Current News
Mar checking on the lung organoids
Publication of Nature article on SARS-CoV2 infection in human distal lung organoids
November 2020
Congratulations to Mar, the lab, and her collaborators for getting her manuscript published in Nature! 2020 did its best to try to keep us out of the lab, but we persisted. Even with shelter-in-place mandates, Mar was able to collaborate with the Kuo lab to characterize the apical-out lung organoid model and SARS-CoV-2 infection.
Our new grad student
Welcome to the lab Youlim!
April 2020
We are excited to announce that Youlim Kim has joined the lab. She found her niche during her rotation with us and is interested in using the organoid model to better understand H. pylori colonization and migration in the human stomach.
15 years of science under one roof
The lab celebrates its first reunion
December 2019
Manuel's promotion to Professor conveniently took place the same year of the lab's 15th anniversary. Naturally that meant a party was in order. It was an evening filled with reminiscing, swapping funny stories about lab shenanigans, competing in a Manuel-themed trivia game, and of course an ambitious sampling of TQ buffer. Enjoy a small insight to those moments here. A very special thanks to Lauren and Shumin for organizing this event and to Ewen and Manuel for opening their home to host.
Dr. Manuel Amieva, Professor
Manuel is promoted to Professor!
July 2019
Congrats to Dr. Manuel Amieva on his promotion to full professor! He has been a longtime member of the Stanford community starting with his M.D./Ph.D. education (completed in 1997). He continued his training here as a Pediatric Resident and Fellow as well as a Post Doctoral Fellow until the time came to start his own lab and teaching career in 2004. Manuel has not only made novel research discoveries, but has also implemented novel teaching methods as he trains up the next generation of medical doctors and scientists. Many lab members (past and present) have benefited from his remarkable mentorship and we all look forward to celebrating this momentous milestone with him.
Dr. Jessica Klein, Walter V. and Idun Berry Postdoctoral Fellow
Jessica is our new Berry Fellow!
July 2019
Congrats to Dr. Jessica Klein on being awarded the Walter V. and Idun Berry Fellowship.
This prestigious and highly-competitive award is granted to select postdoctoral researchers in clinical and basic sciences with projects aimed at improving child health and wellness. With this support, Jessica will construct new molecular tools to study how H.pylori establishes and maintains chronic infection in childhood.
PLoS Biology Cover. The gastric glands harbor unique populations of Helicobacter pylori, labeled in this 3D confocal image with GFP or tdTomato fluorescent proteins.
Publication of PLoS Biology article on how Helicobacter pylori establishes chronic colonization in the gastric mucosa
May 2019
Congratulations to Connie, the lab, and her collaborators for getting her manuscript published in PLoS Biology, and for getting the journal cover of the May 2019 Edition! In this work, Connie used high resolution imaging and mapping techniques to visualize H. pylori populations in whole infected organs and understand how this lifelong mucosal colonizer persists in the stomach. Her results suggest that the bacteria do so by establishing stable reservoirs within a specialized microenvironment, or "microniche", deep in the gastric glands.
Press coverage of Connie's work
Reservoir bugs: Study shows why stomach pathogen is so tough to eradicate
Reservoir bugs: How one bacterial menace makes its home in the human stomach
Pathogens find safe harbor deep in the gastric glands
Why the H. pylori stomach bug is so persistent
Probiotics can't evict this bug from tiny stomach pits
How do cancer-causing bacteria take over our stomachs?
The Scientist Image of the Day: Gastric Colonies
Biomedical Picture of the Day: Stomach problem-causing H. pylori bacteria survive in glands deep in the stomach lining
Journal articles highlighting Connie's work
Helicobacter pylori hideout in gastric glands
Connie's article got recommended on F1000 prime!
F1000 Prime Article Recommendation by Dr. Dirk Bumann
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Retreat 2014 (Poster)
*Stanford Microbiology & Immunology Department Retreat 2015 (Talk)
*Gordon Research Seminar & Conference on Microbial Toxins and Pathogenicity 2016 (Poster)
*Stanford Microbiology & Immunology Department Retreat 2016 (Poster)
*Cold Spring Harbor Microbial Pathogenesis and Host Response Meeting 2017 (Talk)
*Stanford Microbiology & Immunology Department Retreat 2017 (Talk)
*Stanford Bug Club Seminar 2018 (Talk)
Cover painted by Jessica Klein
Publication of Cell Reports article on a novel human enteroid model for studying host-pathogen interactions
February 2019
Congratulations to Julia, the lab, and her collaborators for getting her manuscript published in Cell Reports, and for getting the journal cover of the 9th issue of 2019! In this work, Julia described a method to control the epithelial polarity of human enteroids, thus enabling access to the apical epithelium. Furthermore, Julia showed that these apical-out enteroids can be used to study host-pathogen interactions, epithelial barrier integrity, and nutrient uptake in the gut.
