Alejandra Mejia-Caballero's presentation on the diversity and function of Lactobacillus amylovorus in the pig intestine was selected for an award at the UC Davis Host Microbe Interaction Annual Retreat at held at Granlibakken, Lake Tahoe, October 2025. Congratulations Alejandra!

We were honored for excellent performance maintaining a culture of laboratory safety. This award was the result of hard work by current and former lab members. It was wonderful to be acknowledged in this way. For more information, see here. 

It remains a challenge in microbiology fully enumerage living (viable) microbes. This has implications for probiotics and other biotics research. You can find the blog post here. 

Diet is a major determinant of the gastrointestinal microbiome composition and function, yet our understanding of how it impacts the efficacy of prebiotics and probiotics is limited. In an ISAPP led paper published in Nature Microbiology, we examined current evidence of dietary influence on prebiotic and probiotic efficacy in human studies, including potential mechanisms. The paper outlines reasons to include diet as a variable and provide recommentations on the design, conduct and reporting of human clinical trials of prebiotics and probiotics (and other biotic interventions) to account for any effect of diet and nutrition.  See this blog for more information.

Check out the discussion and resources provided on this recent UC Davis podcast. We talk about the state of the science on probiotics and why the diverse microbes in fermented foods should not be called probiotics. It was fun to taste some different fermented foods and biotic products available in the supermarket today,

Congratulations to Lei on completion of her dissertation research and PhD degree in Microbiology. Her dissertation, "Bioactivity of secreted compounds made by fermented vegetable-associated lactobacill" includes a detailed review on the bioactive compounds in lacto-fermented fruits and vegetables and several chapters dedicated to understanding the impacts of fermented food metabolites broadly and bacteriocins specifically in the digestive tract. We are thrilled that Lei will be continuing her work in the Marco lab as a Postdoc starting November 2024.

The first ever Gordon Research Conference on lactic acid bacteria was held in Ventura, CA from July 23 to 28, 2023. The conference was a fun week of interactive sessions and lots of time for networking and making new friends pursuing research on this fascinating group of bacteria. We had over 120 participants from nearly all corners of the world. The meeting included excellent speakers and impressive posters on a wide-range of topics including lactic acid bacteria metabolism, cell surface composition, and phages, to fermented foods and uses of these bacteria in medicine and engineering.

Be on the lookout for the next meeting expected in 2025!  https://www.grc.org/lactic-acid-bacteria-biology-symbioses-and-applications-conference/2023/

Our collaborative ISAPP group found that foods with higher microbial concentrations are associated with modest health improvements across a range of outcomes. This paper used NHANES participants’ reported food intake to quantify the food they ate that contained medium or high levels of microbes. Then they determined how these intakes correlated with various markers of health such as blood pressure and weight. We found that increased consumption of live microbes in the diet was linked with multiple measurements of better health: more favorable blood pressure, better blood glucose and insulin, lower inflammation, as well as lower waist circumference and body mass index. This established that those who consumed higher quantities of live dietary microbes showed tangible, if modest, health benefits.

https://doi.org/10.1016/j.tjnut.2023.02.019

This published in Applied Environmental Microbiology shows how intraspecies interactions in food fermentations are dependent on metal cation availabilty. We are excited to share these findings because they provide new insight on the ecological interactions and nutritional requirements of microbes in food fermentations which can be used to improve the quality and consistency of those foods.

Glory Bui (PhD student MGG) received the honor of a coveted poster award at the annual International Scientific Association of Probiotics and Prebiotics (ISAPP) meeting in Sitges, Spain. The award was given to two students by the Student Fellows Association (SFA). Congratulations to Glory on her excellent research and presentation on diffusible factors made by L. casei in milk which improve intestinal epithelial barrier function.

We are excited to share the news that we are launching a new project to reduce antibiotic use and risk of antimicrobial resistance in pig production. This $21.2 million, 5-year PIG-PARADIGM project is funded by the Novo Nordisk Foundation. Our lab is teaming up with other researchers at UC Davis and at universities in Denmark and the Netherlands. We will be studying how to prevent the need for antibiotics during pig weaning by improving digestive tract resilience through the gut microbiome. More information about our plans can be found here and here.

