research articles about microbiology

Microbiology

Regenerating Deep-Sea Worms Harness Live-In Algae as They Split into Three

Gutless, solar-powered worms genetically control their resident algae

Rohini Subrahmanyam

See What Gives Sourdough Its Distinctive Taste and Smell

You can thank yeast and bacteria cultivated over generations for the distinctive taste and smell of the oldest leavened bread in history

Daniel Veghte, The Conversation US

Viral Genetics Confirms What On-the-Ground Activists Knew Early in the Mpox Outbreak

Molecular biology could have changed the mpox epidemic—and could stop future outbreaks

Joseph Osmundson

Cannibal Cells Inspire Cancer Treatment Improvement

Giving cells an appetite for cancer could enhance treatments

Kate Graham-Shaw

Is Raw-Milk Cheese Safe to Eat?

Recent bacterial outbreaks from consuming cheese made from unpasteurized milk, or “raw milk,” raise questions about the safety of eating these artisanal products

Riis Williams

Many Pregnancy Losses Are Caused by Errors in Cell Division

Odd cell divisions could help explain why even young, healthy couples might struggle to get pregnant

Gina Jiménez

'Microbiome of Death' Uncovered on Decomposing Corpses Could Aid Forensics

Microbes that lurk in decomposing human corpses could help forensic detectives establish a person's time of death

Christoph Schwaiger, LiveScience

Weird ‘Obelisks’ Found in Human Gut May be Virus-Like Entities

Rod-shaped fragments of RNA called “obelisks” were discovered in gut and mouth bacteria for the first time

Joanna Thompson

Semen Has Its Own Microbiome—And It Might Influence Fertility

Recent research found a species of bacteria living in semen that’s associated with infertility and has links to the vaginal microbiome

Andrew Chapman

Bacteria Make Decisions Based on Generational Memories

Bacteria choose to swarm based on what happened to their great-grandparents

Allison Parshall

Your Body Has Its Own Built-In Ozempic

Popular weight-loss and diabetes drugs, such as Ozempic and Wegovy, target metabolic pathways that gut microbes and food molecules already play a key role in regulating

Christopher Damman, The Conversation US

See Your Body’s Cells in Size and Number

The larger a cell type is, the rarer it is in the body—and vice versa—a new study shows

Clara Moskowitz, Jen Christiansen, Ni-ka Ford

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• Microb Cell
• v.9(4); 2022 Apr 4

A hundred spotlights on microbiology: how microorganisms shape our lives

Didac carmona-gutierrez.

1 Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.

Katharina Kainz

Andreas zimmermann, sebastian j. hofer, maria a. bauer, christoph ruckenstuhl, guido kroemer.

2 Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.

3 Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.

4 Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.

Frank Madeo

5 BioHealth Graz, Graz, Austria.

6 BioTechMed Graz, Graz 8010, Austria.

Viral, bacterial, fungal and protozoal biology is of cardinal importance for the evolutionary history of life, ecology, biotechnology and infectious diseases. Various microbiological model systems have fundamentally contributed to the understanding of molecular and cellular processes, including the cell cycle, cell death, mitochondrial biogenesis, vesicular fusion and autophagy, among many others. Microbial interactions within the environment have profound effects on many fields of biology, from ecological diversity to the highly complex and multifaceted impact of the microbiome on human health. Also, biotechnological innovation and corresponding industrial operations strongly depend on microbial engineering. With this wide range of impact in mind, the peer-reviewed and open access journal Microbial Cell was founded in 2014 and celebrates its 100 th issue this month. Here, we briefly summarize how the vast diversity of microbiological subjects influences our personal and societal lives and shortly review the milestones achieved by Microbial Cell during the last years.

THE MANY IMPLICATIONS AND CHALLENGES OF MICROBIAL RESEARCH

The history of life on Earth is mainly microbial. The emergence of the first microorganisms 3-4 billion years ago [ 1 ] was the initial step for the establishment of terrestrial life. Microorganisms critically contributed to our planet's transformation, with the rise of photosynthetic bacteria allowing for oxygen to build up in the atmosphere [ 2 ]. Nowadays, microorganisms continue to affect the planet's biosphere and are an integral and inextricable part of our lives at different levels. The exploration of the microbial world is not only key to understanding ourselves but can provide answers to many medical, technological and scientific questions we face as humankind. Here, we briefly summarize the main areas, on which microorganisms impact today and will in the future, in particular (i) infectious diseases, (ii) symbiotic interactions, (iii) biotechnological applications and (iv) biological models ( Figure 1 ).

INFECTIOUS DISEASES

Infectious diseases continue to threaten our lives and societies, as revealed by the current COVID-19 pandemic. This applies in particular to persisting, emerging and re-emerging infectious diseases. In that respect, it will be important to monitor the human-animal interface, and recognize that many emerging diseases are zoonotic, i.e. they spread between animals and humans and have an animal reservoir [ 3 ]. This threat emanates from all microbial phyla. Apart from minatory viral infections [ 4 ], bacterial and fungal infections continue to cause millions of deaths worldwide [ 5 , 6 ]. An alarming rise in antibiotic and antifungal resistance exacerbates this menace [ 5 , 7 ], representing one of the most acute challenges in medical microbiology. Finally, protozoan infections remain a public health threat associated with significant morbidity and continue to have a substantial socioeconomic impact [ 8 , 9 ]. The limited advancements in vaccination strategies and the increasing parasite resistance against existing drugs further exacerbate the problem [ 10 ]. Also, coinfections of different pathogens belonging to one or different species can occur, resulting in additional challenges [ 11 – 14 ]. Thus, more work is needed to explore the molecular and pathological interaction between co-infecting microorganisms. This applies to both the direct interplay with each other and the indirect interaction through the host, for instance via the immune system. Altogether, infectious diseases continue to be devastating despite the many medical improvements accomplished in the last decades. Of note, many microbial pathogens also pose a threat to agriculture and livestock farming [ 15 , 16 ], which further aggravates the socioeconomic burden of infectious diseases.

SYMBIOTIC INTERACTIONS

The participation of microorganisms in symbiotic interactions determines a vast range of biological aspects across species. In particular, the human gut microbiota – the collection of bacteria, archaea and eukarya colonizing the gastrointestinal tract [ 17 ] - has attracted much attention in the past decade. The gut microbiota has a deep impact on many instances of human biology, ranging from development, physiology and immune homeostasis to health, nutrition and even behavior [ 18 – 21 ]. In addition, the importance of the human virome is increasingly being recognized. The human virome is composed of bacteriophages that infect bacteria, viruses that infect other cellular microorganisms (archaea, eukarya), viruses that infect human cells and some transitory viruses originating in food [ 22 ]. Their interactions with the human host are only beginning to be understood, but clearly hint towards a decisive role in health (e.g. via interplay with the host immune system) and multiple diseases (e.g. diabetes, hypertension and cancer) [ 22 ]. From a broader perspective, microbial symbiosis affects and co-defines a vast array of ecological aspects, ranging from plant growth [ 23 ] to defensive capacities [ 24 ]. For instance, complete ecosystems like hydrothermal vents and coral reefs exemplify the ecological success of microbial-multicellular symbioses. Finally, symbiosis can uniquely drive evolutionary innovation; this is maybe best embodied in the endosymbiotic origins of mitochondria and chloroplasts in eukaryotic cells [ 25 , 26 ], where the symbiont was cellularly and genomically integrated into the host.

