Gregory B. Gloor
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View article: Author Correction: A roadmap for equitable reuse of public microbiome data
Author Correction: A roadmap for equitable reuse of public microbiome data Open
View article: PHYCUT: Scalable multiplex CRISPR/Cas9 editing for genome engineering in the diatom <i>Phaeodactylum tricornutum</i>
PHYCUT: Scalable multiplex CRISPR/Cas9 editing for genome engineering in the diatom <i>Phaeodactylum tricornutum</i> Open
Diatoms are globally significant microalgae that contribute ∼ 20% of oxygen production and exhibit remarkable metabolic diversity. The marine diatom Phaeodactylum tricornutum has emerged as a promising synthetic biology platform for biopro…
View article: A roadmap for equitable reuse of public microbiome data
A roadmap for equitable reuse of public microbiome data Open
View article: PAM adenine methylation and flanking sequence regulate SaCas9 activity in bacteria
PAM adenine methylation and flanking sequence regulate SaCas9 activity in bacteria Open
SUMMARY Cas9 nucleases are the effectors of the class 2 type II CRISPR system in bacteria and function to restrict invading DNA. They can also be used with single guide RNAs (sgRNAs) as antimicrobials and genome engineering tools in bacter…
View article: Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2
Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2 Open
In high-throughput sequencing (HTS) studies, sample-to-sample variation in sequencing depth is driven by technical factors, and not by variation in the scale (size) of the biological system. Typically a statistical normalization removes un…
View article: Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction
Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction Open
The Cas9 enzyme along with a single guide RNA molecule is a modular tool for genetic engineering and has shown effectiveness as a species-specific anti-microbial. The ability to accurately predict on-target cleavage is critical as activity…
View article: Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization
Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization Open
View article: The impact of progressive chronic kidney disease on hepatic drug metabolism
The impact of progressive chronic kidney disease on hepatic drug metabolism Open
Nonrenal clearance pathways such as drug metabolism are decreased in severe chronic kidney disease (CKD). The impact of progression of CKD on hepatic drug metabolism is unknown. We characterized the effect of progressive CKD on hepatic cyt…
View article: Uropygial gland microbiota of nearctic−neotropical migrants vary with season and migration distance
Uropygial gland microbiota of nearctic−neotropical migrants vary with season and migration distance Open
Symbiotic microbiota are important drivers of host behaviour, health, and fitness. While most studies focus on humans, model organisms, and domestic or economically important species, research investigating the role of host microbiota in w…
View article: Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies
Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies Open
View article: Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies
Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies Open
Background: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and …
View article: Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis
Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis Open
Though statistical normalizations are often used in differential abundance or differential expression analysis to address sample-to-sample variation in sequencing depth, we offer a better alternative. These normalizations often make strong…
View article: <i>De Novo</i> Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials
<i>De Novo</i> Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials Open
Metagenomic sequences represent an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents. However, unlocking the functional potential of …
View article: Multi-site microbiota alteration is a hallmark of kidney stone formation
Multi-site microbiota alteration is a hallmark of kidney stone formation Open
Background Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the…
View article: Explicit Scale Simulation for analysis of RNA-sequencing with ALDEx2
Explicit Scale Simulation for analysis of RNA-sequencing with ALDEx2 Open
In high-throughput sequencing (HTS) studies, sample-to-sample variation in sequencing depth is driven by technical factors, and not by variation in the scale (e.g., total size, microbial load, or total mRNA expression) of the underlying bi…
View article: A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets
A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets Open
The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models struggl…