We are excited to share the news that Ruchita Uttarwar completed her MS research and graduated this June. Her thesis is titled "Effect of amoxicillin clavulanate on the intestinal microbiota and metabolomes of mice administered yogurt and Bifidobacterium animalis subsp. lactis BB-12". We are thrilled for her upcoming manuscript and bright future ahead.

Congratulations to Dr. Eric Stevens on the completion of his dissertation research. Eric's studies have shed new light on extracellular electron transfer metabolism performed by lactic acid bacteria in food fermentations.

Eric Stevens' dissertation research has led to exciting new findings on the metabolism of lactic acid bacteria. Through his research and together with our collaborators at Rice University, we discovered how L. plantarum uses extracellular electron transfer to improve growth and acidify its environment. Read more about our findings here at eLife and the UC Davis press release.

Congratulations to Zach Bendiks on his Journal of Functional Foods paper investigating how the gut microbiome changes in response to different dietary fibers. Resistant starch is highly selective and increases expression of stress-response genes corresponding with reductions in intestinal pH.

Our perspective article on Inuit fermented foods is published in the new journal Microbiome Research Reports. This article provides guidance on how to approach microbiological research questions on Inuit fermented foods so that it centers Inuit knowledge within the specific geographic, social, and cultural contexts in which these foods are made. 

We are excited to be embarking on a new project funded by the California Dairy Research Foundation and the National Dairy Council to compare yogurt and plant-based yogurt products for their digestibilty and delivery of probiotic bacteria to the digestive tract. This project is being conducted together with Professor Gail Bornhorst (FST and BAE, UC Davis). We hope to begin to understand the similarities and differences in how the nutrients and microbes in these foods are made bio-available during digestion in the stomach and small intestine.

Our paper on the development of a molecular diagnostic multiplex qPCR assay for detection of Mycoplasma species in milk as important causes of contagious mastitis in dairy cattle is now published in PeerJ. This article was made possible by a grant from the California Dairy Research Foundation and our amazing collaborators Drs. Aly and Lehenbauer in the UC Davis School of Veterinary Medicine.

Congratulations to Zach Bendiks for receiving the UC Davis 2021 Kinsella Memorial Prize. This award, established in honor of late Dean and Professor John E. Kinsella, is awarded to the best dissertation based on the quality and originality of the work, the multidisciplinary impact of the research, and the importance of the research to the College of Agricultural and Environmental Sciences (CA&ES) mission to serve agriculture, the environment, and human health and development.

We are excited about our new publication on the diversity of Lactiplantibacillus plantarum isolated from plants and plant foods. This paper gives insight into the ecological strategies of L. plantarum and how it as adapted to different plant types and fermented foods and was made possible by funding from the USDA National Institute of Food and Agriculture. http://dx.doi.org/10.1111/1751-7915.13871

Check out our new publication on the microbiota in Cheddar cheese and research which led us to identify the microorganisms responsible for slit defects. This work was made possible by the California Dairy Research Foundation. 10.1128/mSystems.01114-20

The ISAPP consensus paper on fermented foods is now published. The paper provides a new definition of fermented foods and beverages and provides guidance on the difference between probiotics and fermented foods. For more information - see Maria's blog and this summary.

Maria's "Crystal Ball" article was published in Microbial Biotechnology. The article proposes that research defining the precise ways microorganisms benefit human health will be expanding rapidly in the near future. For more reading about this article, see here.

For more information on our EATLAC community science project, see our website here: https://www.eatlac.org/

Congratulations to Dr. Annabelle Yu for completing her dissertation research on the intra-species diversity of plant-associated lactic acid bacteria!

Our comprehensive review on how the gut microbiome changes in response to resistant starch type 2 was published in Nutrition Research. Congrats to Zach on leading the way on this paper!

We published a review on probiotic prevention of antibiotic associated diarrhea (AAD). The crux is that we still know very little about AAD and the molecular mechanisms responsible for probiotic effects.

Congratulations to Zach for winning a poster prize at the 2019 Stanford Microbiome Symposium!

Our paper showing that Lactobacillus plantarum rapidly repairs epithelial barriers in the virally inflammed gut by a PPARalpha derived mechanism was published in the Proceedings of the National Academy of Sciences.
 

