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!