Infections

How Microbes Already Living On and In Us Shape Infections

Infections come from outside the body, but how badly they take hold often depends on microbes already living in it.

Across the pages on this site, from the gut and reproductive tract to the skin and sinuses, the same pattern shows up again and again, sometimes as protection, sometimes as damage.

Some pathogens attack the resident bacterial community directly. Others simply have an easier or harder time depending on what's already there.

Some infections dismantle the resident community itself

HIV wipes out more than half of the gut's immune cells within the first few weeks of infection, faster and more completely than anywhere else in the body, and this damage sets a pattern that persists even once the virus itself is controlled with treatment.

Standard tuberculosis treatment causes a similarly lasting disruption. The combination of antibiotics needed reshapes gut bacteria so severely that the altered community can still be detected nine months to two years after treatment finishes.

A study in Mali showed just how directly gut bacteria can determine outcome. Transplanting stool from malaria-susceptible children into mice produced significantly higher parasite levels than stool from resistant children, in the exact same infection.

Source: The T-Cell Response to HIV

Source: The gut microbiome is associated with susceptibility to febrile malaria in Malian children

In other cases, resident bacteria actively fight the pathogen off

On the skin, a bacterium called Staphylococcus lugdunensis produces its own antibiotic, cutting rates of a common infection-causing bacterium roughly five-fold in people who carry it. In the reproductive tract, Lactobacillus bacteria produce lactic acid that kills the bacterium behind gonorrhoea outright and blocks chlamydia from entering cells.

When that protective community breaks down instead, in bacterial vaginosis, the risk of acquiring HIV rises by around 60%, alongside several other infections, through a specific, identifiable immune mechanism rather than coincidence.

Antibiotic overuse threads through much of this. Around 74% of acute bronchitis cases and over 80% of acute sinus infections are prescribed antibiotics despite being viral, and each unnecessary course can leave protective bacteria measurably altered for months afterwards, in the gut and wherever else they live.

Source: Human commensals producing a novel antibiotic impair pathogen colonization

Source: Bacterial vaginosis and HIV acquisition: A meta-analysis of published studies

What this means for you

Any suspected infection needs proper diagnosis from a doctor, since the right treatment depends entirely on which pathogen is involved and antibiotics only work against bacteria, never viruses. In addition, the research across this section shows resident microbial communities, in the gut, on the skin, and in the reproductive tract, measurably shape whether an infection takes hold, how severe it becomes, and how well the body recovers afterwards. A varied, plant-rich diet supports the same gut bacteria this research ties to stronger defences against infection generally. That's the same idea behind GutLab, everyday gut health starts with regularly feeding the microbiome a broad range of plant-rich ingredients.

Explore infections on this page

The panels on this page group into a few broad types. Respiratory infections, including flu, colds, pneumonia, bronchitis, sinus and throat infections, tonsillitis, TB, and COVID-19, share a strong theme of antibiotic overuse damaging protective bacteria. Infections affecting the reproductive tract, including HIV, hepatitis, HPV, chlamydia, gonorrhoea, syphilis, bacterial vaginosis, and yeast infections, share the vaginal Lactobacillus story running through several of them. Skin infections, fungal skin infections, and scabies concern the skin's own bacterial defences, while malaria and dengue cover mosquito-borne infections with a genuine gut connection, and herpes covers a virus where animal research shows gut bacteria shielding the brain from its worst effects. Use the panels on this page to find the one relevant to you.