BIOTECHNOLOGY

From a historical or even pre-historical perspective, already in ancient times, microorganisms were used as tools to produce, ferment or process a diversity of important food items including vinegar, bread, beer, fish, cheese and wine [ 27 ]. In other words, microorganisms were actively used as biotechnological agents long before the scientific basis underlying these processes was even known. Nowadays, microorganisms represent an essential backbone of many biotechnological applications thanks to their rapid growth for quick production, technical versatility for production design and wide applicability to a number of industrial sectors. Indeed, fundamental and applied microbiology are essential components of modern biotechnology with an ever-increasing economic impact. For instance, the food industry heavily relies on microorganisms for applications that range from fermented food items and alcoholic beverages to food grade components and bio-based ingredients in general. Thus, bacteria are used for the production of thickening or gelling agents, flavor compounds and enhancers, acidulants, vitamins and colorants [ 28 ]. Moreover, microorganisms have a deep impact on biotechnological approaches in agriculture and aquaculture with developments ahead that may use host-microbe interactions and the host microbiome for sustainable production [ 29 ]. Microorganisms also play a significant role in environmental biotechnology, including municipal and industrial water waste management [ 30 ] as well as treatment of solid hazardous waste [ 31 ]. Other applications involve the treatment of oil spillage [ 32 ], radioactive contamination [ 33 ], electronic waste processing [ 34 ], bioleaching (the extraction of metals from their ores through the action of microorganisms) [ 35 ] or even space biomining [ 36 ]. Yet another economically relevant use is energy production. Biofuels are produced by engineered microorganisms that utilize renewable carbon sources. Although they have shown great potential in replacing fossil fuels (especially ethanol and biodiesel), there are still some limitations, including applicability in conventional engines and high costs [ 37 ]. So-called microbial fuel cells (MFCs), which use bacteria to oxidize organic and inorganic matter in order to generate current, may represent an appealing electrogenic approach in the future [ 38 ]. Another example of microbial biotechnology is pharmaceutical production, which includes heterologous expression of human proteins, microbial enzymes or drug compounds for medical and research purposes [ 39 ]. Some of the aforementioned examples are established processes while others are still in development, revealing the huge potential and economic impact of microorganisms in technological approaches [ 40 ].

MODELLING BASIC PRINCIPLES OF BIOLOGY

The short generation time, facile cultivation and ease of genetic manipulation have established a number of microorganisms as widely used model organisms. Escherichia coli has been instrumental in the discovery and understanding of basic molecular biology processes, including DNA replication, DNA-to-RNA transcription and the genetic code allowing for RNA-to-protein translation. To date, a total of twelve Nobel Prizes were awarded for work that used E. coli as a research organism or tool, and its potential to assist in further advancements remains high [ 41 ]. A number of other prokaryotes (including archaea [ 42 ]) are actively used as model organisms. For example, Bacillus subtilis is applied to study biofilms, bacterial asymmetry or morphogenesis [ 43 ], cyanobacteria like Synechocystis sp. PCC 6803 to model photosynthesis [ 44 ], or Caulobacter crescentus for the study of cellular differentiation, motility or mechanosensing [ 45 ]. Green algae, including unicellular Chlamydomonas reinhardtii and multicellular Volvox carteri (Volvox), also serve as model organisms. C. reinhardtii bears both animal-like organelles (cilia) and plant-like organelles (chloroplasts), allowing research into the function of flagella and photosynthesis [ 46 ]. Volvox is mainly used to investigate developmental mechanisms and the evolutionary origins of multicellularity [ 47 ]. Other protists include the giant heterotrichous ciliate Stentor coeruleus as a model for cellular regeneration and wound healing [ 48 ] and the ciliate Oxytricha , which is employed in the areas of genome biology, post-zygotic development and epigenetic inheritance [ 49 ]. The eukaryotic nature of these cells allows for the study of essential and medically relevant molecular processes. Similarly, yeast cells display all advantages of unicellular model organisms paired with a high degree of conservation that has made yeast a fundamental partner in elucidating many aspects of human physiology and pathology [ 50 ]. Work performed in yeast has been awarded five Nobel Prizes in the past two decades. The budding yeast Saccharomyces cerevisiae is used to study a multitude of human diseases (e.g. neurodegeneration, cancer) [ 51 , 52 ], characterize basic physiological processes (e.g. cell death, aging, autophagy, mitochondrial import, vesicle fusion, cell cycle) [ 53 – 64 ] and identify novel medical drugs (e.g. antiaging, anticancer, antiparasitic, antifungal) [ 56 , 65 – 70 ], among many other applications [ 71 ]. Another example is the fission yeast Schizosaccharomyces pombe , which is used to analyze, for example, cell cycle processes or DNA checkpoints [ 72 , 73 ].

A PUBLICATION PLATFORM FOR MICROBIOLOGICAL RESEARCH

Given the many layers of how microorganisms wield huge influence on our lives, the open-access journal Microbial Cell was founded with the idea to generate an online agora for all types of research in the microbiological field. The current issue (Volume 9, Issue 4) marks a milestone in Microbial Cell 's history: it represents the 100 th issue since the journal was launched in January 2014. This occasion is a timely moment to take stock and reflect on how Microbial Cell has developed and contributed to the research fields of unicellular and multicellular microorganisms over the past years.

The mere fact that a journal run by active academic scientists and through an independent publisher (Shared Science Publishers) has established itself in the highly competitive business of peer-reviewed scientific publishing is per se a great achievement. That this has occurred in a radically open-access fashion and in such an important and trending field like microbiology adds even more value to this accomplishment. We take this opportunity to thank all authors who have published their articles in Microbial Cell for their trust put in the journal to run the evaluation and dissemination processes of their work. At the same time, we congratulate the authors for the high quality of their papers: the around 400 articles that have been published since the journal was launched have now cumulatively been cited more than 4000 times (Web of Science, Clarivate Analytics).

We acknowledge all members of the Editorial Board for their long-standing commitment and reliability. Indeed, our Editorial Board has the arduous task to evaluate submissions in ten different thematic subareas: aging, cell death, cell physiology and cell signaling, genome stability and structure, infection biology, microbiome, mitochondria, parasitology, stress response, and structural & systems biology. During the manuscript evaluation process, these editors strongly rely on the expertise and rigor of peer reviewers, who invest a great amount of their time in improving the submitted work. We are very grateful to all our referees throughout the world for their invaluable input. The combined effort of all partners of the ecosystem, authors, editors and reviewers, has consistently improved the journal throughout these years to place it at the apex of microbiology.

A BRIEF HISTORY OF MICROBIAL CELL

Microbial Cell emerged as an academic effort from a group of active scientists to apprehend the thematic heterogeneity of microbial research. Accordingly, the inaugural Editorial from January 2014 outlined that Microbial Cell would have the mission to facilitate “the characterization of unicellular organisms (or multicellular microorganisms) in their response to internal and external stimuli and/or in the context of human health and disease” [ 74 ]. This definition mirrored well the initial and still persisting idea of a publication platform that acknowledges microbiological interdisciplinarity.

