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Article
Open AccessReverse metabolomics for the discovery of chemical structures from humans
Determining the structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here we present reverse metabolomics as a discovery strategy, whereby tandem m...
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Article
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation
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Article
Enhancing untargeted metabolomics using metadata-based source annotation
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotate...
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Article
Open AccessWastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially ...
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Article
Open AccessCandidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome
Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genet...
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Article
Open AccessSARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment
SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic ...
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Article
Open AccessFeasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment
Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to e...
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Article
Global chemical effects of the microbiome include new bile-acid conjugations
A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect on the bal...
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Article
Open AccessPhylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny...
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Article
Healthy infants harbor intestinal bacteria that protect against food allergy
There has been a striking generational increase in life-threatening food allergies in Westernized societies1,2. One hypothesis to explain this rising prevalence is that twenty-first century lifestyle practices, i...
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The Microbiome and Its Potential for Pharmacology
The human microbiota (the microscopic organisms that inhabit us) and microbiome (their genes) hold considerable potential for improving pharmacological practice. Recent advances in multi-“omics” techniques hav...
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Open AccessMicrobiota diversity and gene expression dynamics in human oral biofilms
Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. Although the composition of oral...
