recent research in food microbiology

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Editorial: Insights in food microbiology: 2021

Laurent dufossé.

1 ESIROI agroalimentaire, Université de la Réunion, Saint-Denis, France

Dario De Medici

2 Microbiological Foodborne Hazard Unit, National Institute of Health (ISS), Rome, Italy

This Research Topic is part of the Insights in Frontiers in Microbiology series launched in 2021. As we are entering the third decade of the twenty-first century, and, especially in the last years, the achievements made by scientists in the field of Microbiology have been exceptional, leading to major advancements. Frontiers has organized a series of Research Topics to highlight the latest advancements in science in order to be at the forefront of science in different fields of research. This specific Editorial initiative was focused on new insights, novel developments, current challenges, latest discoveries, recent advances, and future perspectives in the field.

The Research Topic solicited brief, forward-looking contributions from the Editorial board members that describe the state of the art, outlining recent developments and major achieved accomplishments, future challenges and how to address those challenges to move the field forward. Reviews, Mini-Reviews, Perspectives, and Opinions summarizing the current state and future directions of the field were particularly welcome in this Research Topic. This Research Topic aimed to inspire, inform, and provide direction and guidance to researchers in the field.

We are pleased to note that our Research Topic has attracted contributions from many highly regarded researchers deeply involved for many years in Food Microbiology around the world, including from Austria, Brazil, Canada, China, Egypt, Finland, India, Italy, Poland, Portugal, and USA. We received 15 submissions, 13 of which were accepted (10 original research articles, two reviews, one mini-review) for publication after rigorous peer-reviews, with a total of 90 authors.

As usual with food microbiology, articles deal with good and beneficial aspects of microorganisms in food, when others list and investigate detrimental effects of unwanted microorganisms in food. Among the list of microorganisms under scrutiny, we can list the followings (non-exhaustive list): Salmonella, Shigella , Shiga toxins producing Escherichia coli (STEC), Yersinia enterocolitica, Listeria monocytogenes , and Staphylococcus aureus .

The fermentation of foodstuffs is one of the foundations for the past, current and future developments of humanity on the planet Earth. The literature review by Skowron et al. first lists all the advantages of fermented products (extension of the shelf life of food, inhibition of the growth of pathogenic microorganisms, improvement of the organoleptic properties, enhancement of product digestibility…). Fermentation of food can also be a source of risk if carried out under uncontrolled conditions (presence of unwanted, pathogenic microorganisms, enterotoxigenic or enterohemorrhagic bacteria). Even after millennia of practice, much remains to be done to ensure that all countries in the world provide healthy fermented products to their populations.

As a continuation of the previous work, Ghatani et al. investigated soft chhurpi, a traditionally Hymalayan Yak fermented milk, prepared by the indigenous community of Sikkim Himalayas. The two main strains found in this fermented product, Enterococcus durans and Enterococcus lactis present probiotic aspects, such as hypocholesterolemic activity and tolerance to bile salts and acid pH. It is essential for humanity to continue to isolate microbial strains with pro-health effect, from sea level to high mountain altitudes, from oceans to primary forests.

Even if current food research trends are pushing toward insect proteins, cellular meat or meat made up of 100% plant proteins, animal proteins are still widely consumed, and everyone is now aware of the intricacy between animal health and human health (see also the One-Health concept). Monte et al. conducted a large study on the biodiversity of multidrug-resistant Salmonella Heidelberg strains isolated from the poultry production chain across Brazil, one the largest poultry producer in the world. Authors emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen, combining molecular techniques such as WGS and CRISPR-based genotyping.

Pigs are another large source of animal proteins in the world. Large-scale animal production, often synonymous with many animals on a small surface area, induces pathologies treated with antibiotics. The use, abuse, and inappropriate use of antibiotics in livestock farms can lead to the antimicrobial resistance (AMR) in different microorganisms. Koskinen et al. defined the AMR of 1,016 pathogenic porcine Yersinia enterocolitica 4/O:3 strains originating from the United Kingdom, Belgium, Germany, Italy, Russia, Spain, Finland, Latvia, and Estonia. Among the conclusions of these authors, the health situation varies from country to country. More antibiotics for animal health are imported and used by the country and more the AMR increases. Parenteral medications should be preferred to orally administered mass medications, and the prudent use of antimicrobials is essential to control AMR at the farm level.

