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Article
Open AccessAssociations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults
Population-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the consumption of plant-based foods (vegetables, potatoes, fruits, cere...
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Article
Open AccessIntegration of polygenic and gut metagenomic risk prediction for common diseases
Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follo...
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Article
Author Correction: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
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Article
Open AccessAssessing and removing the effect of unwanted technical variations in microbiome data
Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown sour...
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Article
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single larg...
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Article
Open AccessTrycycler: consensus long-read assemblies for bacterial genomes
While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from m...
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Article
Open AccessAuthor Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli
A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22238-5
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Article
Open AccessGenome evolution and the emergence of pathogenicity in avian Escherichia coli
Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat ...
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Article
Open AccessDisease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis
Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differen...
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Article
Open AccessRuminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015
Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Ty** (MLST) data, such studies have identified chicken as a major source of C. j...
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Article
Open AccessMolecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease
Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated ...
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Article
Open AccessGenomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter
Horizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization...
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Article
Open AccessGenomic variations leading to alterations in cell morphology of Campylobacter spp
Campylobacter jejuni, the most common cause of bacterial diarrhoeal disease, is normally helical. However, it can also adopt straight rod, elongated helical and coccoid forms. Studying how helical morphology is g...
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Article
Open AccessImpact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli
Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. Th...
