matched (12 per cent) and almost one in three strains in the mouth (32 per cent). For people from different households it was a fraction of that.

What counted most is remarkable: not age and not relatedness, but how long two people had been living together. An Israeli study of 1,046 people of varied ancestry fits that picture: genes played only a minor role in the composition of the Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity”, while unrelated people from the same household resembled each other clearly, and about a fifth of the differences between individuals was linked to diet, medication and body measurements. In Fiji, where 287 people from closely connected villages were studied, the strongest patterns were within households and between spouses. And in a US study, 94 married couples resembled each other in their gut microbiota more than 83 sibling pairs did, while the siblings were no more similar than strangers. The difference came entirely from couples who described their relationship as close.

The main trading place is the mouth. In a Dutch study of 21 couples, partners had a more similar oral microbiota than unrelated people, and the more often and more recently they kissed, the more similar their saliva was. Using a marker experiment with a Probiotics Live microorganisms that are meant to provide a benefit in sufficient amounts. The effect depends on the individual strain. More in the chapter “Using fermented foods well” yoghurt, the researchers estimated that one intimate ten-second kiss transfers around 80 million bacteria. A single kiss did not measurably change the similarity, though: it takes repetition, otherwise the visitors are gone again quickly. From the mouth things travel downwards. In an analysis of 1,644 samples with both mouth and stool from the same person, 74.5 per cent of the cases in which a species occurred at both sites involved the same strain, mostly common mouth bacteria such as Streptococcus salivarius. So we are constantly swallowing our own oral microbiota.

The airways share something too. Among 1,046 city dwellers in 111 households, people living together, especially couples and siblings, shared a median of 16.7 per cent of their throat strains; for people from different households it was 0 per cent. What was shared included harmless residents as well as pathogens that only cause trouble under certain conditions. How it all begins is covered in a chapter of its own: in the first months an infant takes on about half of its strains from the mother, and that trace stays detectable into adulthood.

Sharing with a dog or cat works differently. In a study of 60 families, household members, especially couples, resembled each other most clearly on the skin; where a dog lived in the house, the adults shared even more skin microbes, and dog owners shared more with their own dog than with other dogs. A Japanese study followed people and dogs from the day they moved in together for three months and found eleven bacterial variants that turned up on both sides of human-dog pairs, mostly ones that were already common in the respective host; the overall composition of the gut microbiota did not change. The largest collection of animal samples, 2,639 metagenomes from dogs and cats, shows why: 198 species occur in dogs, cats and humans, but the strains appear adapted to their host. A permanent move from dog to human therefore seems to be the exception.

Can sharing also help? The clearest hint comes from animal work. Germ-free mice were given stool from twin pairs in which one person was lean and the other severely obese, and each took on that donor’s body composition. When the animals were housed together in one cage, bacteria from the lean donor moved into the other mice and prevented weight gain there – but only when the feed was high in fibre. In humans there are only observations: in the US study, married people had a more species-rich gut microbiota than people living alone, richest among those in close relationships. What an animal in the house has to do with allergies and the immune system is covered in the chapter on pets.

Within a household, bacteria travel back and forth: most through the mouth and kisses, less in the gut, and with the dog mainly across the skin.

Disrupted state: causes and effects

What gets shared is whatever is there, not whatever helps. In the same analysis of 1,644 samples, it was precisely the most easily transmissible gut species that were linked to poorer heart and metabolic measures. That is a snapshot: whether those species do any damage, or are simply more common where conditions are unfavourable anyway, is not settled by it. A "contagious" metabolic disease has not been demonstrated in humans.

For pathogens, by contrast, household transmission is everyday reality. In a US study with 1,479 contacts, 30 per cent of family members fell ill after a gastrointestinal case in the household when norovirus had been detected in the first case, against 15 per cent without that finding. Noroviruses are very robust, a few particles are enough, and they are still shed for days after symptoms stop.

The diarrhoea pathogen Clostridioides difficile A bacterium that can spread after antibiotics and cause severe diarrhoea with its toxins. More in the chapter “After antibiotics: C. difficile and faecal transplants” does not stop at the front door either. An analysis of claims data covering 224,818 cases found that people with a case in the family in the preceding 60 days fell ill about twelve times as often as people without that history, and about 22 times as often among cases with no previous hospital stay. The context: only 4.8 per cent of all cases followed a case in the family, so the absolute risk stays small, and family members often share other things too, such as antibiotic prescriptions. For the stomach bacterium Helicobacter pylori the family clustering is particularly clear: in a Japanese study of 838 children, infected mothers and grandmothers were the strongest indicators of infection in the child, while infected fathers and grandfathers were not.

Resistance is a second theme. Compared with people without a dog, dog owners in a Chinese metagenome study carried more resistance genes against aminoglycosides and tetracyclines in the gut; Enterobacteria were the shared carriers in both humans and dogs. In a family study with 13 dogs and 16 owners, the dogs’ resistance gene profiles resembled those of their own people more than those of strangers. And in households with sick dogs and cats in Portugal and the UK, the same resistant strain was repeatedly found in animal and human, in three Portuguese households at a time that fitted the animal’s illness. Such genes also travel between people: in the throat study, 15 per cent of resistance genes sat on mobile pieces of DNA that can move between bacterial species.

