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Robust microbial classification systems are essential, but their definition is complicated by the large size and high diversity of microbial populations combined with a widespread horizontal genetic exchange. Multi-locus approaches that index gene variation without explicit phylogenetic classification mitigates these problems, but reproducibly defining high-level groups remains problematic. We describe a generalisable machine learning approach, 'NeighbourGroups', that reproducibly, robustly, and rapidly classifies multi-locus sequence types with defined precision.

Despite on-going vaccination programmes, Neisseria meningitidisis a majorcause of septicaemia and meningitis. In 2017-18, the MenW and MenY capsular groups caused 38% of all UK invasive meningococcal disease cases. Current policy is to generate genome sequences of all meningococcal disease isolates. Using this resource, we aim to determine how genetic variation contributes to phenotypic differences between carriage and disease isolates. We have adapted assays, mimicking carriage and disease behaviours, for high-throughput phenotypic testing of 335 MenW cc11 and MenY cc23 isolates. We are currently testing MenW cc11 disease and carriage isolates for cytotoxicity in a human lung epithelial cell line, growth in media and biofilm formation. Phenotypic differences are utilised as inputs for Genome Wide Association Studies enabling linkage of specific genomic variants, or variant combinations, with phenotypic variation. Genomic data include whole genome sequences and repeat-mediated phase variation states. The MenW cc11 isolates span two known phylogenetic clusters, original and 2013. Our preliminary data from high-throughput growth and biofilm assays showed no significant differences between these groups or sources (disease versus carriage); however, variations were observed within groups with, for example, distinctive cytotoxicity or biofilm differences between isolates. These variations may reflect physiological divergence due to minor genetic modifications between highly phylogenetically-related strains. Our assay systems are robust, reproducible, and easily scalable for efficient high-throughput genotypic and phenotypic testing. Thus, large-scale screening of phenotypic variation for infectious diseases is achievable and harnessable for cost-effective, direct evolutionary and epidemiological studies.

Bacteria live in complex communities with multiple species and strains competing with each other. Victories and defeats within these microbial wars are largely ignored unless they have a noticeable impact on the environment or the host, for example when a disease causing strain emerges as a winner. Evolutionary theory typically explains pathogen emergence as a trade-off between virulence and transmissibility. However, for opportunistic pathogens the secondary infection niche is often a dead end, as the host is either killed or cured, so a trade-off can not develop. In this context it is difficult to explain the maintenance of virulence genes in the population as they would be costly. Here, current literature is synthesized to address this apparent conundrum. The potential for adaptations to one niche to provide a benefit in another is described for some pathogenic species and this paradigm is extended to include genetic diversity and competition among individual strains. Finally, considering assemblages of strains in fluctuating immune environments with complex micro-niche structure, a scenario is presented in which commensal organisms can be primed for invasive disease should the opportunity arise.

Accurate, experimental rovibronic energy levels, with associated labels and uncertainties, are reported for 11 low-lying electronic states of the diatomic \TiO\ molecule, determined using the \Marvel\ (Measured Active Rotational-Vibrational Energy Levels) algorithm. All levels are based on lines corresponding to critically reviewed and validated high-resolution experimental spectra taken from 24 literature sources. The transition data are in the 2 $-$ 22,160 \cm{} region. Out of the 49,679 measured transitions, 43,885 are triplet-triplet, 5710 are singlet-singlet and 84 are triplet-singlet transitions. A careful analysis of the resulting experimental spectroscopic network (SN) allows 48,590 transitions to be validated. The transitions determine 93 vibrational band origins of \TiO\, including 71 triplet and 22 singlet ones. There are 276 (73) triplet-triplet (singlet-singlet) band-heads derived from \Marvel\ experimental energies, 123 (38) of which have never been assigned in low or high resolution experiments. The highest $J$ value, where $J$ stands for the total angular momentum, for which an energy level is validated is 163. The number of experimentally-derived triplet and singlet \TiO\ rovibrational energy levels is 8682 and 1882, respectively. The lists of validated lines and levels for \TiO\ are deposited in the Supporting Information to this paper.

Gut-content analyses using molecular techniques are an effective approach to quantifying predator-prey interactions. Predation is often assumed but scavenging is an equally likely route by which animal DNA enters the gut of a predator/scavenger. We used PCR (polymerase chain reaction) to detect scavenged material in predator gut homogenates. The rates at which DNA in decaying slugs (Mollusca: Pulmonata) and aphids (Homoptera: Aphididae) became undetectable were estimated. The detectability of DNA from both carrion types in the guts of the generalist predator Pterostichus melanarius (Coleoptera: Carabidae) was then determined. The effects of carrion age and weight, as well as beetle sex, on detection periods, were quantified. Laboratory trials measured prey preference of beetles between live and decaying prey. Further experiments measured, for the first time, feeding by P. melanarius on dead slugs and aphids directly in the field. In both field and laboratory, P. melanarius preferentially fed on dead prey if available, but preference changed as the prey became increasingly decayed. Disappearance rates for slug carrion in wheat fields and grasslands were estimated and P. melanarius was identified as the main scavenger. Comparison of the retention time for dead slugs in the field, with the detection period for decaying slug material in the guts of the predators, showed that PCR-based techniques are not able to distinguish between predated and scavenged food items. This could potentially lead to overestimation of the impact of predation on slugs (and other prey) by carabids. Possible implications of facultative scavenging by invertebrate predators for biocontrol and food-web research are discussed.