Following these objectives, the first 100 issues of Microbial Cell have accompanied and contributed to several developments in microbiological research during the last eight years. For instance, in a much regarded Microbial Cell paper of 2015, Alexander Varshavsky and colleagues described formylated N-terminal methionine as a novel bacterial degradation signal used in a new branch of the bacterial N-end rule pathway [ 75 ]. Varshavsky's lab was instrumental in the discovery of the ubiquitin system of intracellular protein degradation and was the first to describe the connection between the N-terminal residue of a protein and its half-life [ 76 , 77 ]. As another example, in 2016 Microbial Cell published a highly cited review, in which Daniel J. Klionsky and colleagues provided a brief but comprehensive summary on the roles, regulatory instances and molecular mechanisms of autophagy [ 78 ]. 2016 was also the year, in which Yoshinori Ohsumi was awarded the Nobel Prize in Physiology or Medicine for his discovery of the mechanisms orchestrating this intracellular degradation pathway, which were uncovered in yeast cells [ 79 – 81 ]. In 2018 Microbial Cell published a review by Francisco J.M. Mójica and colleagues that provided an overview of the CRISPR-Cas mechanism as a prokaryotic immune system and discussed a number of evolutionary implications [ 82 ]. Mójica's achievements, particularly his groundbreaking work characterizing CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci [ 83 , 84 ], laid the ground for the development of CRISPR-Cas as the most important tool for genomic editing that exists to date. In 2020, Emmanuelle Charpentier and Jennifer A. Doudna received the Nobel Prize in Chemistry for the development of this method [ 85 ]. One final example for how Microbial Cell has contributed to research deals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the highly infectious disease COVID-19. The multilayered consequences of COVID-19 at the individual, social, political and economic levels are unprecedented in our globalized world. Microbial Cell has been publishing diverse papers on SARS-CoV-2, ranging from mechanistic viewpoints to methodological approaches for viral detection and molecular modelling.

The last 100 issues have seen Microbial Cell grow as a journal and establish itself in the microbiology publishing sphere. The journal's CiteScore (Scopus) is currently 7.1 (provisional score for 2021), which ranks the journal at top positions in all relevant microbiology-related categories. Microbial Cell has established roots in various research communities as highlighted by reviews, research papers, commentaries, as well as by a number of guideline papers that establish unified criteria in a number of fields, for instance in DNA recombination and repair, yeast cell death and antifungal and antibiofilm agents. Furthermore, Microbial Cell has initiated the publication of several Special Issues on a diverse range of topics, following a concept, in which incoming papers are published in regular issues and then collected in the Special Issue repositorium. That way, Special Issues can be updated continuously and refreshed by new articles that capture new evolving knowledge. Until now, Microbial Cell has launched Special Issues on the following topics [ 86 ]: sexually transmitted infections (started in 2016), the human microbiome in health and disease (started in 2019), hygiene in healthcare (started in 2019), microbiology in cultural heritage (started in 2021) and yeast cell death (started in 2022).

In the course of the last eight years, Microbial Cell has strengthened its position in the microbiology-publishing landscape by attaining a number of milestones. In 2014, Microbial Cell partnered with the World Health Organization's HINARI program to support free access to biomedical research literature. That same year, Microbial Cell also became a member of Crossref, an official digital object identifier (DOI) registration agency, providing each article with a persistent interoperable identifier that also enables to precisely link citations across publishers of online academic journals. Also in 2014, Microbial Cell was indexed in Sherpa/RoMEO, an aggregator of open access policies of academic journals. In addition, Microbial Cell secured a partnership with the Austrian National Library to ensure digital long-term archiving and perpetual access to its complete content. After successful applications to the Chemical Abstracts Service (CAS) and the Directory of Open Access Journals (DOAJ), Microbial Cell was accepted in these two renowned repositories in 2015. One year later, Microbial Cell was awarded the very selective DOAJ Seal (allocated to only 10% of DOAJ-indexed journals) for best practice in open access publishing. Also in 2016, Microbial Cell entered the International Committee of Medical Journal Editors (ICMJE) list to acknowledge that it follows the ICMJE's Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals. That same year, Microbial Cell was selected for inclusion in Clarivate Analytics' (formerly Thomson Reuters) Emerging Sources Citation Index (ESCI), thus allowing the journal to be accessed through the Web of Science. This selection subsequently allowed for inclusion into additional Web of Science indexes: Biological Abstracts, BIOSIS Previews, Current Contents Life Sciences and Essential Science Indicators. One of the most important milestones was reached in 2017, when Microbial Cell was accepted in Pubmed Central, the archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). After long evaluation periods, Microbial Cell was further accepted in two of the most selective indexes, Elsevier's Scopus (2019) and Clarivate Analytics' Science Citation Index Expanded SCIE (2021).

THE CONCEPT OF MICROBIAL CELL

Over the past few years, Microbial Cell has persistently paid high attention to the quality of its published material. Content-related aspects like novelty, methodology, data presentation, appropriate interpretation, etc., are certainly the main denominators of quality in any submission. In addition, the increasing number of scientific misconduct cases requires special attention. That is why Microbial Cell implements a very strict and careful evaluation of any submitted material in relation to possible data fabrication, data falsification including inadequate manipulation of images and plagiarism. Thus, each submitted work is tested via CrossCheck, a plagiarism detection service powered by the detection software iThenticate. If concerns are raised, Microbial Cell initiates appropriate procedures as detailed by the Committee on Publication Ethics (COPE).

With respect to article accessibility , Microbial Cell has always followed an open access approach and used a creative commons (CC) license for copyright purposes. Microbial Cell is published under the CC BY license, which is probably the most generous type of CC licenses. The CC BY license authorizes third parties to share and adapt the published work, even for commercial goals, as long as the authors are appropriately credited and changes are indicated. Thereby, the work can be accessed completely free and with no restrictions; the only prerequisite is the connection to the internet, with no other financial, legal or technical limitations. This approach maximizes the visibility of published work and at the same time, ensures that scientific knowledge is universally and freely accessible to every interested individual around the world. This openness reflects the essential values of science and acts as an effective driver of active research, promoting the free exchange of ideas. Incidentally, 2022 marks the 20 th anniversary of the Budapest Open Access Initiative, the public statement of principles relating and defining open access to the research literature.

As mentioned, unrestricted article accessibility promotes visibility and increases the impact of a scientific work. The assessment of such an impact involves citations by scholarly journals (because this assessment is peer-connected), which derives in rankings by dedicated indexes. However, we also do acknowledge that alternative outlets, for instance social media, are important indicators of public interest as they increase the diffusion of information at the item (article)-level. Accordingly, Microbial Cell actively uses the corresponding channels including Twitter and Facebook. The journal also provides a social impact measure for each article through PlumX Metrics, a comprehensive monitoring tool that calculates altmetrics for scholarly works.