Press coverage of Julia's work
To learn secrets of lab-grown "gutballs," scientists turn them inside out
Julia's article got recommended on F1000 prime!
F1000 Prime Article Recommendation by Dr. Frank Seeber
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Retreat 2016 (Talk)
*Stanford Pediatrics Department Retreat 2018 (Poster): Julia was awarded a prize for best poster!
Dr. Connie celebrating after her defense!
Connie successfully defends her thesis!
August 2018
Connie successfully defends her thesis, "Microniches in the gastric glands control Helicobacter pylori colonization of the stomach". Congratulations, Dr. Fung!!!
H. pylori rapidly swims away from the tip of a microinjection needle that is releasing hydrochloric acid.
Publication of PLoS Pathogens article on the role of acid sensing in Helicobacter pylori stomach colonization
January 2017
Congratulations to Julie, the lab, and her collaborators for getting her manuscript published in PLoS Pathogens, and for the article getting highlighted on the front page of the journal website! In this work, Julie investigated how Helicobacter pylori sensing of acid gradients enable it to colonize and survive in the stomach, and also how acid sensing controls the interaction of the bacteria with the gastric epithelium.
Press coverage of Julie's work
Stomach bugs' bad acid trip: Scientists find tools H. pylori uses to sense organ's wicked secretions
Conferences and research presentations on this work
*Sensory Transduction in Microorganisms Gordon Research Seminar 2016 (Talk & Poster)
*Sensory Transduction in Microorganisms Gordon Research Conference 2016 (Poster)
Dr. Lauren celebrating after her defense!
Lauren successfully defends her thesis!
March 2016
Lauren successfully defends her thesis, "The adherens junctions control susceptibility to Staphylococcus aureus α-toxin". Congratulations, Dr. Popov!!!
Dr. Julie celebrating after her defense!
Julie successfully defends her thesis!
February 2016
Julie successfully defends her thesis, "Chemodetection and response to host signals facilitate Helicobacter pylori colonization of the gastric epithelium". Congratulations, Dr. Huang!!!
Adherens junction protein PLEKHA7 (green) in human lung epithelial cells. White = actin, Blue = nuclei.
Time-lapse visualization of lesion development and repair in WT and PLEKHA7 KO mice following MRSA skin infection. Mice that lack PLEKHA7 resolve MRSA skin infection with significantly less tissue loss compared to WT animals.
Publication of PNAS article on Staphylococcus aureus α-toxin and the cellular adherens junctions
October 2015
Congratulations to Lauren, the lab, and her collaborators for getting her manuscript published in PNAS! In this work, Lauren and her collaborators conducted a haploid genetic screen to look for host factors important for Staphylococcus aureus α-toxin virulence. They discovered that components of the host cellular adherens junctions control susceptibility to this important virulence factor. In this study, Lauren focused on the role of the adherens junction protein PLEKHA7 during α-toxin injury and Staphylococcus aureus infections.
Press coverage of Lauren's work
Inside job: Staphylococcus aureus gets critical assist from host-cell protein accomplice
Staphylococcus aureus Achilles' heel
Scientists discover weak spot of the superbug MRSA
Journal articles highlighting Lauren's work
In this issue by PNAS
The ever-emerging complexity of α-toxin's interaction with host cells
Lauren's article got recommended on F1000 prime!
F1000 Prime Article Recommendation by Dr. Drusilla L. Burns
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Noon Seminar 2014 (Talk)
*Stanford Microbiology & Immunology Department Retreat 2014 (Talk)
*Keystone Conference on Innate Immunity and Determinants of Microbial Pathogenesis 2015 (Poster)
*Stanford Pediatrics Department Retreat 2015 (Talk): Lauren was awarded a prize for best talk!
*Gordon Research Seminar on Staphylococcal Diseases 2015 (Talk)
*Gordon Research Conference on Staphylococcal Diseases 2015 (Talk): Lauren was one of few students selected to give an oral presentation at the conference!
*Cold Spring Harbor Laboratory Microbial Pathogenesis and Host Response Meeting 2015 (Talk)
*Stanford Bug Club Seminar 2015 (Talk)
H. pylori is attracted to the tip of a microinjection needle that is releasing media that has been conditioned on epithelial cells.