Congrats to Annabelle on her review on the abundance, diversity, and plant-specific adaptations of plant-associated lactic acid bacteria published in Environmental Microbiology Reports.

We were awarded a new two-year grant to develop educational resources and research on fresh fermented fruits and vegetables from the California Department of Food & Agriculture.

Maria joined the Kerry Health & Nutrition Institute's Scientific Advisory Council.

Our paper showing how the bacterial composition in milk changes dramatically over the course of a day at each processing step was published in Applied Environmental Microbiology.

Our paper on the identification of the bacterial receptor for the bacteriocin Plantaricin EF was published. This paper shows how the bacteriocin targets metal homeostasis in bacterial cells.

Maria joined the International Scientific Association for Probiotics and Prebiotics (ISAPP) Board of Directors.

We published a paper describing rapid assays to detect Mycoplasma bovis, an important bovine mastitis causing pathogen, in the Journal of Dairy Science. This work was brought about by our collaboration with Drs. Sharif Aly and Terry Lehenbauer in the UCD School of. Veterinary Medicine and with support from the California Dairy Resarch Foundation. 

Our studies on how milk and milk fermented by Lactobacillus casei  can prevent impairments to intestinal epithelial barrier integrity in Caco-2 cells was published this month in the Journal of Agricultural and Food Chemistry.

Our paper showing that L. plantarum iconsumption results in reduced weight gain and the barrier-protective properties of of the L.plantarum bacteriocin plantaricin EF was published in Gut Microbes. 

Congratulations to Zeya on being awarded second place in the oral competition at Jiangnan University's Global Food Science Student Competition. She was one of 70 students competing from 60 Universities, representing 36 countries.

Our paper "Microbiota, metabolome, and immune alterations in obese mice fed a high-fat diet containing type 2 resistant starch", published in Molecular Nutrition & Food Research, was one of the journal’s top 20 most downloaded recent papers in the past year

Our paper on how DNA sequencing and bioinformatics methods impact bacterial community analysis was published in mSphere.

Maria joined The Fermentation Association Advisory Board

Ellie's paper on the role of sucrose metabolism for Lactobacillus plantarum in the digestive tract was published in FEMS Microbiology Ecology

Congratulations to Eric Stevens on being selected for a National Science Foundation Graduate Research Fellowship award

Congratulations to Ellie Yin on being selected for the John E. Kinsella Memorial Prize for outstanding research on her doctoral dissertation

Zach Quart and Hiu Mak presented their research at the UC Davis Undergraduate Research Conference. Well-done to two of our excellent undergraduate students!

Congratulations to Annabelle Yu on being selected to travel to Uganda this summer as part of a Trellis Fund Project from the Feed the Future Innovation Lab for Horticulture. 

Maria was the guest editor on this year's Current Opinion in Biotechnology, Food Biotechnology issue

Ellie's paper on the importance of Lactobacillus plantarum plantaricin synthesis in the GI tract was published

Our review on intestinal Lactobacillus and its association with health and disease was published in Current Opinion of Biotechnology. (https://doi.org/10.1016/j.copbio.2017.08.004)

Congratulations to Eric Stevens on his Science Communications Fellowship from the Sacramento Powerhouse Science Center!

Ellie Yin's research on how dietary and intestinal Lactobacillus respond to dietary changes is now published in Scientific Reports: http://rdcu.be/uK9j

Ben's paper describing a novel NRPS/PKS system in Lactococcus lactis is published in Microbiology Open  (https://www.ncbi.nlm.nih.gov/pubmed/28921941​)

Congrats to our ADA project team, and specifically to Javad, for our new comprehensive paper on dietary resistant starch and effects of RS type 2 on the gut and systemic health during consumption of a high fat diet. Journal of Molecular Food & Nutrition Research. (http://onlinelibrary.wiley.com/doi/10.1002/mnfr.201700184/)

Our lab's work on milk and dairy products was featured on the UC Davis One Health Blog

Both Elissa Goldman and Patricia Matus are recipients of the UC Davis Provost's Undergraduate Fellowships.

