Growth-density inversion in Escherichia coli reveals superlinear, not sublinear, density dependence

Sublinear density dependence has been widely reported empirically, but this is at odds with resource competition theory. This study uses a tightly controlled test in a microbial model system to reveal...

doi.org

Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene–host associations in complex communities - Genome Biology

Background Antibiotic resistance genes (ARGs) circulating among clinically relevant bacteria pose serious challenges to public health. Given the ancient and environmental bacterial origins of ARGs, a better understanding of the carriers of ARGs beyond the clinically most relevant species is urgently needed for longer-term resistance monitoring and intervention measures. While the risks of emerging ARGs from environmental sources have been recognized, the identification bottlenecks stem from the limitations of shotgun metagenomic sequencing and bioinformatic methods. Results We use long-read metagenomic sequencing and bacteria-specific methylation profiles to re-establish the links between established (well-described) or latent (absent in databases) ARGs and their bacterial and genetic contexts in wastewater. We analyze base modification data produced by PacBio SMRT sequencing using an in-house pipeline utilizing position weight matrices and UMAP visualizations, which we validate by a synthetic community with known bacterial composition. Our analysis reveals several previously unreported ARGs and ARG-host linkages in wastewater. For instance, we find that Arcobacter, a key wastewater associated taxon and emerging pathogen, carries a latent beta-lactamase gene with high predicted mobility potential. Of the other understudied beta-lactamases, we describe blaMCA within pdif-modules across highly varying contexts suggesting its recent acquisition events. Additionally, we uncover the wastewater resident taxa mediated carriage of clinically important ARGs. Conclusions By linking ARGs to their wider genetic contexts and hosts, our findings shed light on the previously unrecognized carriers of resistance genes in wastewater. The presented approach provides a valuable methodology for early identification of newly arising ARGs and their hosts.

doi.org

Marine Microbiologist Farooq Azam Receives Kyoto Prize

University of California San Diego marine microbiologist and Distinguished Professor Emeritus Farooq Azam has been selected as the 2026 Kyoto Prize laureate in Basic Sciences. Azam is widely recognize...

bit.ly

biorxiv.org

After USDA request, Indiana plant biologist locked out of lab by school

Move comes after Roger Innes complained about the government’s prosecution of Chinese postdocs

scim.ag

The Beautiful Intelligence of Bacteria and Other Microbes

Bacterial biofilms and slime molds are more than crude patches of goo. Detailed time-lapse microscopy reveals how they sense and explore their surroundings, communicate with their neighbors and…

quantamagazine.org

Predator-driven microbial feedback loops promote plant health - Nature Communications

Top-down trophic interactions are critical drivers of microbiome dynamics but are difficult to predict. Here, the authors demonstrate that nematode-driven shifts in microbiomes enhance pathogen suppre...

nature.com

Predator-driven microbial feedback loops promote plant health - Nature Communications

Top-down trophic interactions are critical drivers of microbiome dynamics but are difficult to predict. Here, the authors demonstrate that nematode-driven shifts in microbiomes enhance pathogen suppre...

nature.com

Revised and Extended: What's Happening Inside the NIH and NSF

science.org

OpenAI and the CSU system bring AI to 500,000 students & faculty

The largest deployment of ChatGPT to date will expand the use of AI in education and help the United States build an AI-ready workforce.

openai.com

Were Precambrian oceans devoid of planktonic cyanobacteria? Insights from metabolism

doi.org

Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes

Global marine microbial marketplace for DNA building blocks drives biogeochemical cycling and ecological signaling in the ocean.

science.org

Temporal Changes in the Role of Species Sorting and Evolution Determine Community Dynamics

Evolutionary change within community members and shifts in species composition contribute to community and trait dynamics. To integrate when and how both processes structure communities, we estimated...

onlinelibrary.wiley.com

THE GREEN LIGHT, Episode 3: Seppe Kuehn - Unveiling Mysteries of Microbial Communities

YouTube video by Algae People

youtu.be