Publication of Cell Host Microbe article on how Helicobacter pylori senses and locates the gastric epithelium
August 2015
Congratulations to Julie, the lab, and her collaborators for getting her manuscript published in the August 2015 issue of Cell Host Microbe! In this work, Julie investigated how Helicobacter pylori senses urea emanating from host cells as a chemoattractant to find its epithelial niche. Make sure to check out the videos Julie recorded of the bacteria's swimming responses to the chemoattractant!
Press coverage of Julie's work
When bacteria swarm: H. pylori home in on our stomach cells
Journal articles highlighting Julie's work
H. pylori GPS: Modulating Host Metabolites for Location Sensing
Helicobacter pylori: Lessons in bacterial attraction
Stomach microbe finds a safe haven
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Noon Seminar 2012 (Talk)
*Stanford Microbiology & Immunology Department Retreat 2013 (Talk)
*Bay Area Microbial Pathogenesis Symposium 2014 (Talk)
*Microbial Stress Response Gordon Research Seminar 2014 (Talk & Poster)
*Microbial Stress Response Gordon Research Conference 2014 (Poster)
*5th ASM Conference on Beneficial Microbes 2014 (Talk)
*Genentech Infectious Diseases Department Seminar 2015 (Talk)
*Stanford Bug Club Seminar 2015 (Talk)
Publication of Gastroenterology article on how Helicobacter pylori colonizes and manipulates the progenitor and stem cell compartments in the gastric glands
June 2015
Congratulations to Michael, the lab, and his collaborators for getting his manuscript published in Gastroenterology and for getting the cover of the June 2015 issue! In this work, Michael characterized H. pylori interactions with gastric epithelial progenitor and stem cells and how these interactions contribute to host pathology.
Press coverage of Michael's work
Ulcer-causing bacteria induces stomach stem cell growth in mice, researchers find
Ulcer-causing bacteria manipulate stomach stem cells to their own ends
Science Update Podcast: Bacteria & Stomach Cancer
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Noon Seminar 2014 (Talk)
*Stanford Pediatrics Department Retreat 2014 (Talk): Michael was awarded a prize for best talk!
*United European Gastroenterology Conference 2015 (Talk): Michael was a Top Abstract Prize Awardee!
*Digestive Disease Week 2015 (Talk)
Mar checking on the lung organoids
Publication of Nature article on SARS-CoV2 infection in human distal lung organoids
November 2020
Congratulations to Mar, the lab, and her collaborators for getting her manuscript published in Nature! 2020 did its best to try to keep us out of the lab, but we persisted. Even with shelter-in-place mandates, Mar was able to collaborate with the Kuo lab to characterize the apical-out lung organoid model and SARS-CoV-2 infection.
Our new grad student
Welcome to the lab Youlim!
April 2020
We are excited to announce that Youlim Kim has joined the lab. She found her niche during her rotation with us and is interested in using the organoid model to better understand H. pylori colonization and migration in the human stomach.
15 years of science under one roof
The lab celebrates its first reunion
December 2019
Manuel's promotion to Professor conveniently took place the same year of the lab's 15th anniversary. Naturally that meant a party was in order. It was an evening filled with reminiscing, swapping funny stories about lab shenanigans, competing in a Manuel-themed trivia game, and of course an ambitious sampling of TQ buffer. Enjoy a small insight to those moments here. A very special thanks to Lauren and Shumin for organizing this event and to Ewen and Manuel for opening their home to host.
Dr. Manuel Amieva, Professor
Manuel is promoted to Professor!
July 2019
Congrats to Dr. Manuel Amieva on his promotion to full professor! He has been a longtime member of the Stanford community starting with his M.D./Ph.D. education (completed in 1997). He continued his training here as a Pediatric Resident and Fellow as well as a Post Doctoral Fellow until the time came to start his own lab and teaching career in 2004. Manuel has not only made novel research discoveries, but has also implemented novel teaching methods as he trains up the next generation of medical doctors and scientists. Many lab members (past and present) have benefited from his remarkable mentorship and we all look forward to celebrating this momentous milestone with him.
Dr. Jessica Klein, Walter V. and Idun Berry Postdoctoral Fellow
Jessica is our new Berry Fellow!
July 2019
Congrats to Dr. Jessica Klein on being awarded the Walter V. and Idun Berry Fellowship.
This prestigious and highly-competitive award is granted to select postdoctoral researchers in clinical and basic sciences with projects aimed at improving child health and wellness. With this support, Jessica will construct new molecular tools to study how H.pylori establishes and maintains chronic infection in childhood.
