Gregory B Gloor

The University of Western Ontario | UWO · Department of Biochemistry

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 completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomer...

The worldwide COVID-19 pandemic caused by the SARS-CoV-2 betacoronavirus has highlighted the need for a synthetic biology approach to create reliable and scalable sources of viral antigen for uses in diagnostics, therapeutics and basic biomedical research. Here, we adapt plasmid-based systems in the eukaryotic microalgae Phaeodactylum tricornutum t...

Background Conjugation 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 identification of these systems in metagenomic samples clinically important. ResultsHere, we outline two related methods t...

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 uncertain. MHC effects on odour may be mediated by odour-producing symbiotic microbes whose community structure is sh...

Background Conjugation 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 identification of these systems in metagenomic samples clinically important. ResultsHere, we outline two distinct methods...

High-throughput sequencing datasets comprise millions of reads of genomic data and can be modelled as count compositions. These data are used for transcription profiles, microbial diversity, or relative cellular abundance in culture. The data are sparse and high dimensional. Moreover, they are often unbalanced, i.e. there is often systematic variat...

1. Metabolites produced by symbiotic microbes can affect the odour of their hosts, providing olfactory cues of identity, sex, or other salient features. 2. In birds, preen oil is a major source of body odour that differs between populations and sexes. We hypothesized that population and sex differences in preen oil chemistry reflect underlying diff...

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 completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomer...

Conjugation 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 identification of these systems in metagenomic samples clinically important. Here, we outline two distinct methods to identify conjug...

Pannexin 1 (PANX1) is a glycoprotein that forms large pore channels capable of passing ions and metabolites such as ATP for cellular communication. PANX1 has been implicated in many diseases including breast cancer and melanoma, where inhibition or deletion of PANX1 reduced the tumorigenic and metastatic properties of the cancer cells. We interroga...

Ureteral stents are commonly used to prevent urinary obstruction but can become colonized by bacteria and encrusted, leading to clinical complications. Despite recent discovery and characterization of the healthy urinary microbiota, stent-associated bacteria and their impact on encrustation are largely underexplored. We profile the microbiota of pa...

The assembly and binning of metagenomically-assembled genomes (MAGs) using Illumina sequencing has improved the genomic characterization of unculturable communities. However, short-read-only metagenomic assemblies rarely result in completed genomes because of the difficulty assembling repetitive regions. Here, we present a strategy to complete and...

Spontaneous preterm birth is associated with vaginal microbial dysbiosis. As certain strains of lactobacilli help restore homeostasis in non-pregnant women, the goal was to determine the effect of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 administered orally, twice daily for 12 weeks on the vaginal microbiota, cytokines and chemo...

Background: Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each uses a unique set of statistical assumptions to solve problems on a case-by-case basis. These software packages are typically diff...

The major histocompatibility complex (MHC) is the most polymorphic region of the vertebrate genome. Individuals with more MHC alleles can respond to a broader suite of pathogens, suggesting that selection should favour the ability to assess the MHC genotype of potential mates. Indeed, MHC-based mate choice, particularly preferences for MHC-dissimil...

Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not...

The selective regulation of bacteria in complex microbial populations is key to controlling pathogenic bacteria. CRISPR nucleases can be programmed to kill bacteria, but require an efficient and broad-host range delivery system to be effective. Here, using an Escherichia coli and Salmonella enterica co-culture system, we show that plasmids based on...

Background Next-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. A cornerstone of NGS is the quantification of RNA or DNA presence as counts. However, these counts are not counts per se: their magnitude is determined arbitrarily by the seque...

Transfer RNAs are required to translate genetic information into proteins as well as regulate other cellular processes. Nucleotide changes in tRNAs can result in loss or gain of function that impact the composition and fidelity of the proteome. Despite links between tRNA variation and disease, the importance of cytoplasmic tRNA variation has been o...

Background: A normally developed placenta is integral to a successful pregnancy. Preeclampsia (PE) and intrauterine growth restriction (IUGR) are two common pregnancy related complications that maybe a result of abnormal placental development. Placental microRNAs (miRNAs) have been investigated as potential biomarkers for these complications, as t...

The human gut microbiota composition is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological role. Despite extensive culturing and sequencing efforts, the complete bacterial repertoire of the human gut microbiota remains undefined. Here we identify 1,952 uncultured candidate bacterial sp...

Purpose of review: Not all of the risk of cardiovascular disease can be explained by diet and genetics, and the human microbiome, which lies at the interface of these two factors, may help explain some of the unaccounted risk. This review examines some of the well established links between the microbiome and cardiovascular health, and proposes rel...

The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform futur...

Nonrenal clearance pathways such as drug metabolism are decreased in chronic kidney disease (CKD). Although the mechanism remains elusive, uremic toxin retention and an altered gut microbiota are suspected to influence cytochrome P450s (CYPs) contributing to the unpredictable pharmacokinetics in patients with CKD. We characterized dysbiosis and ure...

The molecular mechanisms of translation are highly conserved in all organisms indicative of a single evolutionary origin. This includes the molecular interactions of tRNAs with their cognate aminoacyl-tRNA synthetase, which must be precise to ensure the specificity of the process. For many tRNAs, the anticodon is a major component of the specificit...

Next-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. Today, NGS is routinely used to understand many important topics in biology from human disease to microorganism diversity. A cornerstone of NGS is the quantification of RNA or DNA presenc...

LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease ac...

LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease ac...

