Michael J. Meehan
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View article: Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes
Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes Open
An essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a va…
View article: The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids Open
N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spe…
View article: Foodomics: Links to cognition and AD markers of disease
Foodomics: Links to cognition and AD markers of disease Open
Background Diet has been associated with memory, emotion/stress regulation, structure and function of the hippocampus and amygdala and attenuation of cognitive aging. There is a well‐recognized lack of reliability in self‐reported dietary …
View article: A Modified Mediterranean Ketogenic Diet reverses signatures and mitigates modifiable risk factors of Alzheimer’s disease
A Modified Mediterranean Ketogenic Diet reverses signatures and mitigates modifiable risk factors of Alzheimer’s disease Open
Background Alzheimer’s disease (AD) is a neurodegenerative disorder with significant environmental factors, including diet, that influence its onset and progression. While the ketogenic diet (KD) holds promise in reducing metabolic risks a…
View article: Possible Missing Sources of Atmospheric Glyoxal Part II: Oxidation of Toluene Derived from the Primary Production of Marine Microorganisms
Possible Missing Sources of Atmospheric Glyoxal Part II: Oxidation of Toluene Derived from the Primary Production of Marine Microorganisms Open
Background: Glyoxal has been implicated as a significant contributor to the formation of secondary organic aerosols, which play a key role in our ability to estimate the impact of aerosols on climate. Elevated concentrations of glyoxal ove…
View article: Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors
Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors Open
View article: The microbiome diversifies<i>N</i>-acyl lipid pools - including short-chain fatty acid-derived compounds
The microbiome diversifies<i>N</i>-acyl lipid pools - including short-chain fatty acid-derived compounds Open
N -acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N -acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference s…
View article: microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data Open
View article: Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics Open
Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpret…
View article: Issue Information
Issue Information Open
View article: Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation Open
View article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data Open
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can s…
View article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data Open
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can s…
View article: Effects of a ketogenic and low‐fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease
Effects of a ketogenic and low‐fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease Open
INTRODUCTION The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential for KD‐mediated neuroprotectio…
View article: Effects of a Ketogenic and Low Fat Diet on the Human Metabolome, Microbiome and Food-ome in Adults at Risk for Alzheimer’s Disease
Effects of a Ketogenic and Low Fat Diet on the Human Metabolome, Microbiome and Food-ome in Adults at Risk for Alzheimer’s Disease Open
STRUCTURED ABSTRACT INTRODUCTION The ketogenic diet (KD) is an intriguing candidate for neuroprotection in Alzheimer’s disease (AD) given its protective effects against metabolic dysregulation and seizures. The diet’s neuroprotective effec…
View article: Enhancing untargeted metabolomics using metadata-based source annotation
Enhancing untargeted metabolomics using metadata-based source annotation Open
View article: Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics
Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics Open
Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpret…
View article: Multi-omics of human plasma reveals molecular features of dysregulated inflammation and accelerated aging in schizophrenia
Multi-omics of human plasma reveals molecular features of dysregulated inflammation and accelerated aging in schizophrenia Open
Schizophrenia is a devastating psychiatric illness that detrimentally affects a significant portion of the worldwide population. Aging of schizophrenia patients is associated with reduced longevity, but the potential biological factors ass…
View article: Reference data-set driven metabolomics
Reference data-set driven metabolomics Open
Human untargeted metabolomics studies succeed in annotating only ~10% of molecular features. We, therefore, introduce reference data-driven analysis that uses the source data as a pseudo-MS/MS reference library to match against human metab…
View article: Identifying the effect of vancomycin on health care–associated methicillin-resistant <i>Staphylococcus aureus</i> strains using bacteriological and physiological media
Identifying the effect of vancomycin on health care–associated methicillin-resistant <i>Staphylococcus aureus</i> strains using bacteriological and physiological media Open
Background The evolving antibiotic-resistant behavior of health care–associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern. They are resistant to a broad class of antibiotics such as macrolide…
View article: ReDU: a framework to find and reanalyze public mass spectrometry data
ReDU: a framework to find and reanalyze public mass spectrometry data Open
View article: Characterizing the response of <i>Acinetobacter baumannii</i> ATCC 17978 to azithromycin in multiple <i>in vitro</i> growth conditions
Characterizing the response of <i>Acinetobacter baumannii</i> ATCC 17978 to azithromycin in multiple <i>in vitro</i> growth conditions Open
Multi-drug resistant (MDR) Acinetobacter baumannii is one of the most concerning pathogens in hospital infections. A. baumannii is categorized as an urgent threat by the U.S. Centers for Disease Control and the highest priority pathogen by…
View article: Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media
Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media Open
Healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern due to their evolving antibiotic resistant. They are resistant to a broad class of antibiotics like macrolides, aminoglycosides…
View article: Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media
Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media Open
Staphylococcus aureus is a leading human pathogen associated with both hospital-acquired and community-acquired infections. The bacterium has steadily gained resistance to β-lactams and other important first-line antibiotics culminating in…
View article: Feature-Based Molecular Networking Analysis of the Metabolites Produced by in vitro Solid-State Fermentation Reveals Pathways for the Bioconversion of Epigallocatechin Gallate
Feature-Based Molecular Networking Analysis of the Metabolites Produced by in vitro Solid-State Fermentation Reveals Pathways for the Bioconversion of Epigallocatechin Gallate Open
Flavan-3-ol B-ring fission derivatives (FBRFDs) are secondary metabolites that contribute to the unique properties of fermented dark teas. However, the FBRFD precursors and biochemistry are unclear. Fungal strains cultured from Fuzhuan bri…
View article: Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Open
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in pub…
View article: Global chemical effects of the microbiome include new bile-acid conjugations
Global chemical effects of the microbiome include new bile-acid conjugations Open
View article: Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media Open
Staphylococcus aureus strains have been continuously evolving resistance to numerous classes of antibiotics including methicillin, vancomycin, daptomycin and linezolid, compounding the enormous healthcare and economic burden of the pathoge…
View article: Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data Open
Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface ( https://redu.ucsd.edu/ ), a community- and data-driven approach that solves this proble…
View article: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids
Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids Open
A mosaic of cross-phyla chemical interactions occurs between all metazoans and their microbiomes. In humans, the gut harbors the heaviest microbial load, but many organs, particularly those with a mucosal surface, associate with highly ada…