Biology subjects

Unitt, A.

Publications and source records attributed to Unitt, A..

3 recordsLinked to original sources

bioRxiv2026

A Life Identification Number Barcoding (LIN Code) System for Neisseria meningitidis: high resolution multi-level typing of meningococci.

Neisseria meningitidis is a commensal member of the human oropharyngeal microbiota that can cause devastating invasive meningococcal disease. This genetically and antigenically diverse accidental pathogen has been a paradigm for the study of bacterial population biology. The meningococcus was the first organism for which a seven-locus multi-locus sequence typing (MLST) scheme was developed. With the addition of sequence-based characterisation of antigen genes, molecular typing has been widely employed to inform surveillance and public health interventions. Following the advent and widespread adoption of whole genome sequencing (WGS), precise delineation of variants is possible. Here, a WGS-based Life Identification Number (LIN) code typing scheme is described, providing a multi-resolution nomenclature for understanding meningococcal population diversity and molecular epidemiology. The LIN codes were developed using a set of 6,131 N. meningitidis genomes, comprising up to 200 isolates from each clonal complex (cc) previously described using MLST. Based on cluster-stability analysis and concordance with ccs, thirteen LIN thresholds described the meningococcal population at different levels of resolution. LIN codes and human-readable nicknames consistent with existent nomenclatures were assigned to the N. meningitidis genomes hosted in the PubMLST. Published outbreaks validated the LIN thresholds, illustrating the potential of this genomic tool in public health management.

microbiology↗

bioRxiv2025

Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to consistently identify N. gonorrhoeae lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect N. gonorrhoeae strain taxonomy in a reliable and stable manner. Here, a N. gonorrhoeae genomic lineage nomenclature, based on the barcoding system of Life Identification Number (LIN) codes, was developed using a refined 1430 core gene MLST (cgMLST). This hierarchical LIN code nomenclature conveys lineage information at multiple levels of resolution within one code, enabling it to provide immediate context to an isolates ancestry, and to relate to familiar, previously used typing schemes such as Ng cgMLST v1, 7-locus MLST, or NG-STAR clonal complex (CC). Clustering with LIN codes accurately reflects gonococcal diversity and population structure, providing insight into associations between genotype and phenotype for traits such as antibiotic resistance. These codes are automatically assigned and publicly accessible via the pubmlst.org/organisms/neisseria-spp database.

genomics↗

bioRxiv2020

RuBisCO adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analysed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically-resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover ([~]21-37 %), and between the Michaelis constants for CO2 and O2 ([~]9-19 %), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9 %) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints (most likely caused by a slow rate of molecular evolution) have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all such trade-offs.

plant biology↗