Filtration-Based Rapid ECM-Hydrogel Elimination Enables Robust MALDI MSI of Intestinal Organoids

The rapid development of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) offers a powerful approach for the 2D metabolic profiling of intestinal organoids. However, i...

pubs.acs.org

A division of labor controls the degradation of fucoidans in the ocean

Fucoidans—complex polysaccharides produced by brown algae and diatoms—contribute to long-term carbon sequestration due to their resistance to microbial degradation[1][1],[2][2]. While individual micro...

biorxiv.org

The role of Akkermansia muciniphila sulfatases in colonic mucin utilisation

Akkermansia muciniphila , an obligate mucin degrader, is a major member of the human colonic microbiota and has been associated positive health outcomes. Mucins are complex glycoproteins that contain ...

biorxiv.org

Relational Graph Convolutional Network for Robust Mass Spectrum Classification

Supervised machine learning methods have shown impressive performance in interpreting mass signals and automatically segmenting spatially meaningful regions in Mass Spectrometry Imaging (MSI). Such se...

pubs.acs.org

Using bioinformatics for identifying and plugging metabolic pathway holes | PNAS

Using bioinformatics for identifying and plugging metabolic pathway holes

pnas.org

Discovery of a widespread chemical signalling pathway in the Bacteroidota - Nature

The N-acyl-cyclolysine system regulates the expression of co-localized operons encoding diverse secreted molecules in Bacteroidota.

nature.com

Futile lipid cycling: from biochemistry to physiology - Nature Metabolism

Sharma et al. review the regulation and biological functions of apparently ‘futile’ dynamic lipid cycle in regulating whole-body metabolic homeostasis.

bit.ly

Polypeptides synthesized by common bacteria in the human gut improve rodent metabolism - Nature Microbiology

Two polypeptides synthesized by common bacterial strains in human gut microbiota lower body fat and blood glucose and increase bone density, improving the metabolism of rodents.

nature.com

Oligosaccharide Elicitors in Plant Immunity: Molecular Mechanisms and Disease Resistance Strategies

Short Summary: This review examines how oligosaccharide elicitors from pathogens and plants activate immune responses through membrane receptors, detailing their types, functions, and signaling pathwa...

cell.com

Identification of gut bacteria reductases that biotransform steroid hormones - Nature Communications

Here, the authors identify and characterize three gut bacterial enzyme families that metabolize endogenous and synthetic steroid hormones, showing to act on diverse substrates, to exhibit gene fusions...

nature.com

Frontpage - Global Microbiome Conservancy

Advancing Microbiome Science Equitably and Ethically Exploring the Microbiome We aim to advance our knowledge of the human microbiome and boost global research capacity. By curating and sharing a high...

microbiomeconservancy.org

De Novo Glycan Annotation of Mass Spectrometry Data

Carbohydrates are fundamental molecules of life that are involved in virtually all biological processes. The chemical diversity of glycans─carbohydrate chains─enables diverse functions but also challe...

pubs.acs.org

Deciphering microbial spatial organization: insights from synthetic and engineered communities

Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between community members, initial growth condition or environmental factors. Under- standing the mechanisms that drive these spatial patterns is essential for uncovering fundamental principles of microbial ecology and for developing applications. Using genetic engineering and synthetic microbial communities allows us to decipher how specific parameters influence spatial organization. In this review, we highlight recent studies that leverage synthetic microbial communities to deepen our understanding of microbial spatial ecology. We begin by exploring how initial conditions, such as cell density and relative species abundance, influence spatial organization. We then focus on studies that examine the role of individ- ual microbial traits, such as cell shape and motility. Next, we discuss the impact of contact-dependent and long-range interactions, including metabolite exchange and toxin release. Furthermore, we highlight the in- fluence of environmental factors on spatial dynamics. Finally, we address the current limitations of synthetic approaches and propose future directions to bridge the gap between engineered and natural systems.

academic.oup.com

From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics | Molecular Systems Biology

EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.

doi.org

Coexistence ecology of pathogen-inhibiting microbes in the phytobiome

Certain microbes have considerable potential as biocontrol agents against various pathogens, but they coexist with other microbial species in complex networks of interactions that influence their function in a host-dependent manner. These interactions and underlying mechanisms are still largely unknown. In this review we focus on Pseudomonas, a versatile genus of bacteria with adaptable physiological and metabolic traits, functioning as both symbionts and pathogens. We review the direct antagonism pathways Pseudomonas uses to inhibit different pathotypes and its role in indirectly inducing systemic defense responses in plants. We provide insights into bacterial coexistence and interactions in host plant–microbe and microbe–microbe relationships, considering pairwise and community dynamics. Understanding these interactions will help optimize synthetic communities and improve practices for sustainable agriculture.

dlvr.it

Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in C. elegans - Nature Communications

Here, Peters et al. report that Pseudomonas fluorescens protects Caenorhabditis elegans against pathogen infection via polyketide synthase-derived sphingolipids, uncovering a non-canonical bacterial s...

doi.org

Microbial Interactions – an alternative taxonomy

Is it mostly Darwin or Marx: ‘survival of the fittest’ vs ‘socialist cooperation’

open.substack.com

Plant Root Exudates: Advances in belowground signaling networks, resilience, and ecosystem functioning for sustainable agriculture

• Plant root exudates characteristically orchestrate diverse ecological interactions on a multi-kingdom scale ranging from microbes to neighboring plants • RE-induced direct and indirect biogeochemical cycling of belowground resources offers a robust tool to promote sustainable cultivation with limited dependence on chemical inputs • Root exudates-mediated interactions exhibit critical implications in modern agricultural settings to design cropping patterns and combinations, diagnostics, plant health monitoring, and highly precise decision making • Despite several benefits of REs, and strong agro-ecological implications, dearth areas exist concerning the composition, mechanistic interactions, and environmental influence; addressing the same will allow leveraging positive societal impacts

sciencedirect.com

PostDoc position (m/f/d) in intestinal metabolomics in health and disease bei Universitätsklinikum Schleswig-Holstein

Jobsuche der Bundesagentur für Arbeit. Hier Stellensuche nach neusten Jobs oder Ausbildungsplätzen starten in einer der größten Jobbörsen Deutschlands.

arbeitsagentur.de

Kiel University in the Excellence Strategy: Success for the two Kiel clusters PMI and ROOTS

The German Research Foundation announced which collaborative research projects will receive funding for the next seven years as Clusters of Excellence.

uni-kiel.de

Spatially structured bacterial interactions alter algal carbon flow to bacteria

academic.oup.com

Cross-feeding creates tipping points in microbiome diversity | PNAS

A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the interactions among their many fun...

pnas.org