MacKenzie Bryant
YOU?
Author Swipe
View article: A resource to empirically establish drug exposure records directly from untargeted metabolomics data
A resource to empirically establish drug exposure records directly from untargeted metabolomics data Open
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: Gut microbiome compositional and functional features associate with Alzheimer's disease pathology
Gut microbiome compositional and functional features associate with Alzheimer's disease pathology Open
BACKGROUND The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited. METHODS Shallow‐shotgun metagenomics was used to …
View article: A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population
A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population Open
Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of thi…
View article: Correction for Tang-Wing et al., “Impact of diet change on the gut microbiome of common marmosets ( <i>Callithrix jacchus</i> )”
Correction for Tang-Wing et al., “Impact of diet change on the gut microbiome of common marmosets ( <i>Callithrix jacchus</i> )” Open
View article: Correction for Taylor et al., “Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome”
Correction for Taylor et al., “Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome” Open
View article: Correction for Brennan et al., “Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution”
Correction for Brennan et al., “Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution” Open
View article: Empirically establishing drug exposure records directly from untargeted metabolomics data
Empirically establishing drug exposure records directly from untargeted metabolomics data Open
Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integ…
View article: Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies
Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies Open
Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time points. However, managing acquisition, processing, and analysis of large numbers o…
View article: Gut microbiome compositional and functional features associate with Alzheimer’s disease pathology
Gut microbiome compositional and functional features associate with Alzheimer’s disease pathology Open
BACKGROUND The gut microbiome is a potentially modifiable factor in Alzheimer’s disease (AD); however, understanding of its composition and function regarding AD pathology is limited. METHODS Shallow-shotgun metagenomic data was used to an…
View article: Impact of diet change on the gut microbiome of common marmosets ( <i>Callithrix jacchus</i> )
Impact of diet change on the gut microbiome of common marmosets ( <i>Callithrix jacchus</i> ) Open
Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets ( Callithrix jacchus ), often affecting the health and welfare of the animal and ultimately their use as a research subject. The micro…
View article: Pangenome comparison of <i>Bacteroides fragilis</i> genomospecies unveils genetic diversity and ecological insights
Pangenome comparison of <i>Bacteroides fragilis</i> genomospecies unveils genetic diversity and ecological insights Open
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequen…
View article: Pathogenic<i>Bacteroides fragilis</i>strains can emerge from gut-resident commensals
Pathogenic<i>Bacteroides fragilis</i>strains can emerge from gut-resident commensals Open
SUMMARY Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathoge…
View article: Pangenome comparison of<i>Bacteroides fragilis</i>genomospecies unveil genetic diversity and ecological insights
Pangenome comparison of<i>Bacteroides fragilis</i>genomospecies unveil genetic diversity and ecological insights Open
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694 B. fragilis whole genome seque…
View article: Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses
Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses Open
Technical bias is a pressing issue in microbiome research, and variability can be introduced at any stage from sample collection to figure generation. In this study, we aim to reduce biases in studying the human vaginal microbiome by exami…
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: Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution
Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution Open
Next-generation sequencing technologies have enabled many advances across diverse areas of biology, with many benefiting from increased sample size. Although the cost of running next-generation sequencing instruments has dropped substantia…
View article: Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection
Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection Open
View article: Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol
Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol Open
Roughly half of the human population lives near the coast, and coastal water pollution (CWP) is widespread. Coastal waters along Tijuana, Mexico, and Imperial Beach (IB), USA, are frequently polluted by millions of gallons of untreated sew…
View article: Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses
Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses Open
The urogenital microbiome is an understudied yet important human microbiome niche. Research has been stimulated by the relatively recent discovery that urine is not sterile; urinary tract microbes have been linked to health problems, inclu…
View article: Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity Open
View article: Enhancing untargeted metabolomics using metadata-based source annotation
Enhancing untargeted metabolomics using metadata-based source annotation Open
View article: Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses
Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses Open
Replicability is a well-established challenge in microbiome research with a variety of contributing factors at all stages, from sample collection to code execution. Here, we focus on voided urine sample storage conditions for urogenital mi…
View article: A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities
A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities Open
Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members o…
View article: SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp.
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp. Open
Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting …
View article: A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities
A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities Open
Microbial communities contain a broad phylogenetic diversity of organisms, however the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems, and are potentially important members o…
View article: Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity Open
View article: SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp Open
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse tr…
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: Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments
Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments Open
As our understanding of the structure and diversity of the microbial world grows, interpreting its function is of critical interest for understanding and managing the many systems microbes influence. Despite advances in sequencing, lack of…