The involvement in, and commitment to, the broad thematic scope of neglected, emerging and trendy microbiology-related topics is a defining characteristic of Microbial Cell . As such, the journal has been continuously supporting the efforts of the microbiology research community well beyond its role as a publication platform. For instance, Microbial Cell runs a waiver program (DevResearch Program) that allows for the partial or complete exemption of article processing charges for corresponding authors based in low-income or lower-middle-income countries. The journal has also sponsored several prizes at and provided support to international conferences, including the Theodor Escherich Symposium on medical microbiome research, the International Symposium “One mitochondrion, many diseases”, or the International Meeting on Yeast Apoptosis.

Since the genesis of Microbial Cell , we have been aware of the plethora of facets that make microorganisms a fundamental part of our lives, including at the historical, medical, diagnostic, evolutionary, ecological, environmental, cultural, biotechnological and modelling levels. In accord with this conviction, we have published 100 issues that reflect the wide-ranging importance of microbial research. As we have outlined in this piece, this involves a number of challenges and opportunities that we will continue to embrace in the future.

Microbiology has long been at the forefront of research and has attained many achievements in diverse areas of life science and medical practice. Its popularity has gained new heights in recent years, not only due to its ever-increasing applicability, but also due to the unprecedented threat of rising antibiotic and antifungal resistance, as well as due to the re-emergence of old infectious diseases and the emergence of new ones. Indeed, microorganisms represent both opportunity and threat. As the Editors of Microbial Cell , we have the responsibility to ensure adequate selection of publications that represent a high level of contemporary science. At the same time, we have the ambition to provide an open interdisciplinary communication space for microbiologists from all subdisciplines around the globe, in the interest of scientific and societal progress.

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BMC Microbiology is an open access, peer-reviewed journal that considers articles on all microorganisms - bacteria, archaea, algae and fungi, viruses, unicellular parasites and helminths. It considers studies on all aspects of the biology and biochemistry of microorganisms including but not limited to cell biology, genomics, signalling, the interaction of the microbes with the environment and host, mechanistic and functional insights into infection and disease, and biotechnological application in science and industry.

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Citation Impact 2023 Journal Impact Factor: 4.0 5-year Journal Impact Factor: 4.6 Source Normalized Impact per Paper (SNIP): 1.081 SCImago Journal Rank (SJR): 0.999 Speed 2023 Submission to first editorial decision (median days): 15 Submission to acceptance (median days): 135 Usage 2023 Downloads: 2,970,572 Altmetric mentions: 1,619

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ORIGINAL RESEARCH article

The microwave bacteriome: biodiversity of domestic and laboratory microwave ovens.

• 1 Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
• 2 Darwin Bioprospecting Excellence S.L., Valencia, Spain

Microwaves have become an essential part of the modern kitchen, but their potential as a reservoir for bacterial colonization and the microbial composition within them remain largely unexplored. In this study, we investigated the bacterial communities in microwave ovens and compared the microbial composition of domestic microwaves, microwaves used in shared large spaces, and laboratory microwaves, using next-generation sequencing and culturing techniques. The microwave oven bacterial population was dominated by Proteobacteria , Firmicutes , Actinobacteria , and Bacteroidetes , similar to the bacterial composition of human skin. Comparison with other environments revealed that the bacterial composition of domestic microwaves was similar to that of kitchen surfaces, whereas laboratory microwaves had a higher abundance of taxa known for their ability to withstand microwave radiation, high temperatures and desiccation. These results suggest that different selective pressures, such as human contact, nutrient availability and radiation levels, may explain the differences observed between domestic and laboratory microwaves. Overall, this study provides valuable insights into microwave ovens bacterial communities and their potential biotechnological applications.

1 Introduction

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.

2.1 Strain collection

Thirty microwave ovens (10 from domestic use, 10 of domestic shared-use, and 10 of laboratory use) were sampled and used to culture microbial strains on Columbia agar, TSA, YM, R2A, and NA. This yielded a collection of 101 isolates dominated by strains belonging to the genera Bacillus , Micrococcus , and Staphylococcus , followed by Brachybacterium , Paracoccus , and Priestia . Members of the genera Acinetobacter , Bhargavaea , Brevibacterium , Brevundimonas , Dermacoccus , Klebsiella , Pantoea , Pseudoxanthomonas , and Rhizobium were found only in domestic microwaves. Strains belonging to the genera Arthrobacter , Enterobacter , Janibacter , Methylobacterium , Neobacillus , Nocardioides , Novosphingobium , Paenibacillus , Peribacillus , Planococcus , Rothia , Sporosarcina , and Terribacillus were isolated only in microwaves of domestic-shared use. A strain of Nonomuraea species was isolated only in laboratory microwaves ( Figure 1 ).

Figure 1 . Main bacterial genera isolated from domestic, domestic-shared and laboratory microwaves.

Moreover, microbial strains of the genera Bacillus , Curtobacterium , Prolinoborus , Pseudomonas , and Staphylococus were isolated from both domestic and domestic-shared microwaves. Kocuria and Moraxella strains were obtained from domestic-shared and laboratory microwaves. Members of four genera were found in all types of microwaves: Brachybacterium , Micrococcus , Paracoccus , and Priestia ( Figure 1 ).

2.2 Analysis of bacterial diversity of microwaves by NGS

NGS (Next Generation Sequencing) analysis of the conserved V3 and V4 regions of the 16S rRNA gene allowed the exploration of bacterial diversity within microwave ovens. The results showed that, at the phylum level, Proteobacteria predominated in microwave bacterial communities, followed by Firmicutes and Actinobacteria to a lesser extent ( Figure 2 ; Supplementary file S1 ). Differential abundance analysis confirmed the higher presence of the phyla Chloroflexi , Acidobacteria , Deinococcus-Thermus , and Cyanobacteria in the laboratory microwaves compared to the household microwaves ( Supplementary file S2 ). The latter phylum was also more abundant in the domestic-shared microwave group compared to the domestic (not shared) microwaves.

Figure 2 . Taxonomic distribution at the phylum level of the bacteria present in the three types of microwaves: laboratory (M1–M10), domestic (M11–M20), and domestic-shared (M21–M34).

At the genus level, laboratory microwaves showed a more homogeneous composition than domestic microwaves ( Figure 3 ). Acinetobacter , Pseudomonas , and Sphingobium were present in all types of microwaves. Among the significantly more abundant genera in laboratory microwaves compared to household microwaves were Delftia , Micrococcus , Deinocococcus , and an unidentified genus of the phylum Cyanobacteria ( Supplementary file S2 ). The opposite trend was observed for the genera Epilithonimonas , Klebsiella , Shewanella , and Aeromonas , among others. In addition, differential abundance analysis between domestic and domestic-shared microwaves showed that two genera, Lawsonella and Methyloversatilis , were significantly more abundant in the latter group. When comparing NGS results with the culturing techniques, it was found that almost all of the isolated genera were detected by 16S rRNA gene sequencing. Interestingly, Bhargavaea , Janibacter , and Nonomuraea , which could be cultured, were not detected by sequencing.