Not everything in the mouth is passed on. In a study on Java, 105 people carried the periodontitis bacterium Porphyromonas gingivalis; among siblings, identical variants were found in 6 of 13 families, but in 13 couples where both partners carried the bacterium, in none. It is probably acquired from parents in childhood rather than between partners later. So the same species being present in a household does not automatically mean it travelled.

Which brings us to the most important limitation: shared strains do not prove transmission. People living together eat the same food, drink the same water and touch the same surfaces – that alone puts the same strains into two people. With these methods the direction explicitly cannot be determined; nobody knows who colonised whom. And whether the bacteria found really live there or are only detectable briefly after contact is left open in most studies. For the worry that you might catch Irritable bowel syndrome Recurring abdominal pain linked to bowel movements, without tests finding another cause. Today it is understood as a disorder of gut–brain interaction. More in the chapter “The gut-brain axis”, bloating or a "bad gut flora" from your household, there is no study that has tested and shown it.

What makes people ill is shared too: diarrhoea pathogens after a case in the family, C. difficile spores, resistant bacteria from a sick animal.

What often helps

Lifestyle

Diet, exercise, sleep, social contact and dealing with stress.

Wash your hands where it actually counts Rather than disinfecting the whole flat, be thorough at the few handover points: before cooking and eating, after the toilet, after nappies, the litter tray, poo bags and garden soil. Soap and 20 to 30 seconds are enough. That handwashing prevents diarrhoeal illness is well documented, best studied in countries with poor water supply. Well supported How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [1]
Be briefly strict during a stomach bug in the household For as long as someone is vomiting or has diarrhoea, and two days beyond: own towel, clean the bathroom and door handles more often, do not prepare food for others, wash laundry hot. With norovirus, 30 per cent of family members fell ill. After a case in the family, that is the window in which hygiene really pays off. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [2]
Stay alert after antibiotics or a hospital stay in the family If someone in the household has had Clostridioides difficile or has just come home from hospital, this is the time for washing hands with soap – hand gel alone works poorly against this bacterium’s spores – and for a thoroughly cleaned bathroom. If another household member develops new watery diarrhoea, especially after an antibiotic, that belongs in a doctor’s office. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [3]
Eat high-fibre meals together If bacteria do travel within a household, the food decides whether they stay. In the mouse experiment, bacteria from the lean donor could only move in and prevent weight gain when the feed was high in fibre. That has not been tested in humans, but vegetables, pulses and wholegrains for everyone at the table are the best-evidenced measure anyway. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [4][5]
Closeness yes, toothbrush no Kissing and cuddling are not a risk you need to avoid for the sake of your gut flora, and similar saliva in couples is normal. What makes sense is simply not sharing toothbrushes and not licking cutlery, glasses or dummies – which matters especially during an acute infection, with inflamed gums or a known stomach bacterium. In one study a periodontitis bacterium passed from parents to children rather than between partners. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [6][7]
With a pet: closeness yes, bowl and kitchen apart Stroke the dog or cat, but do not wash the food bowl, toys and blankets in the kitchen, do not eat off the same dishes and do not let your face be licked. In households with sick animals, the same resistant gut bacterium was found in animal and human. Raw meat as pet food increases the load of resistant bacteria – unsuitable if an infant, a pregnant person or someone with weakened defences lives in the household. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [8][9]

Natural supplements

Supplements do not replace a medical check-up. Discuss dosage and interactions with your doctor or pharmacist.

Probiotics for the whole household add nothing The idea of improving the shared gut flora with one product for everybody has not been studied. Even in individuals, purchased strains often fail to settle at all, and after antibiotics they delayed the return of a person’s own flora in one study. There is no reason to buy a pack for the family. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [10]
The lever is on the table, not in the tub What demonstrably helps everyone in a household is fibre and plant variety: meta-analyses show less bowel cancer, less heart disease and more regular bowel movements. A shared shopping trip changes something for everyone who eats at the table; a capsule for one person does not. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [5][4]

Medical treatments

Information, not a treatment recommendation. Decide together with a doctor. Approval and availability differ from country to country.

Stomach bacterium Helicobacter pylori: think of the family If H. pylori is found in someone, infection in their partner and children is more likely, and professional societies advise thinking about re-infection within the household after successful treatment. Who gets tested depends on symptoms, stomach cancer in the family and the rules in your country – raise it in a doctor’s office rather than deciding it yourself. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [11][12]
With recurring C. difficile infection, ask about the surroundings If the infection keeps coming back, it is worth looking at the household: has there been a case, a hospital stay or antibiotics? That does not change the treatment, but it helps in deciding how strict hygiene needs to be and whether a stool transplant is on the table. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [3]
Resistant bacteria: think vet and doctor together If a resistant bacterium is found in a pet, or the animal is on antibiotics for a longer period, that is information for the people in the household too, especially with weakened defences, wounds or a catheter. The other way round, a resistant bacterium in a person belongs in the conversation at the vet. It is the same household, for the bacteria as well. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [8][13]

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How we rate the evidence

Trust score 5 of 5:Established: Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies.
Trust score 4 of 5:Well supported: Several randomised studies in humans with largely consistent results.
Trust score 3 of 5:Promising: Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies.
Trust score 2 of 5:Plausible: Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms.
Trust score 1 of 5:Experimental: Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.

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