A. Comeau
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Linking microbial taxonomy and function in N and P metabolism: a study of organic amendments in semiarid restored soils Open
Background Arid and semi-arid regions cover approximately 41% of Earth’s surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments a…
JarrVis: Visualising Taxa-function relationships from meta-omic data Open
High-throughput sequencing has necessitated and facilitated the development of various computational tools for dissecting the taxonomic structure and molecular function of microbial communities residing in diverse ecological niches. A wide…
Exploring the long-term impact of organic amendments on restored quarry soil microbial communities by shotgun metagenome sequencing. Open
In quarries, human extractive activities degrade the soil’s physical and chemical qualities, affecting microbial communities. The application of organic amendments is known to improve the soil’s physical, chemical and biochemical propertie…
View article: Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph <i>Candidatus</i> Thalassolituus haligoni
Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph <i>Candidatus</i> Thalassolituus haligoni Open
The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N 2 fixation poses a…
View article: From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools Open
In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxon…
Personalised azithromycin+metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn’s disease (CD): protocol of a pilot study Open
Introduction Early relapse in Crohn’s disease (CD) is associated with a more severe disease course. The microbiome plays a crucial role, yet strategies targeting the microbiome are underrepresented in current guidelines. We hypothesise tha…
Preparing multiplexed 16S/18S/ITS amplicons for the Illumina MiSeq v1 Open
The following detailed protocol is for the generation of paired-end sequencing reads of 16S/18S/ITS PCR amplicons with dual barcodes (i.e.: “indices”) on the Illumina MiSeq machine of length ≈450 bp (ie: 300+300 bp sequencing with ~150 bp …
View article: From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools Open
In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxon…
Preparing multiplexed 16S/18S/ITS amplicon SMRTbell libraries with the Express TPK2.0 for the PacBio Sequel2 v1 Open
The preparation of amplicon libraries using the PacBio Express Template Kit 2.0 (TPK2.0) with fusion primers at the IMR. Based upon PacBio protocol 101-599-700 (Jun.2019).
Preparing Combined Indexed Primer Plates (IDT Standard) for the PacBio Sequel2 - Sequel Dual Indices v1 Open
The preparation of diluted combined (F+R) IDT working primer stocks of PacBio Dual Index primers for use in IMR PCR preps.
Preparing multiplexed WGS/MetaG libraries with the Illumina DNA Prep kit for the Illumina NextSeq or MiSeq v1 Open
The preparation of (meta)genomic libraries using the Illumina Nextera Flex (now "DNA Prep") kit with CD/UDI indices at the IMR. Based upon Illumina protocol 10000000254 16 v10 (Aug.2021).
Preparing multiplexed WGS/MetaG SMRTbell libraries with the Express TPK2.0 for the PacBio Sequel2 v1 Open
The preparation of (meta)genomic libraries using the PacBio Express Template Kit 2.0 (TPK2.0) with the Barcoded Adapter Plate 3.0 at the IMR. Based upon PacBio protocol 101-696-100 (Dec.2019).
Preparing Combined Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - IDT UDIs v1 Open
The preparation of diluted combined (F+R) IDT working primer stocks of Illumina UDI primers for use in IMR PCR preps.
Preparing Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - Nextera Dual Indices v1 Open
The preparation of diluted IDT working primer stocks of Illumina Dual Index primers for use in IMR PCR preps.
View article: Microbiome differential abundance methods produce different results across 38 datasets
Microbiome differential abundance methods produce different results across 38 datasets Open
Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropri…
Characterization of Bacterial Community Dynamics of the Human Mouth Throughout Decomposition via Metagenomic, Metatranscriptomic, and Culturing Techniques Open
The postmortem microbiome has recently moved to the forefront of forensic research, and many studies have focused on the idea that predictable fluctuations in decomposer communities could be used as a “microbial clock” to determine time of…
View article: Microbiome differential abundance methods produce disturbingly different results across 38 datasets
Microbiome differential abundance methods produce disturbingly different results across 38 datasets Open
Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods have been applied for this purpose, which are largely used interchangeably in the literature. Although it has been observed that these to…
Detection of Helicobacter pylori Microevolution and Multiple Infection from Gastric Biopsies by Housekeeping Gene Amplicon Sequencing Open
Despite the great efforts devoted to research on Helicobacter pylori, the prevalence of single-strain infection or H. pylori mixed infection and its implications in the mode of transmission of this bacterium are still controversial. In thi…
Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn’s Disease Open
Background The gut microbiome is extensively involved in induction of remission in pediatric Crohn’s disease (CD) patients by exclusive enteral nutrition (EEN). In this follow-up study of pediatric CD patients undergoing treatment with EEN…
An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa Open
Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational a…
Nitrate Consumers in Arctic Marine Eukaryotic Communities: Comparative Diversities of 18S rRNA, 18S rRNA Genes, and Nitrate Reductase Genes Open
To better understand the diversity of primary producers in the Arctic Ocean, we targeted a nitrogen cycle gene, NR, which is required for phytoplankton to assimilate nitrate into organic forms of nitrogen macromolecules. We compared this t…
View article: Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean
Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean Open
The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribut…
The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome Open
Chemerin is an adipocyte derived signalling molecule (adipokine) that serves as a ligand activator of Chemokine-like receptor 1(CMKLR1). Chemerin/CMKLR1 signalling is well established to regulate fundamental processes in metabolism and inf…
Peer Review #3 of "The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome (v0.1)" Open
Chemerin is an adipocyte derived signalling molecule (adipokine) that serves as a ligand activator of Chemokine-like receptor 1(CMKLR1).Chemerin/CMKLR1 signalling is well established to regulate fundamental processes in metabolism and infl…
View article: Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches Open
High-depth sequencing of universal marker genes such as the 16S rRNA gene is a common strategy to profile microbial communities. Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity thre…
View article: Peer Review #1 of "Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches (v0.2)"
Peer Review #1 of "Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches (v0.2)" Open
High-depth sequencing of universal marker genes such as the 16S rRNA gene are a common strategy to profile microbial communities.Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity thre…
Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production Open
Mice are not natural hosts for influenza A viruses (IAVs), but they are useful models for studying antiviral immune responses and pathogenesis. Serial passage of IAV in mice invariably causes the emergence of adaptive mutations and increas…