Microorganisms that are pathogenic to humans can be spread in animal husbandry but can also be present in the food processing chain. Sometimes food factories are huge and a contamination on a slicing line can cause thousands of food poisoning cases. Spampinato et al. surveyed the microbial load and the chemical–physical features of cooked hams, in modified atmosphere packaging (MAP), from five Italian producers which were monitored for a period of 12 days after the opening of the packages (i.e., the secondary shelf life). A whole set of techniques (sensorial properties, volatile metabolites, microbiota monitored by 16S ribosomal RNA gene profiling, and culture-dependent techniques…) allowed the authors to make some recommendations to the food industry. The current period tends to prohibit the use of nitrites in charcuterie and this type of study is therefore of major importance.

Raw milk, consumed as is, or used to prepare cheeses or other dairy products without any heat treatment, is also a microbiologically sensitive food. Oliveira et al. explored the prevalence and genetic diversity of Staphylococcus aureus and staphylococcal enterotoxins (SEs) in raw milk from the main dairy region of mainland Portugal. Recommendation is done to develop a broader SEs screening in food safety control as the majority of enterotoxigenic isolates were found to contain genes encoding SEs (SEG, SEH, and SEI) not routinely screened.

Another well-known bacterium, Listeria monocytogenes is difficult to control along the whole food production chain. Only long-term studies are indicated to understand how some strains are able to survive and spread as others “disappear.” Gattuso et al. reported the complete sequences of 132 clinical strains, sequences that were used to define the evolutionary relatedness among subtypes of L. monocytogenes isolated in Italy from 2010 to 2016. Authors stressed that phylogenic studies, based on Listeria monocytogenes whole-genome sequence data, using the core genome multilocus sequence type, are able to identify the emergence of highly persistent pathogenic variants, contributing to the improvement of the human hazard characterization of L. monocytogenes .

Listing microbial threats to animals and humans is an important task. Finding ways to better control or defeat them is also of crucial importance.

Bacteriophages are beginning to be used in some parts of the world to fight bacterial infections in humans, especially when no active antibiotics are available. Rogovski et al. propose to use the bacteriophages as bacterial control tools and environmental safety indicators in a food chain context. The ecology of the food chain is a process that is very sensitive to the environment, the microorganisms present and their succession over time. In the past, mistakes have been made, for example in trying to have zero microbial life in processes, thus creating a virgin field for contaminants. Many additional studies will be required in the coming years in order to fully appreciate the benefits of using bacteriophages in the food chain.

The elimination of (pathogenic) microorganisms by disinfectants in food processing plants is desirable and mandatory. However, it is confronted with the appearance of increasing resistance. Gundolf et al. used ionic liquids (ILs), considered as a new class of promising antimicrobials, which have been reported to be effective against resistant strains as they interact with bacterial cells in multiple ways. Structure–activity relationships, side-chain effects, cationic head groups, impact on multidrug efflux pumps were among the characteristics under study.

Food microbiology is also a question of (i) detection of microbial pathogens in a large variety of foods and (ii) development of accurate predictive models for growth, survival, or death of these microbial pathogens, in a large variety of foods, too. The detection of foodborne pathogens is increasingly based on molecular techniques but older techniques, well-established techniques are still relevant and interesting. As an example, McMahon et al. demonstrated that microbial antagonism may occur in food-enrichment culture, resulting in inhibition of Shiga toxin-producing Escherichia coli (STEC) and Shigella species. The impressive production of antimicrobial compounds in cell-free extracts from 200 bacterial strains and 332 food-enrichment broths was assessed in this paper. Considering all the results presented, the recovery of some foodborne pathogens, such as Shigella sonnei is an important challenge for food microbiologists and technicians.