PLoS Biology Cover. The gastric glands harbor unique populations of Helicobacter pylori, labeled in this 3D confocal image with GFP or tdTomato fluorescent proteins.
Publication of PLoS Biology article on how Helicobacter pylori establishes chronic colonization in the gastric mucosa
May 2019
Congratulations to Connie, the lab, and her collaborators for getting her manuscript published in PLoS Biology, and for getting the journal cover of the May 2019 Edition! In this work, Connie used high resolution imaging and mapping techniques to visualize H. pylori populations in whole infected organs and understand how this lifelong mucosal colonizer persists in the stomach. Her results suggest that the bacteria do so by establishing stable reservoirs within a specialized microenvironment, or "microniche", deep in the gastric glands.
Press coverage of Connie's workReservoir bugs: Study shows why stomach pathogen is so tough to eradicate
Reservoir bugs: How one bacterial menace makes its home in the human stomach
Pathogens find safe harbor deep in the gastric glands
Why the H. pylori stomach bug is so persistent
Probiotics can't evict this bug from tiny stomach pits
How do cancer-causing bacteria take over our stomachs?
The Scientist Image of the Day: Gastric Colonies
Biomedical Picture of the Day: Stomach problem-causing H. pylori bacteria survive in glands deep in the stomach lining
Journal articles highlighting Connie's work
Helicobacter pylori hideout in gastric glands
Connie's article got recommended on F1000 prime!
F1000 Prime Article Recommendation by Dr. Dirk Bumann
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Retreat 2014 (Poster)
*Stanford Microbiology & Immunology Department Retreat 2015 (Talk)
*Gordon Research Seminar & Conference on Microbial Toxins and Pathogenicity 2016 (Poster)
*Stanford Microbiology & Immunology Department Retreat 2016 (Poster)
*Cold Spring Harbor Microbial Pathogenesis and Host Response Meeting 2017 (Talk)
*Stanford Microbiology & Immunology Department Retreat 2017 (Talk)
*Stanford Bug Club Seminar 2018 (Talk)
Cover painted by Jessica Klein
Publication of Cell Reports article on a novel human enteroid model for studying host-pathogen interactions
February 2019
Congratulations to Julia, the lab, and her collaborators for getting her manuscript published in Cell Reports, and for getting the journal cover of the 9th issue of 2019! In this work, Julia described a method to control the epithelial polarity of human enteroids, thus enabling access to the apical epithelium. Furthermore, Julia showed that these apical-out enteroids can be used to study host-pathogen interactions, epithelial barrier integrity, and nutrient uptake in the gut.
Press coverage of Julia's workTo learn secrets of lab-grown "gutballs," scientists turn them inside out
Julia's article got recommended on F1000 prime!
F1000 Prime Article Recommendation by Dr. Frank Seeber
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Retreat 2016 (Talk)
*Stanford Pediatrics Department Retreat 2018 (Poster): Julia was awarded a prize for best poster!
Dr. Connie celebrating after her defense!
Connie successfully defends her thesis!
August 2018
Connie successfully defends her thesis, "Microniches in the gastric glands control Helicobacter pylori colonization of the stomach". Congratulations, Dr. Fung!!!
H. pylori rapidly swims away from the tip of a microinjection needle that is releasing hydrochloric acid.
Publication of PLoS Pathogens article on the role of acid sensing in Helicobacter pylori stomach colonization
January 2017
Congratulations to Julie, the lab, and her collaborators for getting her manuscript published in PLoS Pathogens, and for the article getting highlighted on the front page of the journal website! In this work, Julie investigated how Helicobacter pylori sensing of acid gradients enable it to colonize and survive in the stomach, and also how acid sensing controls the interaction of the bacteria with the gastric epithelium.
Press coverage of Julie's workStomach bugs' bad acid trip: Scientists find tools H. pylori uses to sense organ's wicked secretions
Conferences and research presentations on this work
*Sensory Transduction in Microorganisms Gordon Research Seminar 2016 (Talk & Poster)
*Sensory Transduction in Microorganisms Gordon Research Conference 2016 (Poster)
Dr. Lauren celebrating after her defense!
Lauren successfully defends her thesis!
March 2016
Lauren successfully defends her thesis, "The adherens junctions control susceptibility to Staphylococcus aureus α-toxin". Congratulations, Dr. Popov!!!
Dr. Julie celebrating after her defense!
Julie successfully defends her thesis!
February 2016
Julie successfully defends her thesis, "Chemodetection and response to host signals facilitate Helicobacter pylori colonization of the gastric epithelium". Congratulations, Dr. Huang!!!