View article: amIcompositional: Simple Tests for Compositional Behaviour of High Throughput Data with Common Transformations
amIcompositional: Simple Tests for Compositional Behaviour of High Throughput Data with Common Transformations Open
Compositional approaches are beginning to permeate high throughput biomedical sciences in the areas of microbiome, genomics, transcriptomics and proteomics. Yet non-compositional approaches are still commonly observed. Non-compositional ap…
View article: <i>De novo</i>synthesis of a conjugative system from human gut metagenomic data for targeted delivery of Cas9 antimicrobials
<i>De novo</i>synthesis of a conjugative system from human gut metagenomic data for targeted delivery of Cas9 antimicrobials Open
Metagenomic sequence represents an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents. However, unlocking the functional potential of …
View article: Symbiotic microbiota vary with breeding group membership in a highly social joint-nesting bird
Symbiotic microbiota vary with breeding group membership in a highly social joint-nesting bird Open
Symbiotic microbes affect the health, fitness, and behavior of their animal hosts, and can even affect the behavior of non-hosts. Living in groups presents numerous benefits and challenges to social animals, including exposure to symbiotic…
View article: Annotating Metagenomically Assembled Bacteriophage from a Unique Ecological System using Protein Structure Prediction and Structure Homology Search
Annotating Metagenomically Assembled Bacteriophage from a Unique Ecological System using Protein Structure Prediction and Structure Homology Search Open
Emergent long read sequencing technologies such as Oxford’s Nanopore platform are invaluable in constructing high quality and complete genomes from a metagenome, and are needed investigate unique ecosystems on a genetic level. However, gen…
View article: A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets
A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets Open
The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models poorly …
View article: Metabolically-targeted dCas9 expression in bacteria
Metabolically-targeted dCas9 expression in bacteria Open
The ability to restrict gene expression to a relevant bacterial species in a complex microbiome is an unsolved problem. In the context of the human microbiome, one desirable target metabolic activity are glucuronide-utilization enzymes (GU…
View article: Uropygial gland microbiota differ between free-living and captive songbirds
Uropygial gland microbiota differ between free-living and captive songbirds Open
View article: Telomere-to-telomere genome assembly of <i>Phaeodactylum tricornutum</i>
Telomere-to-telomere genome assembly of <i>Phaeodactylum tricornutum</i> Open
Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a c…
View article: Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics
Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics Open
View article: Identification of type IV conjugative systems that are systematically excluded from metagenomic bins
Identification of type IV conjugative systems that are systematically excluded from metagenomic bins Open
BackgroundConjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identificati…
View article: Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi
Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi Open
Fungi are nature's recyclers, allowing for ecological nutrient cycling and, in turn, the continuation of life on Earth. Some fungi inhabit the human microbiome where they can provide health benefits, while others are opportunistic pathogen…
View article: Preen gland microbiota covary with major histocompatibility complex genotype in a songbird
Preen gland microbiota covary with major histocompatibility complex genotype in a songbird Open
Pathogen-mediated selection at the major histocompatibility complex (MHC) is thought to promote MHC-based mate choice in vertebrates. Mounting evidence implicates odour in conveying MHC genotype, but the underlying mechanisms remain uncert…
View article: MP07-12 REVISITING THE ROLE OF <i>OXALOBACTER FORMIGENES</i> IN STONE FORMATION: A DEEP DIVE INTO THE MICROBIOME AT MULTIPLE BODY SITES
MP07-12 REVISITING THE ROLE OF <i>OXALOBACTER FORMIGENES</i> IN STONE FORMATION: A DEEP DIVE INTO THE MICROBIOME AT MULTIPLE BODY SITES Open
You have accessJournal of UrologyStone Disease: Basic Research & Pathophysiology (MP07)1 Sep 2021MP07-12 REVISITING THE ROLE OF OXALOBACTER FORMIGENES IN STONE FORMATION: A DEEP DIVE INTO THE MICROBIOME AT MULTIPLE BODY SITES Kait Al, Benj…
View article: Separation of Cohorts on the Basis of Bacterial Type IV Conjugation Systems Identified From Metagenomic Assemblies
Separation of Cohorts on the Basis of Bacterial Type IV Conjugation Systems Identified From Metagenomic Assemblies Open
BackgroundConjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identificati…