Predicting the number of food microorganisms through modeling is a fast-growing research area. Models presented are numerous and adequation with some foods were demonstrated. Li et al. developed a Dimensional Analysis Model (DAM) they applied for Pseudomonas in Niuganba, a traditional Chinese fermented dry-cured beef. The study showed that the DAM model was a simple, unified and effective model to predict the number of microorganisms and storage time.

At the end of the presentation of the Research Topic content, we are back to fermentation of food, to the use of fermentation in order to produce useful food and feed ingredients. For thousands of years, humans have fermented various agricultural products to produce alcohol. This is spread all around the planet.

In their experiments, about a strong aromatic liquor, also known as strong aromatic Baijiu in China, Tong et al. described the diversity, functionality, and influence of Bacillaceae in the process of this beverage. Multi-microbe mixing and cooperative fermentation process are the key points.

Also initiated in Asia, a few thousand years ago, Monascus pigments are spreading in all the world, year after year, and the use of such pigments in food will soon increase with the development of mycotoxin-free, i.e., citrinin-free filamentous fungi strains. Abdel-Raheam et al. , instead of using steamed-rice, as usually done, chose to produce pigments on a food waste, generated during potato chips manufacturing. The fungal pigments biosynthesized were then incorporated as coloring agents for ice lollies, with high acceptability from consumers.

This Editorial summarizes the articles published in this Research Topic. We hope that this Research Topic of articles will contribute to the advancement of research in Food Microbiology. Feeding the world's inhabitants without depleting the resources of the planet is a major goal for humanity.

Finally, we want to thank all the authors who contributed their original work to our Research Topic and the reviewers for their valuable comments. We would like to express our sincere gratitude to the Editorial office of Frontiers in Microbiology for their excellent support and for providing us with this opportunity to successfully conduct this Research Topic.

Author contributions

LD drafted the manuscript. LD and DD revised the draft. All authors made a direct and intellectual contribution to the work and approved the final version for publication.

Conflict of interest

The 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.

Acknowledgments

LD deeply thanks the Conseil Régional de La Réunion and the Conseil Régional de Bretagne for continuous support of research activities dedicated to food microbiology and food biotechnology. We would like to thank the authors and reviewers for their valuable contributions and constructive criticisms to this Research Topic. Deep thanks to the whole Frontiers team, efficient as usual.

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• Published: 28 January 2021

Microbiome innovations for a sustainable future

• Kathleen D’Hondt 1   na1 ,
• Tanja Kostic 2   na1 ,
• Richard McDowell 3 , 4 ,
• Francois Eudes 5 ,
• Brajesh K. Singh   ORCID: orcid.org/0000-0003-4413-4185 6 , 7 ,
• Sara Sarkar 8 ,
• Marios Markakis 9 ,
• Bettina Schelkle 10 ,
• Emmanuelle Maguin   ORCID: orcid.org/0000-0001-5452-3382 11 &
• Angela Sessitsch   ORCID: orcid.org/0000-0003-0137-930X 2  

Nature Microbiology volume  6 ,  pages 138–142 ( 2021 ) Cite this article

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The United Nations Sustainable Development Goals (SDGs) are being integrated into bioeconomy strategies around the world, including the European Green Deal. We highlight how microbiome-based innovations can contribute to policies that interface with the SDGs and argue that international cooperation in microbiome science is crucial for success.

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Acknowledgements

K.D., T.K., B.K.S., E.M., B.S. and A.S. have received funding from the European Union’s H2020 Research and Innovation Programme under grant no. 818116 (MicrobiomeSupport).

Author information

These authors contributed equally: Kathleen D’Hondt, Tanja Kostic.

