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Article
Open AccessNutrition or nature: using elementary flux modes to disentangle the complex forces sha** prokaryote pan-genomes
Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this ...
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Article
Open AccessBCG-induced trained immunity enhances acellular pertussis vaccination responses in an explorative randomized clinical trial
Acellular pertussis (aP) booster vaccines are central to pertussis immunization programs, although their effectiveness varies. The Bacille Calmette-Guérin (BCG) vaccine is a prototype inducer of trained immuni...
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Article
Open AccessMetabolic models predict bacterial passengers in colorectal cancer
Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic me...
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Article
Towards predicting the environmental metabolome from metagenomics with a mechanistic model
The environmental metabolome and metabolic potential of microorganisms are dominant and essential factors sha** microbial community composition. Recent advances in genome annotation and systems biology now a...
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Article
Open AccessFrom cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems
Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic...
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Article
Open AccessComparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remar...
