Abstract. Chemical stressors in environmental and clinical settings can alter conjugative plasmid transfer, which is a key process driving antibiotic resis

Microbial model communities bridge the gap between pure culture and environmental studies, revealing widespread metabolic interdependencies that shape how natural microbial groups thrive and interact ...

Environmental genomics has focused mainly on prokaryotes, leaving microbial eukaryote diversity poorly understood. Using ~20,000 mitochondrial genomes from 3,400 lake metagenomes worldwide, this study...

A scrappy science project led to a significant discovery: two new species of a rare organism that could elucidate a fundamental transition in the history of life on our planet.

A scrappy science project led to a significant discovery: two new species of a rare organism that could elucidate a fundamental transition in the history of life on our planet.

Corals and lichens, though unrelated and from different ecosystems, both depend on internal photosynthetic symbionts, leading to similar traits in morpholo

Noteworthy — Colibactin, a genotoxic natural product, protects honeybees from the pathogen Serratia marcescens.

Commentary on Seth (2025): Unity is intrinsic to being both an experiencing and an embodied subject. Computational accounts of consciousness, being observer-relative, cannot account for this unity. The thermodynamics of life can but, contra Seth’s suggestion, the free energy principle fails to capture the distinctive metabolic interdependencies by virtue of which a living system constitutes itself as a unified perspective on the world.

Contribute to wtmatlock/plasmid-model-cli development by creating an account on GitHub.

Theory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets.

Resource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether...

SVPG performs accurate pangenome-facilitated structural variant detection and accelerates pangenome graph augmentation using long-read sequencing data.

by Hiroshi Nikaido — LB medium, also known incorrectly as Luria-Bertani medium, is widely used to grow bacterial cultures, mainly because it is easy to prepare and provides a broad base of nutrien…

A guide for new listeners

Plasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...

Plants and other photosynthetic organisms interact with their environment and surrounding microbiota through specialized associations. A global core microbiota has been proposed at high taxonomic levels, such as the order level. However, it remains unclear which environmental factors and how microbe-microbe interactions drive variation of this core microbiota at lower taxonomic resolution. Here, we leveraged the environmental diversity of 141 sites across the southwest of France to characterize algal populations, and their associated bacterial and fungal microbiota. We then performed a meta-analysis, combining these data with published datasets to formally identify the global core microbiota of terrestrial photosynthetic organisms, which comprises seven bacterial and five fungal orders. We next investigated diversity within this core microbiota and the environmental drivers shaping site-specific community composition. While environmental factors have a low impact on the total relative abundance of core orders, the core microbiota at the ASV-level is impacted by climatic factors, edaphic factors, and plant community descriptors. Using interaction network analysis, we finally explored how microbe-microbe interactions contribute to the assembly of stable core communities. Our results show that core ASVs occupy central positions in algal-associated microbial networks and that distinct core orders drive site-specific variation in core microbiota structure. Together, these findings highlight the importance of both environmental context and microbial interactions in shaping the composition and stability of the core microbiota associated with photosynthetic organisms. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, 951444 – PATHOCOM, erc-stg-948219, EPYC Agence Nationale de la Recherche, ANR-10-LABX-41 Biotechnology and Biological Sciences Research Council, https://ror.org/00cwqg982, BB/ X011054/1, BBS/E/F/000PR13631

Abstract. Accurate taxonomic assignment of 16S rRNA gene sequences is essential for the reliable interpretation of microbial community studies based on amp

Neisseria’s pilin antigenic variation remains one of the most sophisticated DNA diversification processes in bacteria, yet the trigger that initiates recombination remains unclear. Here, we show that ...

In this Perspective, Haubrock et al. argue that today’s scientific structures constrain creativity and that strategic conformity is a rational response. They discuss how this holds back early-career r...

Viruses are ubiquitous mobile genetic elements that are obligate symbionts of cellular life forms and replicate exclusively within host cells. The ...

Beyond self-care: How an institutional approach could pay for itself (oh, and also reduce suffering too)

Community ecology has developed a rich and increasingly diverse body of theory, but its rapid expansion has outpaced efforts to compare and synthesize competing frameworks. As a result, semantic ambig...

Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first

Over the last year, our lab has been developing a policy on AI use. To do this, we did three main things: We read a lot of academic publications and tech news. We set up an #ai channel on our la...

A central puzzle in the evolution of individuality is the origin of heredity. Egalitarian transitions integrate formerly independent replicators into a higher-level individual, but this requires the c...

Horizontal gene transfer (HGT) is a major driver of microbial adaptation and evolution, yet how habitat type and anthropogenic pressures shape communi…

There are invaders everywhere.

Research suggests that the combination of incentives to publish and the use of large language models will lead to more papers, but they will be less refined.

Neurodiversity in research, from the perspective of neurodivergent scientists.

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

a blog for miscellaneous bioinformatics stuff