Figure 3 . Taxonomic distribution at the genus level of the bacteria present in the three types of microwaves: laboratory (M1–M10), domestic (M11–M20), and domestic-shared (M21–M34).

In terms of alpha diversity analysis, domestic microwaves had the lowest number of distinct ASVs detected and also lower Shannon index values, although these trends were only significant when comparing this type of sample with laboratory microwaves ( Figure 4 ). No significant differences were found between domestic and domestic-shared microwaves, nor between the latter and laboratory microwaves, in the number of distinct ASVs observed, Shannon index and Simpson index. Overall, between 100 and 300 different ASVs were detected, depending on the type of sample, as well as Shannon indices below 4 in household microwaves and above in laboratory microwaves, while Simpson indices ranged from 0.8 to 1.

Figure 4 . Alpha diversity results (richness or number of ASVs, Shannon index and Simpson index) for the three types of microwaves: laboratory (M1–M10), domestic (M11–M20), and domestic-shared (M21–M34).

At the β-diversity level, when comparing the different groups of samples at a qualitative and quantitative level, it was observed that they were statistically different from each other (PERMANOVA test, p -value < 0.05). Laboratory samples grouped closely together, indicating a greater homogeneity in their bacterial composition ( Figure 5 ). When comparing household microwaves, samples tended to cluster within each of the two groups (domestic and shared-domestic), although this was less evident than with laboratory microwaves. Furthermore, the β-diversity of the microwave samples was also compared with that of two highly irradiated, extreme environments: solar panels and nuclear waste samples; as well as an anthropized indoor environment: kitchen surfaces ( Figure 6 ). The samples were grouped according to their origin, although the solar panel samples and especially the kitchen samples appeared to display a more similar bacterial composition to the household microwave samples. The nuclear waste disposal samples showed the least similarity to the microwave samples.

Figure 5 . Beta diversity (PCoA) based on Bray–Curtis (ASV level) for the three types of microwaves: laboratory (M1–M10), domestic (M11–M20), and domestic-shared (M21–M34).

Figure 6 . Beta diversity (PCoA) based on Bray–Curtis (ASV level) for the three types of microwaves: laboratory (M1–M10), domestic (M11–M20), and domestic-shared (M21–M34) and samples from other studies: four kitchen samples, four samples from solar panels and six from nuclear waste.

3 Discussion

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 ).

4 Conclusion

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.

5 Experimental procedures

5.1 sampling.

The inner cubicle of 10 domestic, 10 shared-domestic and 10 laboratory microwaves was sampled by rubbing a sterile collection swab humidified with Phosphate Buffer Saline solution (PBS, composition in g l-1: NaCl; 8.0, KCl; 2.0, Na 2 HPO 4 ; 1.44, KH 2 PO 4 ; 0.24. pH; 7.4) that was stored in Eppendorf tubes containing 500 μL PBS and transported to the laboratory at ambient temperature (20–25°C). Samples were immediately used for strain isolation and stored at −20°C until genomic DNA was extracted. A detailed list of the samples taken, and the corresponding microwaves characteristics can be found in Supplementary Table S1 .

5.2 Strain isolation and identification

For bacterial isolation through culturing techniques, five different growth media were used in this study: Nutrient Agar (NA, composition in g/L: peptone 5, meat extract 3, NaCl 5, agar 15, pH 7.2), Reasoner’s 2A agar (R2A, composition in g/L: peptone 1, yeast extract 0.5, dextrose 0.5, soluble starch 0.5, K 2 HPO 4 0.3, MgSO 4 0.05, sodium pyruvate 0.3, 15 agar, pH 7.2), Trypticase Soy Agar medium (TSA, contained in g/L: tryptone 15, soya peptone 5, NaCl 5, agar 15, pH 7.2), Yeast Mold Agar medium (YM, contained in g/L: yeast extract 3, malt extract 3, dextrose 10, peptone soybean 4, agar 15, pH; 6.2), Columbia Blood Agar medium (CBA, contained in g/L: special peptone 23, starch 1, NaCl 5, agar 10, pH 7.3).

Samples were homogenized in Eppendorf tubes by vigorously mixing with a vortex, and serial dilutions were plated on the media above and incubated at room temperature for 7 days. After 1 week of incubation, individual colonies were selected and isolated by re-streaking onto fresh medium. Pure cultures were cryo-preserved at −80°C in 15% glycerol.

For the taxonomic identification of the strains, PCRs amplifying a fragment of the 16S rRNA gene were carried out using the universal primers 8F (5′-AGA GTT TGA TCC TGG CTC AG-3′) and 1492R (5′-CGG TTA CCT TGT TAC GAC TT-3′) after extracting the DNA by boiling the cells at 99°C for 10 min in MilliQ-water. The 16S rRNA PCR was performed using the NZYTaq II 2× Green Master Mix, and the following PCR cycle: initial denaturation at 95°C for 3 min; 30 cycles of amplification (15 s at 94°C, 15 s at 50°C, 50 s at 72°C); and 2 min of extension at 72°C. The PCR products were checked by electrophoresis in a 1.2% agarose gel and subsequently precipitated overnight in isopropanol 1:1 (vol:vol) and potassium acetate 1:10 (vol:vol; 3 M, pH 5). DNA pellets were washed with 70% ethanol, resuspended in 15 μL Milli-Q water and Sanger sequenced by Eurofins Genomics (Germany). All the sequences were manually trimmed before comparing them against the EzBioCloud 1 and NCBI online databases. 2 EzBioCloud was used to taxonomically identify the closest type strains.

5.3 Isolation of genomic DNA

Genomic DNA was isolated from the samples using the PowerSoil DNA Isolation kit (MO BIO laboratories, Carlsbad, CA, United States) following the manufacturer’s instructions and quantified using the Qubit dsDNA HS Assay kit (Qubit 2.0 Fluorometer, Q32866). Three DNA extractions of new, unused sterile collection swabs humidified with PBS solution were also carried out, one of them together with the microwave’s samples and the remaining two on different subsequent days. These two later ones were sent for high-throughput rRNA sequencing separately in two other sequencing batches with samples belonging to other projects.

5.4 High-throughput rRNA sequencing and metataxonomic analysis

In order to study the bacterial communities present in the microwaves, the extracted genomic DNA was used to amplify the hypervariable region V3-V4 of the 16S ribosomal RNA gene. The conserved regions V3 and V4 (459 bp) of the 16S rRNA gene were amplified using the following forward and reverse primers: 5′-TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG 3′ and 5′-GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′, and the following PCR cycle: initial denaturation at 95°C for 3 min; 25 cycles of amplification (30 s at 95°C, 30 s at 55°C, 30 s at 72°C); and 5 min of extension at 72°C ( Satari et al., 2020 ). The amplification was carried out using the KAPA HiFi HotStart ReadyMix PCR kit (KK2602). The 16S rRNA amplicons were mixed with Illumina sequencing barcoded adaptors (Nextera XT index kit v2, FC-131-2001), and libraries were normalized and merged. The pools with indexed amplicons were loaded onto the MiSeq reagent cartridge v3 (MS-102-3003) and spiked with 10% PhiX control to improve the sequencing quality, that was finally conducted using paired-ends on an Illumina MiSeq platform (2 × 300 bp) in the Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (Fisabio) (Valencia, Spain).