Adherens junction protein PLEKHA7 (green) in human lung epithelial cells. White = actin, Blue = nuclei.
Time-lapse visualization of lesion development and repair in WT and PLEKHA7 KO mice following MRSA skin infection. Mice that lack PLEKHA7 resolve MRSA skin infection with significantly less tissue loss compared to WT animals.
Publication of PNAS article on Staphylococcus aureus α-toxin and the cellular adherens junctions
October 2015
Congratulations to Lauren, the lab, and her collaborators for getting her manuscript published in PNAS! In this work, Lauren and her collaborators conducted a haploid genetic screen to look for host factors important for Staphylococcus aureus α-toxin virulence. They discovered that components of the host cellular adherens junctions control susceptibility to this important virulence factor. In this study, Lauren focused on the role of the adherens junction protein PLEKHA7 during α-toxin injury and Staphylococcus aureus infections.
Press coverage of Lauren's workInside job: Staphylococcus aureus gets critical assist from host-cell protein accomplice
Staphylococcus aureus Achilles' heel
Scientists discover weak spot of the superbug MRSA
Journal articles highlighting Lauren's work
In this issue by PNAS
The ever-emerging complexity of α-toxin's interaction with host cells
Lauren's article got recommended on F1000 prime!
F1000 Prime Article Recommendation by Dr. Drusilla L. Burns
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Noon Seminar 2014 (Talk)
*Stanford Microbiology & Immunology Department Retreat 2014 (Talk)
*Keystone Conference on Innate Immunity and Determinants of Microbial Pathogenesis 2015 (Poster)
*Stanford Pediatrics Department Retreat 2015 (Talk): Lauren was awarded a prize for best talk!
*Gordon Research Seminar on Staphylococcal Diseases 2015 (Talk)
*Gordon Research Conference on Staphylococcal Diseases 2015 (Talk): Lauren was one of few students selected to give an oral presentation at the conference!
*Cold Spring Harbor Laboratory Microbial Pathogenesis and Host Response Meeting 2015 (Talk)
*Stanford Bug Club Seminar 2015 (Talk)
H. pylori is attracted to the tip of a microinjection needle that is releasing media that has been conditioned on epithelial cells.
Publication of Cell Host Microbe article on how Helicobacter pylori senses and locates the gastric epithelium
August 2015
Congratulations to Julie, the lab, and her collaborators for getting her manuscript published in the August 2015 issue of Cell Host Microbe! In this work, Julie investigated how Helicobacter pylori senses urea emanating from host cells as a chemoattractant to find its epithelial niche. Make sure to check out the videos Julie recorded of the bacteria's swimming responses to the chemoattractant!
Press coverage of Julie's workWhen bacteria swarm: H. pylori home in on our stomach cells
Journal articles highlighting Julie's work
H. pylori GPS: Modulating Host Metabolites for Location Sensing
Helicobacter pylori: Lessons in bacterial attraction
Stomach microbe finds a safe haven
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Noon Seminar 2012 (Talk)
*Stanford Microbiology & Immunology Department Retreat 2013 (Talk)
*Bay Area Microbial Pathogenesis Symposium 2014 (Talk)
*Microbial Stress Response Gordon Research Seminar 2014 (Talk & Poster)
*Microbial Stress Response Gordon Research Conference 2014 (Poster)
*5th ASM Conference on Beneficial Microbes 2014 (Talk)
*Genentech Infectious Diseases Department Seminar 2015 (Talk)
*Stanford Bug Club Seminar 2015 (Talk)
Publication of Gastroenterology article on how Helicobacter pylori colonizes and manipulates the progenitor and stem cell compartments in the gastric glands
June 2015
Congratulations to Michael, the lab, and his collaborators for getting his manuscript published in Gastroenterology and for getting the cover of the June 2015 issue! In this work, Michael characterized H. pylori interactions with gastric epithelial progenitor and stem cells and how these interactions contribute to host pathology.
Press coverage of Michael's workUlcer-causing bacteria induces stomach stem cell growth in mice, researchers find
Ulcer-causing bacteria manipulate stomach stem cells to their own ends
Science Update Podcast: Bacteria & Stomach Cancer
Conferences and research presentations on this work
*Stanford Microbiology & Immunology Department Noon Seminar 2014 (Talk)
*Stanford Pediatrics Department Retreat 2014 (Talk): Michael was awarded a prize for best talk!
*United European Gastroenterology Conference 2015 (Talk): Michael was a Top Abstract Prize Awardee!
*Digestive Disease Week 2015 (Talk)