Motivation: P values derived from the null hypothesis significance testing framework are strongly affected by sample size, and are known to be irreproducible in underpowered studies, yet no suitable replacement has been proposed. Results: Here we present implementations of non-parametric standardized median effect size estimates, dNEF, for high-thr...

Objective: Toxic metabolites produced by the intestinal microbiome from animal proteins, carnitine (mainly from red meat), or phosphatidylcholine (mainly from egg yolk), have important adverse effects on cardiovascular disease. These are renally eliminated and may be termed gut-derived uremic toxins (GDUT). We hypothesized that even moderate renal...

Background While the global market for probiotics is soon to reach in excess of US$50 billion, the continent of Africa has been largely ignored, despite these products having the ability to reduce the burden of disease and death. Trial design The present randomised, blinded, placebo-controlled clinical trial was undertaken in Rwanda, a country dev...

Metabolic products of the intestinal microbiome such as trimethylamine N-oxide (TMAO) that accumulate in renal failure (gut-derived uremic toxins, GDUTs) affect atherosclerosis and increase cardiovascular risk. We hypothesized that patients on a Mediterranean diet and those consuming lower amounts of dietary precursors would have lower levels of GD...

Lactobacillus represents a versatile bacterial genus, which can adapt to a wide variety of ecological niches, including human body sites such as the intestinal and urogenital tract. In this study, the complete genome sequence of the vaginal probiotic Lactobacillus rhamnosus GR-1 was determined and compared to other L. rhamnosus strains at genomic a...

This work was conducted to characterize the 16S rRNA gene profile of a cohort of patients with traditional risk factors for developing atherosclerosis. The patients in the cohort were divided into two extremes; those predicted to develop extreme atherosclerosis who did not (Protected), and those predicted not to develop atherosclerosis who did (Une...

Background and aims: There is increasing awareness that the intestinal microbiome plays an important role in human health. We investigated its role in the burden of carotid atherosclerosis, measured by ultrasound as total plaque area. Methods: Multiple regression with traditional risk factors was used to identify three phenotypes among 316/3056...

With compositional data ordinary covariation indexes, designed for real random variables, fail to describe dependence. There is a need for compositional alternatives to covariance and correlation. Based on the Euclidean structure of the simplex, called Aitchison geometry, compositional association is identied to a linear restriction of the sample s...

Background: It is increasingly recognized that metabolic products of the intestinal microbiome may have important effects on cardiovascular disease. Methods: We studied dietary intake of precursors and plasma levels of toxic metabolic products of the intestinal microbiome in patients at extremes of carotid plaque burden, defined by residual scores...

The proper analysis of high-throughput sequencing datasets of mixed microbial communities (meta-transcriptomics) is substantially more complex than for datasets composed of single organisms. Adapting commonly used RNA-seq methods to the analysis of meta-transcriptome datasets can be misleading and not use all the available information in a consiste...

Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they hav...

Background: The increasing interest on the impact of the gut microbiota on health and disease has resulted in multiple human microbiome-related studies emerging. However, multiple sampling methods are being used, making cross-comparison of results difficult. To avoid additional clinic visits and increase patient recruitment to these studies, there...

The microbiota of the aged is variously described as being more or less diverse than that of younger cohorts, but the comparison groups used and the definitions of the aged population differ between experiments. The differences are often described by null hypothesis statistical tests, which are notoriously irreproducible when dealing with large mul...

High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent analysis of such data can yield information on tran- scription profiles, microbial diversity, or even relative cel...

Previous animal studies have shown that the administration of probiotic Lactobacillus rhamnosus can provide a protective effect against ischemia/reperfusion and necrotic injury to the intestine, liver, and heart, as well as a therapeutic effect to the outcome of ischemic injury to the heart, including cardiac hypertrophy and heart failure. We hypot...

Background The gastrointestinal tract (GIT) microbiota is essential to metabolic health, and the prevalence of the Western diet (WD) high in fat and sugar is increasing, with evidence highlighting a negative interaction between the GIT and WD, resulting in liver dysfunction. Additionally, an adverse in utero environment such as placental insufficie...

ALDEx2 test heat map OTUs divergent between diet groups by Wilcoxon rank-sum test are shown. Colour corresponds to the log2 of the OTUs’ abundance.

Shannon’s diversity of every sample Output from diversity function in R (Vegan 2.3-2) performed on OTU table.

Scripts utilized to generate figures R scripts are provided here to generate figures and data 1, 2, S2, S3, S4, S5, S6 from the provided OTU table (S1)

OTU table OTUs were filtered to 0.1% in any sample.

Shannon’s diversity index and read counts for sample groups Shannon’s diversity and read counts are not different between birth weight or diet groups.

Compositional biplot The samples are coloured according to diet and birth weight groups. The biplot is drawn to show the relationship between the OTUs [scale = 1].

ALDEx2 table Output from ALDEx2 test for significantly different OTUs between diet groups.

Background: The gastrointestinal tract (GIT) microbiota is essential to metabolic health, and the prevalence of the Western diet (WD) high in fat and sugar is increasing, with evidence highlighting a negative interaction between the GIT and WD resulting in liver dysfunction. Additionally, an adverse in utero environment such as placental insufficie...

Background: The gastrointestinal tract (GIT) microbiota is essential to metabolic health, and the prevalence of the Western diet (WD) high in fat and sugar is increasing, with evidence highlighting a negative interaction between the GIT and WD resulting in liver dysfunction. Additionally, an adverse in utero environment such as placental insufficie...