The raw Illumina sequences were loaded into Qiime2 (v2021.2.0) ( Bolyen et al., 2019 ). The quality of the sequences was checked using the plugin Demux and the Qiime2-integrated DADA2 pipeline was used for trimming and joining the sequences, removing chimeras and detecting amplicon sequence variants (ASVs) (>99.9% of similarity). The taxonomy of each sequence variant was determined via the classify-Sklearn module from the feature-classifier plugin, employing Greengenes-SILVA-RDP (GSR) ( Molano et al., 2024 ) as reference database for the 16S rRNA taxonomic assignment (V3-V4 hypervariable region). Results were analyzed and plotted with the phyloseq R package (v. 1.30.0) ( McMurdie and Holmes, 2013 ) and ggplot2 (v3.4.0).

The beta diversity analysis was carried out using the principal component analysis (PCoA) after calculating the distances between samples using the Bray-Curtis method, using phyloseq R package (v. 1.22.3) ( McMurdie and Holmes, 2013 ) with Bray–Curtis dissimilarities. PERMANOVA tests were calculated with vegan using the adonis2 function from the vegan R package (v2.6.4) to detect statistically significant differences in the composition of the microbiome between the groups analyzed. The differential abundance analyses between taxa were conducted using the MaAsLin2 R package (v1.0.0) (Mallick et al., 2021) with the following parameters: min_abundance = 0.01, min_prevalence = 0.33, max_significance = 0.05, normalization = “None,” transform = “LOG,” analysis_method = “LM,” correction = “BH,” standardize = FALSE. Differentially abundant taxa were considered significant if the adjusted p -value was less than or equal to 0.05.

Additionally, the bacterial profile obtained in terms of β-diversity was compared with two extreme environments with high levels of radiation: solar panels and nuclear waste samples, along with a human-modified indoor environment represented by kitchen samples ( Supplementary Table S2 ). For this purpose, publicly available datasets were downloaded from NCBI.

Data availability statement

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

Author contributions

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.

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. Financial support from the European Union H2020 (MIPLACE project ref. PCI2019-111845-2, Natural and Synthetic Microbial Communities for Sustainable Production of Optimised Biogas, MICRO4BIOGAS, Grant agreement ID: 101000470) and the Agencia Estatal de Investigación (AEI) (427 Programación Conjunta Internacional 2019) is acknowledged.

Conflict of interest

DT and MP were employed by Darwin Bioprospecting Excellence S.L.

The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Supplementary material

The Supplementary material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2024.1395751/full#supplementary-material

1. ^ https://www.ezbiocloud.net

2. ^ https://blast.ncbi.nlm.nih.gov/Blast.cgi

Bogino, P., Abod, A., Nievas, F., and Giordano, W. (2013). Water-limiting conditions alter the structure and biofilm-forming ability of bacterial multispecies communities in the alfalfa rhizosphere. PLoS One 8:e79614. doi: 10.1371/journal.pone.0079614

PubMed Abstract | Crossref Full Text | Google Scholar

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857. doi: 10.1038/s41587-019-0209-9

Crossref Full Text | Google Scholar

Boxberger, M., Magnien, S., Antezack, A., Rolland, C., Makoa, M., La-Scola, B., et al. (2022). Brachybacterium epidermidis Sp. Nov., a novel bacterial species isolated from the Back of the right hand, in a 67-year-old healthy woman. Int. J. Microbiol. 2022, 2875994–2875998. doi: 10.1155/2022/2875994

Cao, J.-X., Wang, F., Li, X., Sun, Y.-Y., Wang, Y., Ou, C.-R., et al. (2018). The influence of microwave sterilization on the ultrastructure, permeability of cell membrane and expression of proteins of Bacillus Cereus . Front. Microbiol. 9:1870. doi: 10.3389/fmicb.2018.01870

Carstens, C. K., Salazar, J. K., Sharma, S. V., Chan, W., and Darkoh, C. (2022). Evaluation of the kitchen microbiome and food safety behaviors of predominantly low-income families. Front. Microbiol. 13:987925. doi: 10.3389/fmicb.2022.987925

Checinska, A., Paszczynski, A., and Burbank, M. (2015). Bacillus and other spore-forming genera: variations in responses and mechanisms for survival. Annu. Rev. Food Sci. Technol. 6, 351–369. doi: 10.1146/annurev-food-030713-092332

Chen, Y. Y., and Gänzle, M. G. (2016). Influence of cyclopropane fatty acids on heat, high pressure, acid and oxidative resistance in Escherichia coli . Int. J. Food Microbiol. 222, 16–22. doi: 10.1016/j.ijfoodmicro.2016.01.017

Cho, I., and Blaser, M. J. (2012). The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13, 260–270. doi: 10.1038/nrg3182

Daskalov, H. (2006). The importance of Aeromonas hydrophila in food safety. Food Control 17, 474–483. doi: 10.1016/j.foodcont.2005.02.009

Espinal, P., Martí, S., and Vila, J. (2012). Effect of biofilm formation on the survival of Acinetobacter baumannii on dry surfaces. J. Hosp. Infect. 80, 56–60. doi: 10.1016/j.jhin.2011.08.013

Fujiyoshi, S., Tanaka, D., and Maruyama, F. (2017). Transmission of airborne Bacteria across built environments and its measurement standards: a review. Front. Microbiol. 8:2336. doi: 10.3389/fmicb.2017.02336

Gohli, J., Bøifot, K. O., Moen, L. V., Pastuszek, P., Skogan, G., Udekwu, K. I., et al. (2019). The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities. Microbiome 7:160. doi: 10.1186/s40168-019-0772-9

Hrenovic, J., Durn, G., Goic-Barisic, I., and Kovacic, A. (2014). Occurrence of an environmental Acinetobacter baumannii strain similar to a clinical isolate in Paleosol from Croatia. Appl. Environ. Microbiol. 80, 2860–2866. doi: 10.1128/AEM.00312-14

Jacksch, S., Zohra, H., Weide, M., Schnell, S., and Egert, M. (2021). Cultivation-based quantification and identification of Bacteria at two hygienic key sides of domestic washing machines. Microorganisms 9:905. doi: 10.3390/microorganisms9050905

Jarvis, K. G., Daquigan, N., White, J. R., Morin, P. M., Howard, L. M., Manetas, J. E., et al. (2018). Microbiomes associated with foods from plant and animal sources. Front. Microbiol. 9:2540. doi: 10.3389/fmicb.2018.02540

Kandel, C. E., Simor, A. E., and Redelmeier, D. A. (2014). Elevator buttons as unrecognized sources of bacterial colonization in hospitals. Open Med. 8, e81–e86

PubMed Abstract | Google Scholar

Kubo, M. T., Siguemoto, É. S., Funcia, E. S., Augusto, P. E., Curet, S., Boillereaux, L., et al. (2020). Non-thermal effects of microwave and ohmic processing on microbial and enzyme inactivation: a critical review. Curr. Opin. Food Sci. 35, 36–48. doi: 10.1016/j.cofs.2020.01.004

