The microbes on your lettuce change with the seasons

By Dr. Liji Thomas, MDReviewed by Lauren HardakerNov 6 2026

From farm to fork, lettuce carries billions of microorganisms that change with the seasons. New research links these leaf-dwelling microbes to greater gut bacterial diversity, raising questions about how fresh vegetables may influence our microbiome.

Study: Seasonal dynamics in lettuce phyllosphere microbiota and potential transfer to the human gut. Image credit: Kmpzzz/Shutterstock.com

A recent study published online in the journal npj Science of Food suggests that lettuce may provide bacteria and fungi that could reach the human gut, with possible implications for gut microbial composition and diversity.

Fresh lettuce carries microbes that might reach the gut

Modern Western lifestyles are linked to lower gut microbiome diversity, partly through reduced contact with environmental microbes. Research on how plant foods affect the gut has focused mostly on dietary fiber, which provides fermentable substrates for beneficial gut microbiota. However, fresh plant foods also supply live microbes.

The leaf surface of fresh vegetables, also called the phyllosphere, carries a large and varied microbial community with seasonal differences, as shown by earlier in-field studies. This study examined whether these differences persisted on retail lettuce after post-harvest processing, whether lettuce-associated microbes also appeared in human gut microbiome datasets, and how their presence might relate to resident gut bacteria.

Study compared retail lettuce microbes with human gut datasets

The investigators gathered 143 lettuce samples (72 green, 71 red) every month from October 2021 to September 2022 at six retail stores in Daejeon, South Korea. They counted viable microbes by culturing and profiled the communities by amplicon sequencing: the ITS2 region for fungi and the 16S rRNA gene for bacteria.

They linked the microbial community data to local weather records from NASA (temperature, humidity, wind speed, solar radiation, and soil wetness) and compared the lettuce data with published datasets from 14 other fruits and vegetables.

To investigate potential microbial transfer from lettuce to the human gut, they reanalyzed fecal microbiome data from 13 human studies covering several countries and ethnicities: 2,831 people for fungi and 3,254 for bacteria. They clustered lettuce and gut microbial sequences into operational taxonomic units (OTUs) at 97% similarity. Gut sequences that clustered with lettuce sequences were treated as potentially lettuce-derived.

Lettuce leaves harbor diverse bacterial and fungal communities

The investigators measured about 3.4 log CFU of culturable fungi (8.0 log genomes) and 5.0 log CFU of bacteria (7.7 log genomes) per gram of lettuce. Sequencing identified 5,016 fungal and 5,610 bacterial amplicon sequence variants (ASVs), indicating substantial microbial diversity.

The microbiota of lettuce leaves differed from those of the 14 other fruits and vegetables, with larger differences than those observed in fresh vegetables alone. Specifically, they found abundant fungi, Cladosporium and Bulleromyces, along with two bacterial taxa, Massilia and Sphingomonas, that were particularly characteristic of lettuce. The authors suggest that this points to host-specific adaptation.

Sampling month was the strongest factor associated with microbial community variation, followed by distributor. Lettuce type contributed the least.

Seasonal conditions shape fungal and bacterial communities differently

The communities showed seasonal variations in the form of an early and a late season, rather than a steady drift over the course of the year. The early season (S1) ran from December to June, and the late season (S2) from July to November.

Most samples clustered with their sampling period (87.3% of green lettuce samples and 75.6% of red lettuce samples). A random forest classifier supported this seasonal distinction, with area under the receiver operating characteristic curve values above 0.75.

The microbial community patterns were closely correlated with agricultural/meteorological conditions (temperature, relative humidity, wind speed, solar radiation, and soil wetness). This suggests that pre-harvest seasonal patterns persist through to the retail shelf, which the authors suggest may be related to lettuce's short farm-to-consumer cycle.

About 75% of all ASVs were season-specific, and approximately 66% of those were more common in S2. Thus, diversity rose in the late season. The remaining 25% were persistent taxa found in both seasons, but their seasonal responses differed between fungi and bacteria.

