CHOP Microbiome Center Publications

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View a compilation of publications by researchers who used resources in the CHOP Microbiome Center.

Total:
144

2024

Metal availability shapes early life microbial ecology and community succession
MBio · October, 2024
Bacterial metabolites influence the autofluorescence of Clostridioides difficile
Frontiers In Microbiology · October, 2024
Staphylococcus aureus adapts to exploit collagen-derived proline during chronic infection
Nature Microbiology · October, 2024
Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro
MBio · June, 2024
Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro
Frontiers In Nutrition · May, 2024
Challenges in IBD Research 2024: Environmental Triggers
Inflammatory Bowel Diseases · May, 2024
Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts
Cellular And Molecular Gastroenterology And Hepatology · May, 2024
Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae
The Journal Of Clinical Investigation · March, 2024
Bile salt hydrolase catalyses formation of amine-conjugated bile acids
Nature · February, 2024
Human Intestinal Microbiome Determines Individualized Inflammatory Response to Dietary Emulsifier Carboxymethylcellulose Consumption
Cellular And Molecular Gastroenterology And Hepatology · January, 2024
Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease
Cellular And Molecular Gastroenterology And Hepatology · January, 2024
The intestinal microbiome of inflammatory bowel disease across the pediatric age range
Gut Microbes · January, 2024
Microbiome Profiling Demonstrates Concordance of Endotracheal Tube Aspirates With Direct Lower Airway Sampling in Intubated Patients
Chest · January, 2024
Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection
MBio · January, 2024
Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome
Gut Microbes · January, 2024

2023

An integrated analysis of fecal microbiome and metabolomic features distinguish non-cirrhotic NASH from healthy control populations
Hepatology (Baltimore, Md.) · December, 2023
Evolution of Invasive and Colonizing Pediatric Staphylococcus aureus Isolates
Journal of the Pediatric Infectious Diseases Society · November, 2023
Impact of Ivermectin on the Gut Microbial Ecosystem
International Journal Of Molecular Sciences · November, 2023
RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro
Frontiers In Microbiology · November, 2023
Changes in fecal lipidome after treatment with ivacaftor without changes in microbiome or bile acids
Journal Of Cystic Fibrosis : Official Journal Of The European Cystic Fibrosis Society · October, 2023
Tracking gut microbiome and bloodstream infection in critically ill adults
PloS One · October, 2023
Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV
Research Square · October, 2023
Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis
Microbiology Spectrum · September, 2023
Effects of Mask Reuse on the Oropharyngeal, Skin, and Mask Microbiome
The Journal Of Infectious Diseases · August, 2023
2-Hydroxyisovalerate Is Produced During Bacterial Vaginosis and Boosts HIV Infection in Resting T Cells
AIDS Research And Human Retroviruses · August, 2023
Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016)
Microbiol Spectr · August, 2023
Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis
Journal Of Cystic Fibrosis : Official Journal Of The European Cystic Fibrosis Society · July, 2023
The Role of Gut Dysbiosis in the Loss of Intestinal Immune Cell Functions and Viral Pathogenesis
Microorganisms · July, 2023
Infrequent intrahousehold transmission of Clostridioides difficile between pet owners and their pets
Zoonoses And Public Health · June, 2023
Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities
Microbiome · June, 2023
Colonization and Dissemination of Klebsiella pneumoniae is Dependent on Dietary Carbohydrates
BioRxiv : The Preprint Server For Biology · June, 2023
Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction
American Journal Of Physiology. Gastrointestinal And Liver Physiology · May, 2023
Administration of Bifidobacterium animalis subsp. lactis strain BB-12(®) in healthy children: characterization, functional composition, and metabolism of the gut microbiome
Frontiers In Microbiology · May, 2023
Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Latin America
BioRxiv : The Preprint Server For Biology · May, 2023
Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME)
Foods (Basel, Switzerland) · May, 2023
IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation
Sci Immunol · May, 2023
Human tooth as a fungal niche: Candida albicans traits in dental plaque isolates
mBio · January, 2023
Fructooligosaccharide (FOS) from chicory root differentially modifies the in vitro gut microbiota in an age-dependent manner
Front in Nutr · January, 2023
Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification
Front Cell Infect Microbiol · January, 2023