Ellie's paper on Lactobacillus delbrueckii ssp. bulgaricus milk- and low-temperature-associated proteomes was published in mSystems. This paper is a result of our collaboration with Drs. Velitchka Gotcheva and Angel Angelov at the University of Food Technologies, Bulgaria. (http://msystems.asm.org/content/2/5/e00027-17)

Check out our new review article on the health benefits of fermented foods: https://authors.elsevier.com/a/1UEQe_LoKFta2w

Casper Jamin, an MS student from Wageningen University, joined our lab for a six-month internship.

Koen Askamp,  an MS student from Wageningen University, joined our lab for a six-month internship.

Ya-Yun (Jenny) Wang, a PhD student from the National Chung Hsing University, joined the lab for a year long internship.

New publication in Frontiers in Microbiology on comparisons of fecal processing methods for metagenomics analyses: http://journal.frontiersin.org/article/10.3389/fmicb.2016.01643/full

New publication on the bacterial composition in raw milk in tanker trucks and silos at CA dairy processors. This article has a press release and has been covered by a number of news media sources: https://www.ucdavis.edu/news/milk-truck-microbial-study-aims-improve-dairy-food-safety-and-quality

ASM Microbe Magazine feature article on Fermented Foods: http://www.asmscience.org/content/journal/microbe/11/8

Congratulations to Dustin for his poster award at the ISAPP meeting in Turku, Finland!

Nathan Lee and Kane Tian join our lab for the UCD Young Scholar's Program (YSP). Nate and Lee are impressive high school students here to take classes and perform research for 6 weeks this summer. 

The lab welcomes Dr. Kanika Chauhan, a new postdoctoral scholar, to the lab. She will be studying pathogens that cause bovine mastitis.

Welcome to Natalia Ribeiro, an undergraduate student from the University of Campinas, Brazil. She will be performing a summer internship in our lab through a Science Without Borders Scholarship program.

New publication in Scientific Reports on the transcriptome of Lactobacillus plantarum and the indigenous bacteria in the small intestine. Congrats to Ben for his lead authorship on this paper- http://www.nature.com/articles/srep24723
For more information, see the press release on the paper: http://blogs.ucdavis.edu/egghead/

Ben Golomb was awarded the Max Kleiber Thesis Research Prize. Congratulations to Ben on this impressive honor.

Zeya wins the IFT Feeding Tomorrow Graduate Scholarship. Way to go Zeya! 

Congratulations to Zeya for her admittance into the Food Science Graduate Group PhD program.

Dustin was awarded a prestigious NSF Research Fellowship award. Way to go, Dustin!

Congratulations to Ben Golomb for completing his PhD on the adaptations of Lactococcus lactis and Lactobacillus plantarum to their hosts. We wish you much success at your new job!
 

Check out Dorothy Kieffer's new paper on resistant starch amelioration of chronic kidney disease and effects on the gut microbiota and metabolome just published in The AMJ Renal Physiology (http://www.ncbi.nlm.nih.gov/pubmed/26841824). UPDATE (April 2016) This paper was selected by the American Physiological Society to be recognized as among the best recently published articles in physiological research!

New paper in Frontiers in Microbiology (http://journal.frontiersin.org) on the limitations of using PMA and RNA to quantify viable bacterial cells on plants. This paper was featured on the Barfblog (http://barfblog.com/)

New paper in Journal of Applied Microbiology (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-2672/accepted)  This paper details our investigations on the metabolic capacities of Lactobacillus florum and specifically the production of erythritol and mannitol. Congrats to Charlotte on her dedication to this project!

Dr. Zhengyuan Zhai has joined our group. Dr. Zhai joins us from the China Agricultural University and has a fellowship from the China Postdoctoral Science Foundation (CPSF).

Two new publications from our lab on probiotic - dairy connections for health benefits:
http://blogs.ucdavis.edu/egghead/2015/07/13/dairy-products-boost-effectiveness-of-probiotics-new-studies-show/
http://www.davisenterprise.com/local-news/ucd/ucd-study-dairy-products-boost-effectiveness-of-probiotics/

Pujita Munnagni, a very talented high school student, joins our lab through the UC Davis Young Scholar's Program (http://ysp.ucdavis.edu/). Welcome Pujita!

The USDA announced our new NIFA AFRI grant in the Food Quality program:
http://nifa.usda.gov/resource/usda-awards-nearly-19-million-grants-enhance-food-safety-research 
With this grant, we will investigate plant-associated lactic acid bacteria for novel functional traits relevant to food processing and human health. We will employ genetic and functional screening methods to better understand these bacteria in plant-based foods.