Authors and Affiliations

Department of Economy, Science and Innovation – Flemish Government, Brussels, Belgium

Kathleen D’Hondt

Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria

Tanja Kostic & Angela Sessitsch

AgResearch, Lincoln Science Centre, Christchurch, New Zealand

Richard McDowell

Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand

Lethbridge Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada

Francois Eudes

Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia

Brajesh K. Singh

Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia

International Engagement Division, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada

Sara Sarkar

Bioeconomy & Food Systems Unit, Healthy Planet Directorate, Directorate-General for Research and Innovation, European Commission, Brussels, Belgium

Marios Markakis

European Food Information Council, Brussels, Belgium

Bettina Schelkle

UMR1319 MICALIS, Université Paris Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France

Emmanuelle Maguin

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A.S., K.D. and T.K. drafted the manuscript. All authors contributed to the revisions and final draft of the manuscript.

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D’Hondt, K., Kostic, T., McDowell, R. et al. Microbiome innovations for a sustainable future. Nat Microbiol 6 , 138–142 (2021). https://doi.org/10.1038/s41564-020-00857-w

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EMCC STEM Students Pursue Pollinator Projects

Undergrads Study Wildflower Growth; Conduct Native Bee Survey

Estrella Mountain Community College (EMCC) STEM students are busy, busy bees having engaged in Undergraduate Research Experiences, or UREs this semester. Some of our Mountain Lions just wrapped up a study of wildflower growth across different soil types while others are conducting a native bee survey — two things that can’t live without the other.

The wildflower study started last fall when  Quail Forever , a wildlife habitat conservation group, donated a rather large sum of wildflower seeds to EMCC Biology Professor Dr. Catherine Parmiter to use in her classes. They couldn’t have come at a better time as her colleague, Professor Thasanee Morrissey, who also teaches biology and is the Program Analyst for the STEM Center, just happened to be looking for a research opportunity for her students.

They decided to create a URE for five of their students and the Pollinator-Wildflower Research Initiative was born. The goal of the initiative was to determine which type of soil wildflowers would grow best in, with the understanding that more healthy wildflowers attract pollinators such as bees.

First, with the help of their Life Sciences Division colleagues Drs. Neil Raymond, Rachel Smith, and Jarod Raithel, along with the Facilities Department, an area was cleared next to the EMCC Community Teaching Garden where they constructed 16 research plots with four different soil types — native soil, pea gravel, compost, and sand. Next, they asked the MakerSpace to create some appealing signage to mark off the area. Then they planted nine different varieties of wildflower seeds and turned on the irrigation. After that, they monitored the plots weekly and kept track of the plants’ growth with written observations and digitized images.

Natalia Quinones, one of Dr. Parmiter’s students who is graduating this spring with an Associate in Biological Sciences and then transferring to  Arizona State University (ASU) to study microbiology, said one of the reasons she signed up for the URE was to boost her resume.

“I hope that this experience will allow me to join other research projects when I transfer to ASU,” she said.

Dr. Parmiter said the selection process for research opportunities at the university level is very competitive.

“Gaining research experience at the pre-Associate Degree level is essential for students such as Natalia as she navigates her transfer to ASU and later to medical school,” Dr. Parmiter said. 

For this URE, Natalia and her lab partner were responsible for identifying the types of flowers in each substrate of soil and measuring the nitrogen, phosphorus, potassium, and pH content in each plot. 

“I learned more about plant growth and development,” Natalia said. “I gained more knowledge and new vocabulary about the subject. And I learned how to edit and rewrite procedures.”

Dr. Parmiter said Natalia’s field observations and attention to detail were an asset to the team.

“She is an excellent student researcher,” Dr. Parmiter said.

Natalia also works as a part-time lab technician in EMCC’s Life Science Lab, another gold star on her resume.

“I started as a student worker in September 2022 and the lab technicians were always patient and allowed me to make mistakes and learn from them,” she said. “And since they knew I wanted to pursue an education in microbiology, they educated and taught me skills that would apply to my field of study.”

Students who participated in the Pollinator-Wildflower Research Initiative will earn  Western Alliance to Expand Student Opportunities (WAESO) scholarships after they submit their research summaries.

