Communities of microorganisms (microbiota) are present in all habitats on Earth and are
relevant for agriculture, health, and climate. Deciphering the mechanisms that determine …

Meta'omic data on microbial diversity and function accrue exponentially in public
repositories, but derived information is often siloed according to data type, study or sampled …

Profiling metagenomes against databases allows for the detection and quantification of
microorganisms, even at low abundances where assembly is not possible. We introduce …

Accurate species identification and abundance estimation are critical for the interpretation of
whole metagenome sequencing (WMS) data. Yet, existing metagenomic profilers suffer from …

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing
features. However, many bacteria carry" cryptic" plasmids that do not confer clear beneficial …

The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and
Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic …

Determining the taxonomic composition (taxonomic profiling) is a fundamental task in
studying environmental and host-associated microbial communities. However, genome …

Abstract The NEREA (Naples Ecological REsearch for Augmented observatories) initiative
aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to …

Motivation The growing number of microbial reference genomes enables the improvement
of metagenomic profiling accuracy but also imposes greater requirements on the indexing …

Biofiltration is used worldwide to provide safe potable water due to its low energy demand
and excellent treatment performance. For instance, in Denmark, over 95% of drinking water …