Ivica Letunić

A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases

Kanta Chechi, Rima Chakaroun, Antonis Myridakis, Sofia Kirke Forslund-Startceva et autres

Cardiovascular diseases (CVD) remain a major global health challenge. Early markers of disease initiation and progression are urgently needed. We, and others, have previously shown changes in the gut microbiome in association with metabolic and CVD. Here, we demonstrate that gut microbiome-related …

us, gb, de, se, fr, dk, be, nl, jp, it (code pays fourni par la source)

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes

Anthony Fullam, Ivica Letunić, Oleksandr M. Maistrenko, Alexandre Areias Castro et autres

The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a …

de, au, us, ie, jp (code pays fourni par la source)

SMART v10: three decades of the protein domain annotation resource

Ivica Letunić, Peer Bork

SMART (Simple Modular Architecture Research Tool, https://smart.embl.de) is a web-based platform for identifying and annotating protein domains and analyzing domain architectures. SMART version 10 features manually curated models for over 1300 protein domains. Approaching its 30th anniversary, SMART's user interface has been …

de (code pays fourni par la source)

A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.

Kanta Chechi, Rima Chakaroun, Antonis Myridakis, Sofia Kirke Forslund et autres

gb, de, fr, dk, be, jp, it, se, ca (code pays fourni par la source)

InterPro: the protein sequence classification resource in 2025

Matthias Blum, Antonina E. Andreeva, Laise Cavalcanti Florentino, Sara Chuguransky et autres

InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences into families and predict the presence of domains and significant sites. The InterPro …

gb, de, ch, us, it (code pays fourni par la source)

Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes

Marisa Isabell Keller, Suguru Nishijima, Daniel Podlesny, Chan Yeong Kim et autres

Summary Background Enterotypes describe human fecal microbiomes grouped by similarity into clusters of microbial community composition, often associated with disease, medications, diet, and lifestyle. Numbers and determinants of enterotypes have been derived by diverse frameworks and applied to cohorts that often lack …

de (code pays fourni par la source)

OS-073 Linking gut microbiome enterotypes and dysbiosis to liver disease severity and prognosis

Marisa Isabell Keller, Suguru Nishijima, Daniel Podlesny, Chan Yeong Kim et autres

Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool

Ivica Letunić, Peer Bork

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modernized and completely rewritten user interface, together …

de (code pays fourni par la source)

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

Thomas Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek N Orakov et autres

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 microbial environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived …

de, ch, cn, nl, gb, au (code pays fourni par la source)

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

Petros Andrikopoulos, Judith Aron‐Wisnewsky, Rima Chakaroun, Antonis Myridakis et autres

The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied "explainable" machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in …

us, gb, fr, se, de, dk, be, ca, kr (code pays fourni par la source)

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants

Pamela Ferretti, Jakob Wirbel, Oleksandr M. Maistrenko, Thea Van Rossum et autres

Abstract Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. difficile, in particular in C. difficile infection (CDI) cases, remains poorly characterised. To investigate the gut microbiome composition in CDI patients, we analysed 534 …

de, nl, kr (code pays fourni par la source)

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants

Pamela Ferretti, Jakob Wirbel, Oleksandr M. Maistrenko, Thea Van Rossum et autres

Abstract Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. difficile, in particular in C. difficile infection (CDI) cases, remains poorly characterised. To investigate the gut microbiome composition in CDI patients, we analysed 534 …

de, nl, kr (code pays fourni par la source)