Does lower gut microbiome diversity really increase infection risk?
Yes, the evidence is clear: a less diverse gut microbiome is consistently linked to a higher risk of infections. This isn't just a correlation—it's seen across many different patient groups and infection types. For instance, in a study of 121 heart transplant recipients, those who developed a post-operative infection had significantly lower gut microbiome diversity at the time of transplant compared to those who did not get infected [2]. The difference was statistically significant (p=0.0026), meaning it's very unlikely to be due to chance. Similarly, in a study of 150 ICU patients, those who developed hospital-acquired infections (like pneumonia or bloodstream infections) had a marked decrease in microbial diversity during their ICU stay, especially if they received broad-spectrum antibiotics [5]. The patients with the greatest microbiome disruption had the highest risk of infection, longer ICU stays, and higher mortality [5].
This pattern holds true for specific infections as well. Newborns exposed to gestational diabetes had reduced gut microbiome diversity and a two- to threefold increased risk of neonatal infections [1]. In a study of diarrheal patients, those infected with a pathogenic subtype of the parasite *Blastocystis* (ST7) had significantly lower bacterial diversity than those without the parasite [8]. Even in the context of *C. difficile* infection in patients with inflammatory bowel disease, bacterial diversity was lower in those with the infection [6]. The consistent finding across these diverse scenarios—from newborns to ICU patients, from surgical patients to those with parasitic infections—strongly supports the idea that a diverse gut microbiome is protective against infection.
How does a diverse microbiome protect against infection?
A diverse gut microbiome protects against infection through several key mechanisms. First, it helps maintain a strong intestinal barrier. In the study of newborns exposed to gestational diabetes, the reduced diversity was accompanied by a significant drop in beneficial short-chain fatty acids (SCFAs)—acetate fell by 49%, butyrate by 41%, and propionate by 18% [1]. These SCFAs are crucial for gut health, and their loss led to a weakened intestinal barrier, allowing bacteria and toxins to leak into the bloodstream and trigger inflammation [1]. This was confirmed in mice that received fecal transplants from the low-diversity newborns: they developed systemic inflammation and compromised gut barrier function [1].
Second, a diverse microbiome helps train the immune system. In cockroaches, a higher diversity of gut bacteria was linked to better resistance against *Salmonella* infection, not because the good bacteria outcompeted the bad, but because they primed the host's immune system to produce antimicrobial peptides that fight off the infection [7]. Third, a diverse community of beneficial bacteria, like *Bacteroidetes*, *Lachnospiraceae*, and *Ruminococcaceae*, keeps potentially dangerous bacteria in check. In heart transplant patients who did not get infections, these beneficial bacteria were abundant, while in those who got infections, they were replaced by expansions of single species like *Enterococcus* and *Enterobacterales*—the very bacteria that caused the infections [2]. This pattern was also seen in ICU patients, where a loss of *Faecalibacterium prausnitzii* and *Bacteroides* was replaced by overgrowths of *Enterococcus*, *Klebsiella*, and *Pseudomonas* [5].
What factors reduce gut microbiome diversity and increase infection risk?
Several factors can reduce gut microbiome diversity, making you more vulnerable to infections. Broad-spectrum antibiotics are a major culprit. In the ICU study, patients receiving broad-spectrum antibiotics had the most dramatic loss of diversity and the highest infection rates [5]. Cesarean section delivery is another factor: babies born by C-section have lower gut diversity and a different microbiome composition compared to vaginally delivered babies, and this was linked to a higher risk of respiratory infections [3]. However, this study also showed that exclusive breastfeeding could help restore the microbiome and reduce that infection risk [3].
Even lifestyle factors play a role. A study of 47 adults found that higher levels of sedentary behavior and screen time were independently associated with lower gut microbiome diversity, even after accounting for physical activity and other health factors [4]. This suggests that a sedentary lifestyle might increase infection risk indirectly by harming your gut microbiome. Finally, aging itself reduces diversity. In a rat study, transferring blood plasma from old rats to young rats caused the young rats' gut microbiome to become less diverse and more like that of an old rat, while transferring young plasma to old rats increased their diversity [9]. This suggests that age-related changes in the body's internal environment can directly reduce microbiome diversity.