The number of persistent fungal species increased in S2, as did their abundance. Persistent bacterial communities instead changed composition without comparable overall increases in richness or abundance, although families such as Sphingomonadaceae and Enterobacteriaceae became enriched.

Functionally, S2 fungi were mostly classified as saprotrophs (decomposers). S1 fungi covered diverse lifestyles, including wood decomposers, animal parasites, leaf endophytes, and ectomycorrhizal fungi. Bacterial S2 genera in green lettuce were mostly associated with hydrocarbon degradation, but S1 bacteria had more diverse predicted metabolic functions.

Association with pathogens

Neutral model fits weakened from S1 to S2 for both fungi and bacteria, on green and red lettuce samples. This suggests stronger environmental or host-driven selection in the late season. In addition, the S2 microbial networks contained more connections among microorganisms, including links within and between the fungal and bacterial kingdoms, despite having similar numbers of microbial taxa.

During S2, fungal genera associated with potential pathogens were less frequently enriched compared to S1, with one genus in S2 versus 11 and 7 for green and red lettuce in S1, respectively. The authors propose that higher diversity, stronger selection, and dense cross-kingdom interactions may help limit the enrichment of potentially pathogenic fungal genera.

Lettuce microbes detected in human gut samples

Researchers identified microbial sequences closely related to lettuce-associated bacteria and fungi in human gut datasets. Lettuce-associated bacteria were detected in an average of 67.5% of individuals and fungi in 33.1%, although both occurred at relatively low abundances.

Season-specific lettuce microbes, particularly those associated with S2, were detected more often than microbes present year-round. However, their abundance on lettuce did not correlate with their abundance in the gut, suggesting that factors within the digestive tract may influence which microorganisms are detected.

Genetic similarities support the possibility of food-to-gut microbial transfer but cannot establish that lettuce was the source or that these microorganisms survived digestion or colonized the gut.

Lettuce-associated bacteria linked to greater gut diversity

Lettuce-associated bacteria co-occurred more frequently with resident gut microorganisms than lettuce-associated fungi, particularly among late-season taxa. These patterns suggest possible microbial interactions beyond the effects of dietary fiber, although the study did not demonstrate direct interactions.

Notably, gut samples containing lettuce-associated bacteria showed significantly greater microbial richness and diversity, even after excluding those bacteria from the analysis. No comparable association was observed for fungi.

The findings suggest a potential relationship between exposure to vegetable-associated bacteria and gut microbial diversity, but do not establish that lettuce consumption directly increases diversity or improves gut health.

Fresh lettuce may provide seasonal microbial exposure

The researchers estimated that a typical serving of lettuce salad could contain microbial material corresponding to approximately 4.3 billion bacteria and 8.5 billion fungi before household washing.

Some lettuce-associated bacterial genera detected in gut datasets include species with probiotic potential or traits that may support gastrointestinal survival. Nevertheless, their detection does not establish health benefits.

The authors suggest that fresh vegetables could contribute to seasonal changes in gut microbial communities, although this possibility remains untested.

Study limitations and conclusions

The study examined retail lettuce from one South Korean region over a single year, limiting the generalizability of its seasonal findings. Lettuce and human gut samples came from independent datasets, without recorded dietary intake, preventing researchers from confirming direct microbial transfer.

Household washing, possible postharvest contamination, and the inability to establish microbial viability or colonization introduce further uncertainty.

Overall, the findings identify lettuce as a potential source of seasonally varying environmental microorganisms associated with the human gut. However, controlled dietary studies and strain-level analyses are needed to establish whether lettuce microbes reach and persist in the gut, interact with resident bacteria, or influence gut microbial diversity.

As the authors conclude:

This study highlights the lettuce phyllosphere as an underappreciated source of environmental microbiota… Furthermore, it provides both a theoretical framework and proof-of-concept evidence that lettuce-associated microorganisms could interact with commensal gut bacteria.