2022

An in-vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner
Front in Nutr · December, 2022
Diet standardization reduces intra-individual microbiome variation
Gut Microbes · December, 2022
Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance
Microbiome · October, 2022
Gut microbiota-bile acid-skeletal muscle axis
Trends Microbiol · October, 2022
Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome
Int. J. Mol. Sci · October, 2022
The Lung Allograft Microbiome Associates with Pepsin, Inflammation, and Primary Graft Dysfunction
Am J Respir Crit Care Med · September, 2022
Imaging sensitive and drug-resistant bacterial infection with [11C]-trimethoprim
J Clin Invest · September, 2022
Successful dietary therapy in paediatric Crohn's Disease is associated with shifts in bacterial dysbiosis and inflammatory metabotype towards healthy controls
J Crohns Colitis · September, 2022
High frequency of increased triclosan MIC among CC5 MRSA and risk of misclassification of the SCCmec into types
J Antimicrob Chemother · September, 2022
Dysbiosis-induced secondary bile acid deficiency promotes intestinal inflammation
Cell Host Microbe · August, 2022
Outcomes and predictors of sustained remission after drug withdrawal in pediatric Crohn's disease
J Pediatr Gastroenterol Nutr · August, 2022
Gardnerella vaginalis alters cervicovaginal epithelial cell function through microbe-specific immune responses
Microbiome · August, 2022
Innate type 2 immunity controls hair follicle commensalism by Demodex mites
Immunity · August, 2022
A microbial signature for paediatric perianal Crohn's Disease
J Crohns Colitis · August, 2022
SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens
Sci Immunol · July, 2022
Risk for post-colonoscopy irritable bowel syndrome in patients with and without antibiotic exposure: A retrospective cohort study
Clin Gastroenterol Hepatol · June, 2022
The pediatric virome in health and disease
Cell Host Microbe · May, 2022
Long-term outcomes following multiply recurrent Clostridioides difficile infection and fecal microbiota transplantation
Clin Gastroenterol Hepatol · April, 2022
Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations
Anaerobe · April, 2022
The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production
FEMS Microbiol Ecol · April, 2022
Randomized controlled-feeding study of dietary emulsifier carboxymethylcellulose reveals detrimental impacts on the gut microbiota and metabolome
Gastroenterology · March, 2022
The macronutrient composition of infant formula produces differences in gut microbiota maturation that associate with weight gain velocity and weight status
Nutrients · March, 2022
SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through Summer 2021
mBio · February, 2022
Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infection
Gut · February, 2022
Polymicrobial aggregates in human saliva build the oral biofilm
mBio · February, 2022
A microbial signature for pediatric perianal Crohn's Disease
J Crohns Colitis · February, 2022
Dietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease
Gut Microbes · January, 2022
Early stool microbiome and metabolome signatures in pediatric patients undergoing allogeneic hematopoietic cell transplantation
Pediatric Blood and Cancer · January, 2022
Evolution of FMT - From early clinical to standardized treatments
Biologicals · January, 2022
Effects of prebiotics, probiotics, and synbiotics on the infant gut microbiota and other health outcomes: A systematic review
Crit Rev in Food Sci and Nutr · January, 2022
Causes of readmissions for patients discharged on enteral nutrition
PEN J Parenter Enteral Nutr · January, 2022

2021

The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis
Gut Microbes · December, 2021
Jumping a Moving Train: SARS-CoV-2 Evolution in Real Time
Journal Of The Pediatric Infectious Diseases Society · December, 2021
Global Microbiota-Dependent Histone Acetylation Patterns Are Irreversible and Independent of Short Chain Fatty Acids
Hepatology (Baltimore, Md.) · December, 2021
Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil
Emerging Infectious Diseases · November, 2021
Effects of Vancomycin on Persistent Pain-Stimulated and Pain-Depressed Behaviors in Female Fischer Rats With or Without Voluntary Access to Running Wheels
The Journal Of Pain · November, 2021
Copper Resistance Promotes Fitness of Methicillin-Resistant Staphylococcus aureus during Urinary Tract Infection
MBio · October, 2021
Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales
Journal Of Virology · October, 2021
A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults With Crohn's Disease
Gastroenterology · September, 2021
Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing
Genome Biology And Evolution · September, 2021
Insights into the skin microbiome of sickle cell disease leg ulcers
Wound Repair Regen · September, 2021
Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome
MBio · August, 2021
Understanding the Gut Microbiota in Pediatric Patients with Alopecia Areata and their Siblings: A Pilot Study
JID Innovations : Skin Science From Molecules To Population Health · August, 2021
Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection
Viruses · August, 2021
The human virome: assembly, composition and host interactions
Nature Reviews. Microbiology · August, 2021
The lung microbiome in lung transplantation
The Journal Of Heart And Lung Transplantation : The Official Publication Of The International Society For Heart Transplantation · August, 2021
Structure-guided microbial targeting of antistaphylococcal prodrugs
ELife · July, 2021
Sex-dependent compensatory mechanisms preserve blood pressure homeostasis in prostacyclin receptor-deficient mice
The Journal Of Clinical Investigation · July, 2021
Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
Microbiome · June, 2021
Excess dietary fructose does not alter gut microbiota or permeability in humans: A pilot randomized controlled study
Journal Of Clinical And Translational Science · June, 2021
Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates
Open Forum Infectious Diseases · June, 2021
Genetic variation of staphylococcal LukAB toxin determines receptor tropism
Nature Microbiology · June, 2021
Breastfeeding influences the neonatal virome
Nature · May, 2021
Rengasvirus, a circular replication-associated protein-encoding single-stranded DNA virus-related genome that is a common contaminant in metagenomic data
Microbiol Resour Announc · May, 2021
Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design
Appl Microbiol Biotechnol · April, 2021
Adaptation by ancient horizontal acquisition of butyrate metabolism genes in Aggregatibacter actinomycetemcomitans
mBio · March, 2021
Decreased intestinal microbiome diversity in pediatric sepsis: A conceptual framework for intestinal dysbiosis to influence immunometabolic function
Crit Care Explor · March, 2021
Maternal gut microbiota reflecting poor diet quality is associated with spontaneous preterm birth in a prospective cohort study
Am J Clin Nutr · March, 2021
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome
Cell Host Microbe · March, 2021
Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines
J Clin Invest · January, 2021
Fecal microbiota transplantation is highly effective in real-world practice: Initial results from the FMT national registry
Gastroenterology · January, 2021