Kumar, K. V., Pal, A., Bai, P., Kour, A., E, S., P, R., et al. (2019). Co-aggregation of bacterial flora isolated from the human skin surface. Microb. Pathog. 135:103630. doi: 10.1016/j.micpath.2019.103630

Lacap, D. C., Warren-Rhodes, K. A., McKay, C. P., and Pointing, S. B. (2011). Cyanobacteria and chloroflexi-dominated hypolithic colonization of quartz at the hyper-arid core of the Atacama Desert, Chile. Extremophiles 15, 31–38. doi: 10.1007/s00792-010-0334-3

Lax, S., Hampton-Marcell, J. T., Gibbons, S. M., Colares, G. B., Smith, D., Eisen, J. A., et al. (2015). Forensic analysis of the microbiome of phones and shoes. Microbiome 3:21. doi: 10.1186/s40168-015-0082-9

Leung, P. H. M., Subramanya, R., Mou, Q., Lee, K. T., Islam, F., Gopalan, V., et al. (2019). Characterization of mucosa-associated microbiota in matched Cancer and non-neoplastic mucosa from patients with colorectal Cancer. Front. Microbiol. 10:1317. doi: 10.3389/fmicb.2019.01317

Liedert, C., Peltola, M., Bernhardt, J., Neubauer, P., and Salkinoja-Salonen, M. (2012). Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium. J. Bacteriol. 194, 1552–1561. doi: 10.1128/JB.06429-11

Madueño, L., Coppotelli, B. M., Festa, S., Alvarez, H. M., and Morelli, I. S. (2018). Insights into the mechanisms of desiccation resistance of the Patagonian PAH-degrading strain Sphingobium sp. 22B. J. Appl. Microbiol. 124, 1532–1543. doi: 10.1111/jam.13742

Maleki, F., Khosravi, A., Nasser, A., Taghinejad, H., and Azizian, M. (2016). Bacterial heat shock protein activity. J. Clin. Diagn. Res. 10:BE01–BE03. doi: 10.7860/JCDR/2016/14568.7444

Mallick, H., Rahnavard, A., McIver, L. J., Ma, S., Zhang, Y., Nguyen, L. H., et al. (2021). Multivariable association discovery in population-scale meta-omics studies. PLOS Computational Biology , 17:e1009442. doi: 10.1371/journal.pcbi.1009442

Malta, R. C. R., Ramos, G. L. De, and Nascimento, J. S. (2020). From food to hospital: we need to talk about Acinetobacter spp. Germs , 10, 210–217. doi: 10.18683/germs.2020.1207

Mattimore, V., and Battista, J. R. (1996). Radioresistance of Deinococcus radiodurans : functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. J. Bacteriol. 178, 633–637. doi: 10.1128/jb.178.3.633-637.1996

McMurdie, P. J., and Holmes, S. (2013). Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. doi: 10.1371/journal.pone.0061217

Molano, L.-A. G., Vega-Abellaneda, S., and Manichanh, C. (2024). GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis. mSystems 9, e00950–e00923. doi: 10.1128/msystems.00950-23

Moskovicz, V., Ben-El, R., Horev, G., and Mizrahi, B. (2021). Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice. BMC Microbiol. 21:231. doi: 10.1186/s12866-021-02295-y

Munteanu, A.-C., Uivarosi, V., and Andries, A. (2015). Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria. Extremophiles 19, 707–719. doi: 10.1007/s00792-015-0759-9

Nayak, T., Sengupta, I., and Dhal, P. K. (2021). A new era of radiation resistance bacteria in bioremediation and production of bioactive compounds with therapeutic potential and other aspects: an in-perspective review. J. Environ. Radioact. 237:106696. doi: 10.1016/j.jenvrad.2021.106696

Paczosa, M. K., and Mecsas, J. (2016). Klebsiella pneumoniae : going on the offense with a strong defense. Microbiol. Mol. Biol. Rev. 80, 629–661. doi: 10.1128/mmbr.00078-15

Pinna, A., Usai, D., Sechi, L. A., Zanetti, S., Jesudasan, N. C. A., Thomas, P. A., et al. (2009). An Outbreak of Post-Cataract Surgery Endophthalmitis Caused by Pseudomonas aeruginosa. Ophthalmology , 116, 2321–2326.e4. doi: 10.1016/j.ophtha.2009.06.004

Podschun, R., and Ullmann, U. (1998). Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin. Microbiol. Rev. 11, 589–603. doi: 10.1128/CMR.11.4.589

Porcar, M., Louie, K. B., Kosina, S. M., Van Goethem, M. W., Bowen, B. P., Tanner, K., et al. (2018). Microbial ecology on solar panels in Berkeley, CA, United States. Front. Microbiol. 9:3043. doi: 10.3389/fmicb.2018.03043

Raghupathi, P. K., Zupančič, J., Brejnrod, A. D., Jacquiod, S., Houf, K., Burmølle, M., et al. (2018). Microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities. Appl. Environ. Microbiol. 84, e02755–e02717. doi: 10.1128/AEM.02755-17

Rodrigues, C., Hauser, K., Cahill, N., Ligowska-Marzęta, M., Centorotola, G., Cornacchia, A., et al. (2022). High prevalence of Klebsiella pneumoniae in European food products: a multicentric study comparing culture and molecular detection methods. Microbiol. Spectr. 10:e0237621. doi: 10.1128/spectrum.02376-21

Roy, S., and Roy, M. (2019). Characterization of plant growth promoting feature of a neutromesophilic, facultatively chemolithoautotrophic, Sulphur oxidizing bacterium Delftia sp. strain SR4 isolated from coal mine spoil. Int. J. Phytoremediation 21, 531–540. doi: 10.1080/15226514.2018.1537238

Ryan, M. P., and Pembroke, J. T. (2018). Brevundimonas spp: emerging global opportunistic pathogens. Virulence 9, 480–493. doi: 10.1080/21505594.2017.1419116

Satari, L., Guillén, A., Vidal-Verdú, À., and Porcar, M. (2020). The wasted chewing gum bacteriome. Sci. Rep. 10:16846. doi: 10.1038/s41598-020-73913-4

Sghaier, H., Ghedira, K., Benkahla, A., and Barkallah, I. (2008). Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria. BMC Genomics 9:297. doi: 10.1186/1471-2164-9-297

Shaker, R., Osaili, T., Al-Omary, W., Jaradat, Z., and Al-Zuby, M. (2007). Isolation of Enterobacter sakazakii and other Enterobacter sp. from food and food production environments. Food Control 18, 1241–1245. doi: 10.1016/j.foodcont.2006.07.020

Shaw, P., Kumar, N., Mumtaz, S., Lim, J. S., Jang, J. H., Kim, D., et al. (2021). Evaluation of non-thermal effect of microwave radiation and its mode of action in bacterial cell inactivation. Sci. Rep. 11:14003. doi: 10.1038/s41598-021-93274-w

Shen, Q., Ji, F., Wei, J., Fang, D., Zhang, Q., Jiang, L., et al. (2020). The influence mechanism of temperature on solid phase denitrification based on denitrification performance, carbon balance, and microbial analysis. Sci. Total Environ. 732:139333. doi: 10.1016/j.scitotenv.2020.139333

