Microorganisms that thrive in ecosystems characterized by extreme environmental conditions have been well studied to elucidate the evolutionary mechanisms that have favored their adaptation. Natural extreme environments represent an exceptional source of novel microbial species, as well as a source of novel secondary metabolites with biotechnological applications (Shu and Huang, 2022). However, one does not need to travel that far in search for extreme environments.

As a result of human activity and modernization, many different man-made artificial devices were built in the last century. Many studies have described the microbial populations present in highly anthropized artificial environments such as elevator buttons (Kandel et al., 2014), the underground (Gohli et al., 2019), and small electronic devices (Lax et al., 2015). Other works have unveiled that some man-made devices, machines, and appliances, despite being in constant contact with humans or human activities, have their own microecosystems with their own selective pressures and conserved microbiomes. This is the case, for example, of coffee machines (Vilanova et al., 2015) or dishwashers (Raghupathi et al., 2018).

Microwave irradiation has been used for decades to reduce the presence of microorganisms in food and extend food shelf life. The application of an electromagnetic wave in the range of 300 MHz to 300 GHz to a dielectric medium such as food, also known as microwave heating, generates heat to reach lethal temperatures that inactivate most microorganisms, such as Escherichia coli, Enterococcus faecalis, Clostridium perfringens, Staphylococcus aureus, Salmonella spp. and Listeria spp. (Woo et al., 2000; Kubo et al., 2020). Recent work has shown that cell inactivation is associated with deactivation of oxidation-regulating genes, DNA damage and increased permeability and disrupted integrity of cell membranes (Cao et al., 2018; Shaw et al., 2021). Despite this extensive characterization of the biological effects of microwave radiation on foodborne bacteria, to our knowledge there are no reports of microwaves as microbial niches, that is, environments where specific selective pressures (in this case, thermal shock, microwave radiation, and desiccation) can shape a specifically adapted microbiome.

In the present work, we describe the bacterial composition of 30 microwaves from different environments (domestic, domestic of shared use, and laboratory) to explore the intricacies of the microwave microbiome, with a particular focus on identifying variations based on usage patterns. The goal is to determine whether microwaves harbor a distinct microbiome shaped by prolonged exposure to microwave radiation, or whether their bacterial communities are influenced by food interactions and user habits.

In this study, we describe the bacterial communities of microwaves by NGS and compare the results obtained in domestic microwaves, domestic use microwaves located in large shared spaces, and laboratory microwaves. In parallel, this work was complemented with the isolation of culturable microorganisms from the same samples.

Through culturing techniques, we found that many of the isolated strains belonged to typically commensal and anthropic genera such as Bacillus, Micrococcus, Staphylococcus, Micrococcus, and Brachybacterium (Moskovicz et al., 2021; Skowron et al., 2021; Boxberger et al., 2022). As might be expected, human skin-related microorganisms are often found on artificial devices with which humans have frequent contact (Fujiyoshi et al., 2017). In addition, strains belonging to genera potentially pathogenic to humans, such as Klebsiella or Brevundimonas, were identified in some samples (Podschun and Ullmann, 1998; Ryan and Pembroke, 2018). Although these genera are less common on the skin, they can be found in the human microbiome on mucosal surfaces (Paczosa and Mecsas, 2016; Leung et al., 2019).

Analysis of the 16S rRNA gene revealed that the bacterial communities of the microwaves were dominated by members of the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, which also correspond to the predominant phyla in the human skin microbiome (Cho and Blaser, 2012), serving as an indicator of microwave anthropization. In this regard, the relevant presence of taxa that can be found in human skin such as Acinetobacter, Pseudomonas, Moraxella, Bacillus, and Staphylococcus (Kumar et al., 2019) was also detected at the genus level. Despite the similarities found between the samples due to the frequent use of microwaves by humans, differences were also detected between the three types of microwaves, especially between laboratory and domestic microwaves. In the latter, an enrichment of food-associated genera was anticipated due to their primary culinary application. Consequently, it was logical to observe more abundant genera such as Shewanella, Enterobacter, Aeromonas, Lactococcus, or Klebsiella in this type of microwaves, as they are frequently detected in food matrices and food-related habitats, typically associated with degradation or spoilage processes (Jarvis et al., 2018). It is important to note that certain species belonging to some of these genera, such as A. hydrophila, K. pneumoniae, and E. cloacae, are common contaminants in various food-related habitats and they pose potential health risks due to their pathogenic properties and antibiotic resistance (Daskalov, 2006; Shaker et al., 2007; Rodrigues et al., 2022). Their presence in the microwaves, as well as on other surfaces in the built environment, suggests the importance of regular cleaning practices to mitigate potential health risks, as frequent and adequate cleaning with appropriate disinfectants helps to prevent the presence of pathogens associated with these domestic environments (Carstens et al., 2022). As for laboratory microwaves, their use is completely different, as they are never used to heat food, but mainly to heat aqueous solutions, biological samples, synthetic materials or chemical reagents. Since food cannot be a shaping factor of their microbiomes, we hypothesize that the primary factor determining the microbiome in laboratory microwaves is the extreme conditions created within them (with heating processes that often require longer exposure times). In fact, some of the genera that were significantly more abundant in this group of samples included species known for their resistance to high doses of radiation, such as Deinococcus, Hymenobacter, Kineococcus, Sphingomonas, and Cellulomonas (Nayak et al., 2021). Some of the mechanisms used by bacteria to withstand such adverse conditions include expression of heat shock proteins (HSPs) (Maleki et al., 2016) and antioxidant enzymes (Munteanu et al., 2015), maintenance of cell integrity through changes in membrane fatty acid composition (Chen and Gänzle, 2016), biofilm formation (Bogino et al., 2013), or DNA repair (Sghaier et al., 2008). In particular, Deinococcus species such as D. radiodurans and D. geothermalis are known for their ability to withstand extreme environmental conditions such as ionizing radiation, desiccation, or high temperatures due to their highly efficient DNA repair mechanisms and protective cellular components (Mattimore and Battista, 1996; Liedert et al., 2012). Moreover, a previous study by Shen et al. (2020) showed that Acidovorax and Aquabacterium, two other genera enriched in laboratory samples, were differentially more abundant than others at higher temperatures. The phylum Cyanobacteria and Chloroflexi, which were also more common in laboratory microwaves, have also been described as extremophiles that can withstand environments with high levels of radiation and temperature (Lacap et al., 2011; Uribe-Lorío et al., 2019). The greater presence of bacteria resistant to these types of selective pressures could explain the higher alpha diversity values found in laboratory versus domestic microwaves. In addition, the more frequent use of domestic-shared microwaves and by more people could also favor greater diversity in this group with respect to domestic microwaves, as seen in other devices like washing machines (Jacksch et al., 2021).