2020

Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease
Journal Of Crohn's & Colitis · November, 2020
Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease
Cell Host & Microbe · September, 2020
Natural Infection with Giardia Is Associated with Altered Community Structure of the Human and Canine Gut Microbiome
MSphere · August, 2020
Bacterial colonization reprograms the neonatal gut metabolome
Nature Microbiology · June, 2020
Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians
Genome Biology · May, 2020
Dietary Guidance From the International Organization for the Study of Inflammatory Bowel Diseases
Clinical Gastroenterology And Hepatology : The Official Clinical Practice Journal Of The American Gastroenterological Association · May, 2020
The stepwise assembly of the neonatal virome is modulated by breastfeeding
Nature · May, 2020

2019

Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant
Annals Of The American Thoracic Society · November, 2019
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids
Microbiome · August, 2019
Gut microbiota features associated with Clostridioides difficile colonization in puppies
PloS One · August, 2019
Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents
PloS One · May, 2019
Challenges in IBD Research: Environmental Triggers
Inflammatory Bowel Diseases · May, 2019
Innate lymphoid cells support regulatory T cells in the intestine through interleukin-2
Nature · April, 2019
Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study
Lancet (London, England) · April, 2019
Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation
American Journal Of Transplantation : Official Journal Of The American Society Of Transplantation And The American Society Of Transplant Surgeons · April, 2019
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Microbiome · March, 2019
A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells
Mucosal Immunology · March, 2019
De-Discovery of the Placenta Microbiome
American Journal Of Obstetrics And Gynecology · March, 2019
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Genome Biology · January, 2019
Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response
Nature Communications · January, 2019

2018

T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency
Genome Medicine · September, 2018
Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile
Gut · May, 2018
Allometry and Ecology of the Bilaterian Gut Microbiome
MBio · March, 2018
Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12
JCI Insight · February, 2018
Lack of Detection of a Human Placenta Microbiome in Samples from Preterm and Term Deliveries
Microbiome · January, 2018
Enterotypes in the landscape of gut microbial community composition
Nature Microbiology · January, 2018
Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples
American Journal Of Respiratory And Critical Care Medicine · January, 2018
Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees
American Journal Of Primatology · January, 2018

2017

A Pilot Characterization of the Human Chronobiome
Scientific Reports · December, 2017
Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates
PeerJ · December, 2017
Functional imaging of the interaction between gut microbiota and the human host: A proof-of-concept clinical study evaluating novel use for 18F-FDG PET-CT
PloS One · December, 2017
A role for bacterial urease in gut dysbiosis and Crohn's disease
Science Translational Medicine · November, 2017
Colonic Microbiota Encroachment Correlates With Dysglycemia in Humans
Cellular And Molecular Gastroenterology And Hepatology · September, 2017
Increasing Incidence of Multiply Recurrent Clostridium difficile Infection in the United States: A Cohort Study
Annals Of Internal Medicine · August, 2017
Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome
JAMA Pediatrics · July, 2017
A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data
Statistics In Biosciences · June, 2017
The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction
American Journal Of Transplantation : Official Journal Of The American Society Of Transplantation And The American Society Of Transplant Surgeons · May, 2017
Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors
AIDS (London, England) · April, 2017
Genome Sequence of a Toxin-Positive Clostridium difficile Strain Isolated from Murine Feces
Genome Announcements · April, 2017
Human and rat gut microbiome composition is maintained following sleep restriction
Proceedings Of The National Academy Of Sciences Of The United States Of America · February, 2017
Diet as a Trigger or Therapy for Inflammatory Bowel Diseases
Gastroenterology · February, 2017
Optimizing methods and dodging pitfalls in microbiome research
Microbiome · January, 2017

2016

Viral communities of the human gut: metagenomic analysis of composition and dynamics
Mobile DNA · December, 2016
Evolutionary and functional implications of hypervariable loci within the skin virome
PeerJ · December, 2016