Shu, W.-S., and Huang, L.-N. (2022). Microbial diversity in extreme environments. Nat. Rev. Microbiol. 20, 219–235. doi: 10.1038/s41579-021-00648-y

Silby, M. W., Nicoll, J. S., and Levy, S. B. (2009). Requirement of polyphosphate by Pseudomonas fluorescens Pf0-1 for competitive fitness and heat tolerance in laboratory media and sterile soil. Appl. Environ. Microbiol. 75, 3872–3881. doi: 10.1128/AEM.00017-09

Singh, A., Pandey, A. K., and Dubey, S. K. (2023). Genome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2. J. Biomol. Struct. Dyn. 41, 3821–3834. doi: 10.1080/07391102.2022.2057360

Skowron, K., Bauza-Kaszewska, J., Kraszewska, Z., Wiktorczyk-Kapischke, N., Grudlewska-Buda, K., Kwiecińska-Piróg, J., et al. (2021). Human skin microbiome: impact of intrinsic and extrinsic factors on skin microbiota. Microorganisms 9:543. doi: 10.3390/microorganisms9030543

Speirs, J. P., Anderton, A., and Anderson, J. G. (1995). A study of the microbial content of the domestic kitchen. Int. J. Environ. Health Res. 5, 109–122. doi: 10.1080/09603129509356839

Tanner, K., Martí, J. M., Belliure, J., Fernández-Méndez, M., Molina-Menor, E., Peretó, J., et al. (2018). Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles. Environ. Microbiol. Rep. 10, 75–79. doi: 10.1111/1758-2229.12608

Tanner, K., Molina-Menor, E., Latorre-Pérez, A., Vidal-Verdú, À., Vilanova, C., Peretó, J., et al. (2020). Extremophilic microbial communities on photovoltaic panel surfaces: a two-year study. Microb. Biotechnol. 13, 1819–1830. doi: 10.1111/1751-7915.13620

Thomas, P. (2012). Long-term survival of Bacillus spores in alcohol and identification of 90% ethanol as relatively more spori/bactericidal. Curr. Microbiol. 64, 130–139. doi: 10.1007/s00284-011-0040-0

Uribe-Lorío, L., Brenes-Guillén, L., Hernández-Ascencio, W., Mora-Amador, R., González, G., Ramírez-Umaña, C. J., et al. (2019). The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. Microbiologyopen 8:e893. doi: 10.1002/mbo3.893

Vilanova, C., Iglesias, A., and Porcar, M. (2015). The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach. Sci. Rep. 5:17163. doi: 10.1038/srep17163

Woo, I. S., Rhee, I. K., and Park, H. D. (2000). Differential damage in bacterial cells by microwave radiation on the basis of cell wall structure. Appl. Environ. Microbiol. 66, 2243–2247. doi: 10.1128/AEM.66.5.2243-2247.2000

Keywords: microwave, 16S rRNA gene sequencing, taxonomic classification, radiation, desiccation, selective pressure

Citation: Iglesias A, Martínez L, Torrent D and Porcar M (2024) The microwave bacteriome: biodiversity of domestic and laboratory microwave ovens. Front. Microbiol . 15:1395751. doi: 10.3389/fmicb.2024.1395751

Received: 04 March 2024; Accepted: 19 June 2024; Published: 08 August 2024.

Reviewed by:

Copyright © 2024 Iglesias, Martínez, Torrent and Porcar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Manuel Porcar, [email protected]

† ORCID: Alba Iglesias, http://orcid.org/0000-0002-6582-9747 Daniel Torrent, http://orcid.org/0000-0002-3997-0974 Manuel Porcar, http://orcid.org/0000-0002-7916-9479

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Your Microwave Is Teeming With Bacteria, Study Suggests

Researchers found thriving communities of microbes in microwave ovens used in home kitchens, shared spaces and laboratories

Daily Correspondent

You’ve heard of the gut microbiome —the community of bacteria, viruses and fungi that help keep humans and other animals healthy. But what about the microwave microbiome?

New research finds that microwave ovens are hosts to their own distinct communities of microbes, whether in home kitchens or office spaces. Many of these microorganisms can survive the radiation that warms food, challenging the long-held belief that microwaves successfully kill bacteria that may be harmful to human health.

Researchers described their findings in a new paper published Wednesday in the journal Frontiers in Microbiology .

Home cooks shouldn’t panic, however—their microwaves likely aren’t any dirtier than any other parts of the kitchen. However, the findings should serve as a reminder that these appliances need to be cleaned regularly, too.

“A microwave is not a pure, pristine place,” says study co-author Manuel Porcar , a microbiologist at the University of Valencia in Spain, to Nature News ’ Alix Soliman.

Past studies have found microbiomes in other household appliances, including coffee makers and dishwashers . But researchers were curious to know whether the same communities exist inside microwave ovens , which use invisible electromagnetic waves to excite water molecules inside foods. As the molecules vibrate, they produce heat.

The team swabbed the insides of 30 microwaves in homes, scientific laboratories and shared kitchens, such as in office spaces and cafeterias. Then, they cultured their samples and waited to see which, if any, microorganisms flourished. They also sequenced the DNA in their samples.

In the end, they cultivated 101 strains from the samples, representing 747 different genera of bacteria. Many were strains that are often found on human skin, and a few were known to cause food-borne illnesses.

As suspected, each microwave’s location affected its microbiome. For instance, microwaves used in laboratories had the most diverse bacteria—including “ extremophiles ,” or microbes that can withstand harsh conditions.

“We hypothesize that microwaves actually select, from the pool of bacteria present in the air and surfaces, those able to resist radiation,” Porcar tells Newsweek ’s Pandora Dewan.

The discovery of extremophiles in microwaves is not all that surprising, given that they can live in “almost any extreme-exposure environment,” says Belinda Ferrari , a microbiologist at the University of New South Wales in Australia who was not involved in the research, to New Scientist ’s James Woodford. Extremophiles have been found in hydrothermal vents , inside Earth’s crust, on Antarctica , in the stratosphere and beyond.

“They can adapt to everything,” she adds.

Those hardy microorganisms dwelling in microwaves could have other possible uses, such as cleaning up toxic waste, per Nature News .

In the future, the team hopes to explore how extremophiles evolve within microwaves over time. Another possible experiment might involve sampling microwaves both before and after cleaning, Ferrari suggests to New Scientist .

But for now, microwave users might want to brush up on their cleaning skills.

“We recommend regularly disinfecting microwaves with a diluted bleach solution or a commercially available disinfectant spray,” says study co-author Daniel Torrent, a researcher at the biotechnology startup Darwin Bioprospecting Excellence SL, in a statement . “In addition, it is important to wipe down the interior surfaces with a damp cloth after each use to remove any residue and to clean up spills immediately to prevent the growth of bacteria.”

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Sarah Kuta | READ MORE

Sarah Kuta is a writer and editor based in Longmont, Colorado. She covers history, science, travel, food and beverage, sustainability, economics and other topics.

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