Johannes Bj{\"o}rk

Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs.
@quadraminstitute.bsky.social

rdcu.be/eMmcT

Distinguishing diet- and microbe-derived metabolites in the human gut - Microbiome 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...

Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....

Using cross-species co-expression to predict metabolic interactions in microbiomes 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...

New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...

Synergy between Enterobacteriaceae and dietary components shapes the competition between the dominant anaerobes of the human gut 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 ...

www.biorxiv.org/content/10.1...

#microsky #microbiome

A defined microbial community reproduces attributes of fine flavour chocolate fermentation - Nature Microbiology 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...

Cool application of microbiome in food science

Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters!

www.nature.com/articles/s41...

PHLAME calls strains at multiple levels of phylogenetic resolution, including the lineage leve.

Evan benchmarked PHLAME rigorously, including on both simulated data and samples from which we have both isolates and metagenomes.

The disciplinary matrix of holobiont biology Uniting life’s seen and unseen realms guides a conceptual advance in research

Microbiomes are the foundation of the biosphere. Hosts such as humans, bees, and plants have never been just hosts. They are complex units of biological organization upon which various forces act to shape composition, form, and function. www.science.org/doi/10.1126/...

PhD position - bioinformatica / microbioom - Werkenbijumcg.nl - UMCG DXP 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.

Come and join us at the Groningen Microbiome Hub! 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.
bit.ly/4fBt38H

Wow! 🤩🤩🤯
"We demonstrate that a single #tree hosts approximately one trillion bacteria in its woody tissues, with microbial communities distinctly partitioned between heartwood and sapwood, each maintaining unique #microbiomes with minimal similarity to other plant tissues or ecosystem components."

A misplaced microbiome - Nature Reviews Microbiology 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...

www.nature.com/articles/s41...

Controlled colonization of the human gut with a genetically engineered microbial therapeutic 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...

www.science.org/doi/10.1126/...

Non-antibiotics disrupt colonization resistance against enteropathogens - Nature 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.

www.nature.com/articles/s41...

Antimicrobial resistance ( #AMR ) is a silent pandemic that has been attributed to over a million deaths per year worldwide. Socio-demographic factors contribute to the emergence and spread of AMR.🧵

Multi-omics time-series analysis in microbiome research: a systematic review www.biorxiv.org/content/10.1... #jcampubs

Mapping pesticide-induced metabolic alterations in human gut bacteria - Nature Communications 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...

🦠 Pesticides alter your gut & your health

A new study maps how pesticides disrupt gut bacteria, changing hundreds of metabolites & triggering inflammation through lipid metabolism.

🔗 www.nature.com/articles/s41...

#SciComm #Microbiome 🧪 #GutHealth

Intraspecies warfare restricts strain coexistence in human skin microbiomes - Nature Microbiology 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.

🚨Out now!

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 @contaminatedsci.bsky.social @mancusosci.bsky.social #MicrobiomeSky

www.nature.com/articles/s41...

read here: rdcu.be/et7VP

Why don’t people who live together have the same strains of microbes? Tami Lieberman (@contaminatedsci.bsky.social) and I put forward one underexplored reason in our new preprint:
Intraspecies warfare restricts strain coexistence in human skin microbiomes

Thank you for inviting me to the 11th edition of the Barcelona debates on the human microbiome. It was a great meeting! Always nice to be back in Barcelona! Moltes gràcies!

Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model 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...

Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI
doi.org/10.1080/1949...

Figure on how the use of antibiotics and prebiotics modulates gut microbial composition and affects similar mechanisms in microbial function, although in opposite directions.

In this Review, Ellen Blaak and colleagues discuss the effect of antibiotic-induced perturbations of the gut #microbiome on host #metabolic health (£) bit.ly/3TpFUjQ #EndoSky #Microsky

Single microorganism RNA sequencing of microbiomes using smRandom-Seq - Nature Protocols 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…

Single microorganism RNA sequencing of microbiomes using smRandom-Seq. #RNAseq #SingleMicrobeSequencing #RNAseq @natprot.nature.com‬ 🧬
www.nature.com/articles/s41...

The gut microbiome in cancer immunotherapy

The gut microbiome as a target in cancer immunotherapy: opportunities and challenges for drug development www.nature.com/articles/s41...
rdcu.be/eo6l2

This new Review highlights key advances in clinical microbiome characterization and their implications for immunotherapy #ASCO2025

Genomics of host–microbiome interactions in humans - Nature Reviews Genetics 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.

A new review suggests that genetic mechanisms driving host– #microbiome interactions will ultimately contribute to the development of personalized medicine and targeted therapies @natgenet.nature.com www.nature.com/articles/s41...

You can do it! 💪

"The Microbiome for Clinicians" a new, open-access review of progress, limitations, and next steps
@cellpress.bsky.social
www.cell.com/cell/fulltex...

Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia 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,...

Excited to share our new paper! We show how Bilophila wadsworthia uses clever metabolic tricks to thrive in the gut — with links to high-fat diet🦠🔬
📖 rdcu.be/eoI4o
Published at @natcomms.nature.com with @springernature.com
#Microbiome #GutHealth #Bilophila

Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes - Nature Communications 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.

Genetic compatibility and environmental co-occurrence drive the dissemination of #AntibioticResistance genes

Co-occurrence of bacteria in the human #microbiome and #wastewater contributes to gene transfer

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

🧫 Not all gut microbes play well with others.

People with inflammatory bowel diseases tend to have more self-sufficient microbes—the kind that survive alone, not in teams. This suggests that gut problems might change the microbiome, not be caused by it.

Secretory IgM regulates gut microbiota homeostasis and metabolism - Nature Microbiology Rainbow trout with depleted secretory IgM reveal interesting insights into the elusive role of this immunoglobulin in maintaining gut microbiota.

www.nature.com/articles/s41...

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution - Nature Biotechnology The evolution of microbial strains is revealed by analyzing structural variation.

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution

@natbiotech.nature.com from @microbiome.bsky.social

www.nature.com/articles/s41...