Vincent Somerville
YOU?
Author Swipe
View article: ReCycled: A Tool to Reset the Start of Circular Bacterial Chromosomes
ReCycled: A Tool to Reset the Start of Circular Bacterial Chromosomes Open
Summary (two sentences) For many publicly available bacterial genomes the chromosome start is not set at the replication initiation protein. This is a burden for comparative genomics studies as the synteny between such genomes cannot readi…
View article: Strain-level and phenotypic stability contrasts with plasmid and phage variability in water kefir communities
Strain-level and phenotypic stability contrasts with plasmid and phage variability in water kefir communities Open
Microbial communities can change in response to top-down factors, such as phages, and bottom-up factors, such as nutrient availability. Previous studies have successfully investigated bacterial species-level dynamics, but diversity and int…
View article: Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake
Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake Open
Giant viruses (GVs; Nucleocytoviricota) impact the biology and ecology of a wide range of eukaryotic hosts, with implications for global biogeochemical cycles. Here, we investigated GV niche separation in highly stratified Lake A at the no…
View article: Genomic and phenotypic imprints of microbial domestication on cheese starter cultures
Genomic and phenotypic imprints of microbial domestication on cheese starter cultures Open
Domestication – the artificial selection of wild species to obtain variants with traits of human interest– was integral to the rise of civilization. During the neolithic, the oversupply of food enabled by the domestication of crop plants a…
View article: Fermentation Practices Select for Thermostable Endolysins in Phages
Fermentation Practices Select for Thermostable Endolysins in Phages Open
Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular…
View article: Dairy practices select for thermostable endolysins in phages
Dairy practices select for thermostable endolysins in phages Open
Endolysins are phage lytic enzymes that degrade the bacterial cell wall to release phage progeny. We found that the diversity of endolysins is unsuspectedly low and dominated by a single structural type in distinct phages that infect Strep…
View article: Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees
Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees Open
Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found …
View article: Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees
Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees Open
Social bees harbor conserved gut microbiota that may have been acquired in a common ancestor of social bees and subsequently co-diversified with their hosts. However, most of this knowledge is based on studies on the gut microbiota of hone…
View article: Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities Open
Background Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that …
View article: Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities Open
Background Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that …
View article: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities Open
Background Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that …
View article: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities Open
Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such divers…
View article: Additional file 2 of Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Additional file 2 of Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities Open
Additional file 2: Table S2. Sample description of 16S community analysis.
View article: Additional file 1 of Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Additional file 1 of Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities Open
Additional file 1: Table S1. Sample description of shotgun metagenomic samples.
View article: Use and limitations of genome-scale metabolic models in food microbiology
Use and limitations of genome-scale metabolic models in food microbiology Open
Microbes are key to creating safe, edible and enriched fermented food products. This is largely achieved by their metabolism. Thus, the ability to understand the wiring of the complete cellular metabolism is critical to control the ferment…
View article: Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures Open
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly c…
View article: Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures Open
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly c…
View article: Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture
Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture Open
Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbi…
View article: Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture
Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture Open
Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbi…
View article: An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1
An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1 Open
Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associa…
View article: An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in<i>Pseudomonas aeruginosa</i>MPAO1
An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in<i>Pseudomonas aeruginosa</i>MPAO1 Open
Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resi…
View article: Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system Open
Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamen…
View article: Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast <i>Metschnikowia pulcherrima</i>
Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast <i>Metschnikowia pulcherrima</i> Open
Summary Metschnikowia pulcherrima synthesises the pigment pulcherrimin, from cyclodileucine (cyclo(Leu‐Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi. This yeast therefore has great p…
View article: DNA Methylation Patterns in the Round Goby Hypothalamus Support an On-The-Spot Decision Scenario for Territorial Behavior
DNA Methylation Patterns in the Round Goby Hypothalamus Support an On-The-Spot Decision Scenario for Territorial Behavior Open
The question as to how early life experiences are stored on a molecular level and affect traits later in life is highly topical in ecology, medicine, and epigenetics. In this study, we use a fish model to investigate whether DNA methylatio…
View article: Additional file 2: of Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Additional file 2: of Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system Open
Overview of the various metrics employed to evaluate each genome polishing step for NWC_2 using QUAST. (XLSX 15â kb)
View article: Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation
Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation Open
Phosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how co…
View article: DNA methylation patterns in the round goby hypothalamus support an on-the-spot decision scenario for territorial behaviour
DNA methylation patterns in the round goby hypothalamus support an on-the-spot decision scenario for territorial behaviour Open
How early life experiences are stored on a molecular level and affect behavioural phenotypes later in life is not well understood. In fish, reproductive phenotypes are often easily discernible and frequently depend on previous life experie…
View article: Long read-based <i>de novo</i> assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Long read-based <i>de novo</i> assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system Open
Background Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bact…
View article: Species-Specific Root Microbiota Dynamics in Response to Plant-Available Phosphorus
Species-Specific Root Microbiota Dynamics in Response to Plant-Available Phosphorus Open
Summary Phosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However…