Biology subjects

Lyras, D.

Publications and source records attributed to Lyras, D..

6 recordsLinked to original sources

bioRxiv2025

Bacterial species and surface structures shape gene transfer and the transcriptional landscape during early conjugation

Conjugative plasmids drive bacterial evolution and niche adaptation, yet how their active acquisition reshapes host transcription remains poorly understood. Most studies focus on stable plasmid carriage, overlooking the dynamic transcriptional changes during conjugation itself. Here, we show that active RP4 conjugation triggers an immediate, host- and surface factor-dependent transcriptional response. This includes activation of non-SOS stress pathways, motility, exopolysaccharide production, anaerobic respiration, and metabolic adaptation. These responses do not inhibit conjugation, suggesting they serve to maintain host homeostasis. Capsule expression blocks these responses by preventing conjugation, and also inhibits RP4 activation by physically blocking donor-recipient contact. Unexpectedly, RP4 overcomes this barrier by exploiting single-cell variation in recipient capsule thickness, successfully conjugating with thin-capsulated recipients. These findings reveal a striking interplay between plasmid, host, and surface architecture in shaping the conjugation transcriptional landscape, with broad implications for plasmid dissemination and bacterial evolution.

microbiology↗

bioRxiv2024

MLL1 directs gut-associated antibody responses to helminth and bacterial infections

Soil-transmitted helminths are one of the most common infections globally, yet how to promote effective gut-associated humoral responses is not well understood. We identify the histone methyltransferase MLL1 as a key target to promote IgA-driven responses. Mll1 was increased in germinal center B cells in gut-associated lymphoid tissues, and Mll1-deficiency led to changes in the histone modification H3K4me3 on key B cell and immune-regulatory genes. Correspondingly, MLL1-deficient B cells had defective germinal centers and IgG1 in response to the helminth Trichuris muris. Yet, Mll1f/fCd23cre/+ mice expelled worms more rapidly compared to control mice. Accelerated worm clearance correlated with elevated IgA+ plasma cells, as well as both serum and fecal IgA. RNA-sequencing identified CCR9 as a key MLL1-regulated molecule. As such, Mll1f/fCd23cre/+ mice infected with T. muris had increased IgA+CCR9+ PC localized in the large intestine. Regulation of IgA by MLL1 was confirmed beyond T. muris infection. In vitro cultures confirmed Mll1-deficiency increased IgA+ plasma cells in a B cell-intrinsic manner, and IgA production was also increased in Mll1f/fCd23cre/+ mice infected with the bacterium C. rodentium. This study reveals MLL1 as a key target to promote IgA responses to gut-associated infections.

immunology↗

bioRxiv2024

A widespread hydrogenase drives fermentative growth of gut bacteria in healthy people

Molecular hydrogen (H2) is among the most central, but least understood, metabolites in the human gastrointestinal tract (gut). H2 gas is produced in large quantities during bacterial fermentation and consumed as an energy source by bacteria and archaea. Disruption of H2 cycling is linked to gastrointestinal disorders, infections, and cancers, with H2 used as an indicator of gut dysfunction through breath tests. Despite this, the microorganisms, pathways, and enzymes mediating H2 production remain unresolved. Here we show that a previously uncharacterised enzyme, the group B [FeFe]-hydrogenase, drives most fermentative H2 production in the human gut. Analysis of stool, biopsy, and isolate (meta)genomes and (meta)transcriptomes show this hydrogenase is encoded by most gut bacteria and is highly expressed. Through analysis of 19 taxonomically diverse gut isolates, the group B [FeFe]-hydrogenase produces large amounts of H2 gas and supports fermentative growth of both Bacteroidetes and Firmicutes. Bacteroides particularly dominate H2 production. Biochemical and spectroscopic characterisation shows purified group B [FeFe]-hydrogenases are catalytically active and bind a di-iron active site. These hydrogenases are highly enriched in the guts of healthy individuals, but significantly depleted in favour of other fermentative hydrogenases in Crohns disease. Furthermore, we show that metabolically flexible respiratory bacteria are the most abundant H2 oxidizers in the gut, not sulfate reducers, methanogens, and acetogens as previously thought. This combination of enzymatic, cellular, and ecosystem-level analysis provides the first detailed understanding of H2 cycling in the human gut and reveals new links between microbiota function and gastrointestinal health.

microbiology↗

bioRxiv2023

Temperate gut phages are prevalent, diverse, and predominantly inactive

Large-scale metagenomic and data mining efforts have uncovered an expansive diversity of bacteriophages (phages) within the human gut1-3. These insights include broader phage populational dynamics such as temporal stability4, interindividual uniqueness5,6 and potential associations to specific disease states7,8. However, the functional understanding of phage-host interactions and their impacts within this complex ecosystem have been limited due to a lack of cultured isolates for experimental validation. Here we characterise 125 active prophages originating from 252 diverse human gut bacterial isolates using seven different induction conditions to substantially expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 17% of computationally predicted prophages were induced with common induction agents and these exhibited distinct gene patterns compared to non-induced predictions. Active Bacteroidota prophages were among the most prevalent members of the gut virome, with extensive use of diversity generating retroelements and exhibiting broad host ranges. Moreover, active polylysogeny was present in 52% of studied gut lysogens and led to coordinated prophage induction across diverse conditions. This study represents a substantial expansion of experimentally validated gut prophages, providing key insights into their diversity and genetics, including a genetic pathway for prophage domestication and demonstration that differential induction was complex and influenced by divergent prophage integration sites. More broadly, it highlights the importance of experimental validation alongside genomic based computational prediction to enable further functional understanding of these commensal viruses within the human gut.

microbiology↗

bioRxiv2021

Using antibody synergy to engineer a high potency biologic cocktail against C. difficile

Here we show that transgenic spirulina may solve key challenges of developing effective monoclonal protein therapeutics for diseases afflicting gastrointestinal (GI) tissues. We describe, as a paradigm for this novel approach, LMN-201: an investigational four-component treatment for Clostridioides difficile (C. difficile) infection comprising four monoclonal protein therapeutics produced and delivered within spirulina biomass. Three antibody-like moieties within LMN-201 were rationally designed using a multiplicative potency framework, termed synthetic avidity, that increased in vitro toxin neutralization potency by >200-fold relative to the individual components. The fourth moiety, a lysin enzyme protein, adds direct, toxinotype-agnostic antibacterial activity. In rodent challenge models, species-relevant LMN-201-like cocktails reduced disease burden and mortality. In a human GI pharmacokinetic study, LMN-201 was present at concentrations 100- to 1,000-fold above the estimated minimally effective therapeutic threshold at the distal intestine. In a Phase 2 study in participants suffering from C. difficile infection (CDI), seven days of treatment with LMN-201 plus standard-of-care antibiotics achieved initial clinical cure in 21/21 (100%) participants, sustained clinical cure through four weeks in 19/21 (90.5%) participants, and had a favorable safety profile. These findings support LMN-201 with standard-of-care antibiotics as a viable treatment option for CDI, validate spirulina as a scalable platform for oral biologics, and establish a generalizable strategy for engineering high-potency combination protein therapeutics for diseases with a GI tissue nexus.

bioengineering↗

bioRxiv2021

PGfinder, a novel analysis pipeline for the consistent, reproducible and high- resolution structural analysis of bacterial peptidoglycans

Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan, the essential and major component of bacterial cell envelopes. It is comprised of glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGfinder for the analysis of peptidoglycan structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial peptidoglycans. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.

microbiology↗