Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

Background Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbio...

In microbial ecosystems, metabolic interactions are key determinants of species’ relative abundance and activity. Given the immense number of possible interactions in microbial communities, their expe...

The human gut microbiota is frequently dominated by the Bacteroidota phylum, with Bacteroidaceae and Prevotellaceae families prevailing in modern and traditional lifestyles, respectively. While these ...

An in-depth microbiological and metagenomic analysis of Colombian farm and fermentation facilities resulted in the design of a defined microbial community that can reproduce the flavour of fine chocol...

Uniting life’s seen and unseen realms guides a conceptual advance in research

We are seeking a motivated and enthusiastic PhD student with a focus on computational biology, bioinformatics, and microbiome analysis to join a fully funded project on the role of the gut microbiome in cancer and cancer immunotherapy.

This study shows that regional mismatches between transplanted microbiota and the host gut environment alter the metabolic and immune states of host tissues as well as the composition of regional micr...

Precision microbiome programming for therapeutic applications is limited by challenges in achieving reproducible colonic colonization. Previously, we created an exclusive niche that we used to engraft...

Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of such drugs.

Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. Thus, we performed a systematic literature review on data science methods for longitudinal multi-omics, with a particular focus on microbiome research. ### Competing Interest Statement The authors have declared no competing interest. European Union’s Horizon 2020 research and innovation programme, 952914

Pesticide exposure induces significant alterations in gut bacterial metabolism. Here, the authors perform a multi-omics mapping of pesticide-gut microbiota-metabolite interactions, identifying pestici...

About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota.

Clostridioides difficile infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism – whether infection risk is due...

This Protocol outlines the steps for high-throughput single microorganism isolation and microfluidic droplet-based encapsulation and barcoding to obtain single cell transcriptomes from both cultured…

In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

Nature Communications - Here, the authors show that Bilophila wadsworthia uses bacterial microcompartments and anaerobic respiration of host-derived compounds to thrive in the inflamed gut,...

The dynamics of antimicrobial resistance gene transfer remain unclear. Here, by integrating bacterial genome and metagenome data with machine learning the authors show that genetic incompatibility is a main limiting factor, while co-occurrence of bacteria in the human microbiome and wastewater contributes to gene transfer.

New research suggests that changes in gut microbial diversity are a result of disease, not the cause of it.

Rainbow trout with depleted secretory IgM reveal interesting insights into the elusive role of this immunoglobulin in maintaining gut microbiota.

The evolution of microbial strains is revealed by analyzing structural variation.

There is a large heterogeneity among individuals in their therapeutic responses to the same drug and in the occurrence of adverse events. A key factor increasingly recognized to contribute to this var...

In this Review, Delzenne et al. explore how dietary fibres interact with and modulate the gut microbiota, and discuss their effects on human physiology, particularly in the context of obesity, cardiom...

In this Review, Belzer and colleagues explore the diversity of the gut bacterium Akkermansia muciniphila, its biological functions and interactions with the host, diet and other members of the microbi...

Covering: 1974 to 2024 Human microbiota consist of a diverse array of microorganisms, such as bacteria, Eukarya, archaea, and viruses, which populate various parts of the human body and live in ...

The human intestinal microbiota ferments dietary fibre to short-chain fatty acids, which make an important contribution to host health. In this Review, Mukhopadhya and Louis discuss the luminal microb...

In this study, 19 overweight participants, with or without type 2 diabetes mellitus, underwent 14 days of normal-diet observation followed by 14 days of dietary fiber intervention. Fecal samples and ....

Tryptophan-derived indoles produced by the gut microbiota, particularly indole-3-propionate (IPA), are key compounds associated with gastrointestinal balance and overall health. Reduced levels of I...

Contribute to statdivlab/radEmu development by creating an account on GitHub.

Nearly all humans host Cutibacterium acnes and Staphylococcus epidermidis on their facial skin throughout life. Baker et al. reveal remarkable strain-level dynamism beneath this apparent stability. Sp...

The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

“Paradox of the sub-plankton: Plausible mechanisms and open problems underlying strain-level diversity in microbial communities” by Akshit Goyal* and Griffin Chure*. This work highlights the limitati...

Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure a...

Results of multi-omic profiling of the microbiome and host immunity of individuals treated with VE303 to prevent recurrent Clostridioides difficile infection in the context of a phase 2 trial show rob...