Irene Yim, a McNair Scholar, joins the lab to perform her undergraduate research. Welcome Irene!

Bokyung Lee completed her PhD in Food Science. Her studies have shown the significant impact that the food delivery matrix has on probiotic efficacy in the digestive tract. Congratulations Bokyung!

Wentin Ju (postdoc) accepted a position at Mérieux NutriSciences. He will be working on food safety programs closer to home in China. Congratulations Wenting!

Ben Golomb's paper was published in the Journal of Bacteriology on the transcriptome and metabolome of Lactococcus lactis KF147 during growth on plant tissues.

Commentary published in the ASM monthly magazine Microbe on the contributions of Herbert Conn to microbiology. This paper was the result of an ASM Milestones in Microbiology at the University of Connecticut event to honor this pioneer in dairy microbiology in the USA.

Galya Blagoeva returns to the lab as a USDA FAS Borlaug Fellow. Galya's 3 month project is to investigate the unique properties of starch-degrading lactic acid bacteria. Her work here is an extension of her PhD thesis project at the UFT, Bulgaria.


Paper published in mBio showing how it is possible to transplant microbial communities from one plant to another. This technique is useful for dissecting microbial community interactions in the phyllosphere.

Charlotte Tyler completed her MS degree. Charlotte studied the metabolism of plant-associated lactic acid bacteria and the function of yeasts and bacteria in olive fermentations. We will miss you Charlotte!

The lab welcomes Galya Blagoeva from the University of Food Technologies, Bulgaria for a PhD fellowship visit

Paper published in the Annuals of the New York Academy of Science on factors influencing probiotic efficacy and guidelines for evaluating probiotic safety and efficacy.

Xiaochen Yin's paper on the effects of dairy and probiotic consumption on the indigenous intestinal microbiota was published in the Journal of Dairy Science. Consistent but non-overlapping effects were found with the ingestion of Lactobacillus casei and milk.

Lauren Kopit and Eun Bae Kim's examination of the safety of Enterococcus faecium NRRL B-2354 was published in Applied Environmental Microbiology. Using a combined genomics and phenotyping approach, we confirmed the suitability of this strain for use as a surrogate organism in place of Salmonella in tests of thermal processing procedures for food products.

Eun Bae Kim's paper on Enterococcus faecium and Enterococcus faecalis comparative genomics was published in Applied Environmental Microbiology. This paper shows that community (non-clinical) strains of E. faecium but not E. faecalis have different genomic features from clinical (hospital-associated) strains.

Congratulations to Tom Williams for winning first place in the Robert Mondavi Institute graduate poster prize. His poster was selected out of 14 entries. Well done Tom!

Congratulations to Eun Bae on his new job as a faculty member at the Department of Animal Products and Food Science, College of Animal Life Sciences, Kangwon National University, Republic of Korea

Sybille Tachon's paper was published in Environmental Microbiology. This paper provides compelling evidence that probiotics can be more or less effective depending on the diet consumed by the host. Probiotic Lactobacillus survived in higher numbers in the digestive tract and was more protective against intestinal inflammation in mice consuming a high-fat, high-sugar diet.

New publication on the detection of viable E. coli O157:H7 on field and growth chamber lettuce:
Assessments of total and viable Escherichia coli O157:H7 on field and laboratory grown lettuce
Moyne, Harris, and Marco in PLoSOne. e70643
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0070643

Congratulations to Yelizaveta (Liza) Luchkovska on her award of the Provost's Undergraduate Fellowship! She will use the funds she received in this award to support her investigations on the microbial diversity of olive fermentations.