In addition, when the bacterial communities of microwaves were compared with those of other highly irradiated environments—solar panels and nuclear waste residues—and kitchens (food-related habitats in constant contact with humans), it was found that domestic microwaves were more similar to kitchen surface samples. However, laboratory microwaves appeared to have similarities to kitchen and, to a lesser extent, solar panel samples. Thus, genera such as Acinetobacter, Pseudomonas, Bacillus, and Staphylococcus, widely present in the vast majority of microwaves analyzed, are typical of kitchens (Speirs et al., 1995; Malta et al., 2020). Interestingly, many of the genera significantly more present in laboratory microwaves (such as Deinococcus, Hymenobacter, Sphingomonas, Ralstonia, or Micrococcus) are typically identified in solar panels (Porcar et al., 2018; Tanner et al., 2018, 2020). These results confirm that all microwave samples resembled each other, although the laboratory microwaves showed greater similarities with microbiomes from environments with relatively low organic matter and subjected to intense radiation or desiccation.

Further work is needed to study the microbial adaptations of strains isolated from microwaves to high temperatures, desiccation, and electromagnetic radiation. For example, although the ability of bacteria to tolerate high temperatures can greatly vary depending on species and strains, those present in higher abundance in microwaves -Acinetobacter, Pseudomonas, Delftia, Bacillus, and Sphingobium- are known to exhibit a range of tolerance to high temperatures, where Acinetobacter has been reported to tolerate up to 50°C (Hrenovic et al., 2014), Pseudomonas up to 45°C (Silby et al., 2009), Delftia up to 40°C (Roy and Roy, 2019), Bacillus up to 80°C (Thomas, 2012) and Sphingobium up to 40°C (Singh et al., 2023). Some strains of Acinetobacter and Pseudomonas have been found to survive for extended periods of time in dry environments, including hospital surfaces (Espinal et al., 2012) and air filters (Pinna et al., 2009) respectively, while Bacillus species are well-known for their ability to form spores that can survive in a desiccated state for many years (Checinska et al., 2015). Similarly, some species of Sphingobium have been found to survive in dry soil and sediment environments (Madueño et al., 2018).

Three types of microwaves were studied in order to shed light on their bacterial communities. Our findings revealed the intricate interplay between microwave radiation exposure, food interactions, and user habits in shaping the bacteriome of microwaves. The distinct microbial composition observed between laboratory and household microwaves underscored the influence of usage patterns on microbial communities. Household microwaves, enriched in food-associated genera, reflected their primary culinary use, while laboratory microwaves harbored radiation-, desiccation-, and high-temperature-resistant taxa, indicating prolonged exposure to microwave radiation and suggesting a selective pressure of such harsh factors in shaping the distinctive microbial profile we found. However, more research is needed to understand how certain bacterial strains commonly found in microwaves adapt to these selective pressures. Indeed, this analysis could provide relevant information regarding the biotechnological potential of the microwave bacteriome.

Raw reads of the samples analyzed in this study are available at NCBI’s Sequence Read Archive (SRA) (Bioproject Accession PRJNA977132).

AI: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing. LM: Data curation, Formal analysis, Investigation, Methodology, Writing – review & editing. DT: Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft, Writing – review & editing. MP: Conceptualization, Funding acquisition, Investigation, Project administration, Resources, Supervision, Validation, Writing – original draft, Writing – review & editing.