Microbial communities of the romaine lettuce phylloplane

In the USA, two multi-state outbreaks of Shiga toxin-producing Escherichia coli strain O157:H7 resulted in 121 people being hospitalized and five deaths in 2018. These outbreaks were linked to consumption of raw romaine lettuce.

Lettuce leaves are nearly always consumed raw rather than cooked. As a result, the microbes on the lettuce leaf surface (phylloplane) are often ingested by the consumer. Despite this, our knowledge about natural fungal species associated with the phylloplane of romaine lettuce is still very limited. Yet this knowledge is necessary for understanding how this naturally occurring flora interacts with introduced human pathogens on the phylloplane. Characterizing these microbial communities is crucial from a public health point of view.

Purdue University has taken a lead in understanding the microbiota of the leaf surface of romaine lettuce. At Purdue, the fungal microbiome of romaine lettuce is being characterized using an integrative approach. Lettuce plants were bought in grocery stores, and culturing techniques and Sanger sequencing technology were applied to identify species of yeasts on the phylloplane of romaine lettuce, several of which turned out to be undescribed. One of them was the most commonly encountered species in our samples—a Sporobolomyces red yeast.

Preliminary data from next-generation sequencing (NGS) have shown that the fungal communities in organic lettuces are primarily represented by yeasts, in contrast to the primarily filamentous fungi that comprise the leaf surface of conventionally managed lettuces. Yeasts are a non-pathogenic source of various vitamins that may play a role in protecting plants from pathogen invasion or other community disruptions. Filamentous fungi are the major drivers of plant disease and of food spoilage (e.g., Botrytis). Whether one community type or the other also favors the establishment of human pathogens such as Escherichia coli O157:H7 on the phylloplane is not known. It is, however, critical to understand the ability of human pathogenic bacteria to enter and persist in these fungal communities in developing effective strategies to mitigate against future outbreaks.


Haelewaters D, Toome M, Albu S, Aime MC. 2020. Red yeasts from leaf surfaces and other habitats: three new species and a new combination of Symmetrospora (Pucciniomycotina, Cystobasidiomycetes). Fungal Systematics and Evolution 5: 187-196. https://doi.org/10.3114/fuse.2020.05.12 [pdf]

Haelewaters D, Urbina H, Brown S, Newerth-Henson S, Aime MC. 2021. Isolation and molecular characterization of the romaine lettuce phylloplane mycobiome. Journal of Fungi 7(4): 277. https://doi.org/10.3390/jof7040277 [pdf]

Urbina H, Aime M.C., 2018. A closer look at Sporidiobolales: ubiquitous microbial community members of plant and food biospheres. Mycologia 110(1): 79-92. https://doi.org/10.1080/00275514.2018.1438020 [pdf]