Jakob Russel
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View article: Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts
Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts Open
Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here,…
View article: CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome
CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome Open
Introduction Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive t…
View article: CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome
CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome Open
Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed …
View article: Insights into the ecology of the infant gut plasmidome
Insights into the ecology of the infant gut plasmidome Open
Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate the gut microbi…
View article: MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies
MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies Open
Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with fu…
View article: Prophages in the infant gut are induced and modulate the functionality of their hosts
Prophages in the infant gut are induced and modulate the functionality of their hosts Open
Background Gut microbiome (GM) composition and function plays a pivotal role in human health and disease. The gut virome is increasingly being recognised as an important GM player and has been implicated in disease states. However, these s…
View article: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition
Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition Open
Background In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence gen…
View article: Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth
Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth Open
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities esta…
View article: Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults
Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults Open
Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic …
View article: Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs
Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs Open
Many bacteria use CRISPR–Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids 1 . In turn, these invasive elements have evolved anti-CRISPR proteins to block host immunity 2,3 . Here we unveil a distinct type …
View article: Fungi and bacteria in the beds of rural and urban infants correlate with later risk of atopic diseases
Fungi and bacteria in the beds of rural and urban infants correlate with later risk of atopic diseases Open
Introduction Rural children have a lower risk of asthma and atopic diseases than urban children. However, whether indoor microbiota in non‐farming rural homes provides protection is unclear. Methods Here, we examine if microbes in the beds…
View article: MAGinator enables strain-level quantification of<i>de novo</i>MAGs
MAGinator enables strain-level quantification of<i>de novo</i>MAGs Open
Motivation Metagenomic sequencing has provided great advantages in the characterization of microbiomes, but currently available analysis tools lack the ability to combine strain-level taxonomic resolution and abundance estimation with func…
View article: Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers<i>in trans</i>
Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers<i>in trans</i> Open
Type IV-A CRISPR-Cas systems are primarily encoded on plasmids and form multi-subunit ribonucleoprotein complexes with unknown biological functions. In contrast to other CRISPR-Cas types, they lack the archetypical CRISPR acquisition modul…
View article: The role of plasmids in the gut microbiome during the first year of life
The role of plasmids in the gut microbiome during the first year of life Open
Plasmids are extrachromosomal self-replicating genetic elements that play a key role in bacterial ecology and evolution by shuttling diverse host-beneficial traits between bacteria. However, our understanding of plasmids is still limited, …
View article: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition
Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition Open
Even in the absence of antibiotic exposure, the gut microbiome of infants has been shown to contain numerous antibiotic resistance genes (ARGs), but the mechanism for this remains unclear. In environmental bacteria, the selective advantage…
View article: The developing airway and gut microbiota in early life is influenced by age of older siblings
The developing airway and gut microbiota in early life is influenced by age of older siblings Open
Background Growing up with siblings has been linked to numerous health outcomes and is also an important determinant for the developing microbiota. Nonetheless, research into the role of having siblings on the developing microbiota has mai…
View article: IncHI1A plasmids potentially facilitate horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage
IncHI1A plasmids potentially facilitate horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage Open
Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic r…
View article: Unexpected diversity among small-scale sample replicates of defined plant root compartments
Unexpected diversity among small-scale sample replicates of defined plant root compartments Open
Community assembly processes determine patterns of species distribution and abundance which are central to the ecology of microbiomes. When studying plant root microbiome assembly, it is typical to sample at the whole plant root system sca…
View article: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids Open
Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comp…
View article: IncHI1A plasmids potentially facilitate a horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage
IncHI1A plasmids potentially facilitate a horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage Open
Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic r…
View article: Plasmid Loss images and scripts
Plasmid Loss images and scripts Open
Image dataset and their corresponding R scripts.
View article: Plasmid Loss images and scripts
Plasmid Loss images and scripts Open
Image dataset and their corresponding R scripts.
View article: Plasmid Loss data and scripts
Plasmid Loss data and scripts Open
Plasmid loss data and corresponding scripts.
View article: Plasmid Loss data and scripts
Plasmid Loss data and scripts Open
Plasmid loss data and corresponding scripts.
View article: Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts
Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts Open
Background Bacteriophages are the most abundant biological entity on the planet, and are key components of any ecosystem they are present in. The gut virome is increasingly being implicated in disease states although these studies largely …