Congratulations to Lauren! Lauren Kopit won 3rd place in developing scientist competition at the International Association of Food Protection meeting held in Charlotte, North Carolina, July 29-Aug 1. She presented her work on the surrogate strain Enterococcus faecium NRRL B-2354.
She also recently received her MS in Viticulture and Enology and is the first to graduate from the lab. We will miss you Lauren

New publication on the microbiota in the lettuce phyllosphere:
Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere. by Williams, Moyne, Harris, and Marco in PLoSOne. e68642 http://www.ncbi.nlm.nih.gov/pubmed/?term=phyllosphere+marco+and+williams

Our lab was featured in the journal International Innovation  (see publications page)

Congratulations to Xiaochen (Ellie) Yin on her publication in The Journal of Immunology (http://www.ncbi.nlm.nih.gov/pubmed/23585682). The
study, led by the group of Richard A Flavell (Yale University) shows the role of  IL-22 in shaping the intestinal microbiota and the transmissible susceptibility to inflammatory colitis due to altered microbiota in IL-22-deficient mice. Ellie performed the gut microbiota analyses in this study. The paper was also highlighted by the journal (http://www.jimmunol.org/content/190/10/4913).
 

Kick-off on our new project "Bacterial signatures of milk quality" sponsored by the California Dairy Research Foundation. See here for the interview and press release: http://cdrf.org/2013/05/15/meet-maria-marco-a-microbiologist-determined-to-apply-advanced-microbial-genomics-research-to-dairy-product-innovations/
 

Congratulations to Tom Williams! He won both the Chancellor's Grand prize and the Dean's prize in the College of Agriculture and Environmental Science for his oral presentation at the UC Davis Interdisciplinary Graduate Symposium (http://gradstudies.ucdavis.edu/about/igps.html).
Way to go Tom!

Eun Bae Kim is the first author on a paper describing the first genome sequence of Lactobacillus florum

Check out our new publication on fermented olives and pectinolytic yeast from olives associated with spoilage in Food Microbiology. http://attach.sciencedirect.com/science/article/pii/S0740002012001967
 

Lauren Kopit won 2nd place in the annual RMI graduate student poster competition for her poster entitled "Evaluation of the safety of Enterococcus faecium NRRL B-2354 used in thermal process validation". Lauren is a 2nd year MS student in V&E. Her project is funded by the Almond Board of California. Congratulations Lauren!

The genome announcement for Enterococcus faecalis ATCC29212 was just published in the Journal of Bacteriology. http://jb.asm.org/content/194/21/6006.full.pdf+html

Review article by Sybille Tachon and Maria entitled "Environmental factors influencing the efficacy of probiotic bacteria" was published in the Current Opinion in Biotechnology. http://www.sciencedirect.com/science/journal/aip/09581669

Visit from Roland Siezen and Lex Overmars from Nijmegen University to develop our collaboration on enterococcal genomes

The Marco lab has a new collaboration to investigate Lactobacillus bulgaricus together with faculty at the University of Food Technologies, Plovdiv, Bulgaria through the America Bulgaria Foundation http://www.americaforbulgaria.org
 

Probiotics for cleaning countertops?  See article published in the Bay Area News Group. http://newsle.com/article/0/28726504/

New lab publication on how the intestinal microbiota in aged mice is modified by the consumption of dietary resistant starch and correlated to improvements in host feeding responses, weight, and production of proglucagon. Tachon et al in FEMS Microbiology Ecology. In press. http://www.ncbi.nlm.nih.gov/pubmed/22909308

The Scientist highlights probiotics and Maria and the Marco lab is cited. : http://the-scientist.com/2012/07/01/alternative-medicines/#probiotic

The Marco lab was awarded funds through the UC Davis RISE grant program. The grant is for 3 years of support to develop new RNA-Based, Amplification Free, Pathogen Identification methods Using Nano-Enabled Electronic Detection (RAPID-NEED). http://www.research.ucdavis.edu/pgc/fo/RISE

Maria was nominated for a  2012 ASUCD Excellence in Education Award. This award is completely student-funded, student-nominated, and student-chosen. Maria sends her thanks to the students in FST104 for the nomination. It is an amazing honor and such an amazing award considering that Food Microbiology is definitely not an easy A!

 Tom Williams is featured by the UC Davis Office of Graduate Studies
http://gradstudies.ucdavis.edu/publications/news/studenthighlights.html

Maria was selected to be a Lecturer for the 2012-2014 American Society for Microbiology Branch Lectureships (ASMBL) program.
http://www.asm.org/index.php/membership/about-the-asm-branch-lectureships.html

The Marcolab was featured in a KQED QUEST video on the making of Sourdough.
http://science.kqed.org/quest/video/science-on-the-spot-secrets-of-sourdough/