About These Sources
This answer is built on 9 peer-reviewed studies — published from 2022 to 2025, 4 from 2024 or later, 5 in Q1 journals, collectively cited 105 times — selected as the most relevant from 15 studies that passed quality screening, drawn from 60 papers retrieved from a database of over 500 million.
Sources used in this answer
Gestational diabetes mellitus alters neonatal gut microbiota and increases infection susceptibility
In a study of 139 mother-child pairs, gestational diabetes reduced neonatal gut microbiome diversity and beneficial short-chain fatty acids (acetate -49%, butyrate -41%, propionate -18%), and was linked to a 2-3x increased risk of neonatal infections. Fecal transplants in mice confirmed the causal role of the altered microbiome in increasing inflammation and gut barrier damage.
434. Reduced Gut Microbiome Diversity and Compositional Characteristics are Associated with Postoperative Infection in Heart Transplant Recipients
In a cohort of 121 heart transplant recipients, lower stool microbiome diversity at the time of transplant was significantly associated with a higher risk of post-operative infection (p=0.0026). Infected patients had expansions of *Enterococcus* and *Enterobacterales* and a loss of beneficial anaerobes like *Bacteroidetes* and *Lachnospiraceae*.
A health-promoting role of exclusive breastfeeding on infants through restoring delivery mode-induced gut microbiota perturbations
In a longitudinal cohort of 139 infants, cesarean section delivery reduced gut microbiome diversity and increased respiratory infection risk. Exclusive breastfeeding restored the microbiome of C-section babies to a profile similar to vaginally delivered babies by 6 months, reducing infection susceptibility.
Sedentary Behavior And Screen Time Are Associated With Human Gut Microbiome Diversity
In a study of 47 adults, higher sedentary behavior and screen time were independently associated with lower gut microbiome diversity, even after controlling for physical activity, BMI, and blood glucose. This suggests lifestyle factors can directly impact microbiome diversity and potentially infection risk.
Gut Microbiome Alterations And Risk Of HospitalAcquired Infections In ICU Patients
In a prospective cohort of 150 ICU patients, a marked decrease in gut microbial diversity during the ICU stay was associated with a higher risk of hospital-acquired infections. Patients with the greatest loss of beneficial bacteria like *Faecalibacterium prausnitzii* and overgrowth of pathogens like *Enterococcus* had the worst outcomes.
Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection
In a study of 25 IBD patients with *C. difficile* infection, bacterial alpha diversity was lower compared to IBD patients without the infection and healthy controls. Specific bacteria like *Enterococcus faecium* and *Ruminococcus gnavus* were overrepresented in the infected group.
The gut microbiota confers resistance against Salmonella Typhimurium in cockroaches by modulating innate immunity
In cockroaches, the gut microbiota protected against *Salmonella* infection by priming the host's innate immune system (antimicrobial peptide expression), not by direct competition. Overall diversity was not linked to susceptibility; instead, specific minority bacterial taxa were key indicators of infection risk.
Infection with pathogenic Blastocystis ST7 is associated with decreased bacterial diversity and altered gut microbiome profiles in diarrheal patients
In diarrheal patients, infection with the pathogenic *Blastocystis* subtype ST7 was associated with significantly lower bacterial diversity and an altered microbiome structure, with an increase in *Enterobacteriaceae* and a decrease in *Bacteroides* compared to uninfected patients.
Role of age-related plasma in the diversity of gut bacteria
In a rat study, transferring young blood plasma to old rats significantly increased gut microbiome diversity, while transferring old plasma to young rats decreased diversity. This shows that age-related changes in blood plasma can directly alter gut microbiome composition and diversity.