“This scholarship is encouragement for all of the hard work that has gone into this project,” Natalia said. “It also shows that the school supports undergraduate students to work outside the classroom and gain hands-on experiences.”

Cierra Herrera, one of Professor Morrisey’s students who participated in the Pollinator-Wildflower Research Initiative, is also big on hands-on experiences. 

“I learn best when I am doing, and I learned a lot,” Cierra said. “I love to learn and put that knowledge into practice and that is exactly what UREs do.”

Cierra, who is also one of EMCC’s  Animal Ambassadors , will graduate this spring and then transfer to the  University of Hawaiʻi at Mānoa . She plans to double major in Animal Science and either Plant and Environmental Protection Services or Marine Biology.

“I’ve always been caring and conserving before I even knew what that meant,” she said. As unusual as it might sound for a 10-year-old, I hated wasting paper, always recycled, loathed littering, and it always hurt me to see animals suffering, especially because of us, and when we can do something about it. As I continued to go to school and learned more about biology, endangered species, and why they are being endangered, there was no doubt in my mind that I wanted to help these animals.”

Naturally, when Cierra heard about the native bee survey URE, she signed up for that one, too. A perfect complement to the Pollinator-Wildflower Research Initiative, the EMCC Native Bee Project officially kicked off in March. It’s part of a collaborative effort with community colleges in Arizona and California conducting surveys to find out how many different types of bees exist across the two states, something that is currently unknown.

“One out of every three bites of your food you owe to bees,” Dr. Raithel said. “We don’t even have a baseline to know how many bees we have. They are crucial to our survival, yet we know so little about them.”

The EMCC Native Bee Project began over spring break with Drs. Parmiter, Raithel, and Smith spending four days at the  College of the Canyons in Santa Clarita, Calif., learning how to identify, or “key,” native bees so that they could pass that knowledge on to their URE students. Since then, they have begun teaching their students how to catch, clean, dry, pin, key, and photograph native bees caught on and around campus. It’s a lengthy and sometimes nerve-racking process, but for Cierra, the keys are the bee’s knees.

“Looking at the bee under the microscope is my favorite part,” she said. “They are majestic creatures and so beautiful. It is crazy to see the variation of bees in our lab! They are all so unique.”

The  National Science Foundation -funded native bee URE will last three years with six students participating each semester. The data collected will be verified and entered into  Symbiota , a public database, and each bee will have an identification number that corresponds to the student who keyed it.

“It is mind-blowing just thinking about the fact that a native bee that I, myself, keyed will go into a national database with my name!” Cierra said. “That’s absolutely surreal to me, but it is really happening. It makes me a little emotional just thinking about it because I see it as a big deal and I’m only 20 years old and this is happening along with my fellow peers. I can only think about my future and what it has in store for me.”

Cierra’s professors describe her as a problem solver who never hesitates to roll up her sleeves and dive into the action.

“She was like our wildflower research group’s secret weapon — always diving fearlessly into problems and asking all the right questions,” Professor Morrisey said. “With her sharp critical thinking skills, she was like the Sherlock Holmes of our research team! But what’s even better is her team spirit — she’s the ultimate collaborator, bringing fresh ideas to the table.”

Professor Morrisey’s students wrapped up their wildflower growth URE and presented their findings at the  Arizona-Nevada Academy of Science Annual Meeting on April 13 at Glendale Community College. 

“They did great and had a great experience at their first science conference,” Professor Morrisey said.

Cierra said she was nervous but ultimately enjoyed herself.

“It was really good!” she said. “One of the judges said our poster was eye-catching and easy to follow. He was really happy with our experiment in the design aspect — how we eliminated a lot of bias, controlled all of our variables well, and the quadrat sampling. It was really rewarding to hear that feedback.”

Are you an Estrella Mountain Community College student who would like to join the EMCC Native Bee Project or any other STEM Undergraduate Research Experience? Email Dr. Catherine Parmiter at  [email protected] .