Consideration of future requirements for Raman microbiology as a examplar for the ab initio development of informatics frameworks for emergent OMIC technologies

Raman spectroscopy of single bacteria provides an OMIC-like view of the chemical status of individual cells, reporting on metabolism, cell stress and growth, and is likely to become a significant tool in environmental and medical microbiology. We advocate the early development of integrated data models and informatics frameworks, in parallel with the development of Raman hardware and experimental protocols, in order to maximize the benefits of this emerging OMIC technology to the research community

Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks.

Outbreaks of virulent and/or drug-resistant bacteria have a significant impact on human health and major economic consequences. Genomic islands (GIs; defined as clusters of genes of probable horizontal origin) are of high interest because they disproportionately encode virulence factors, some antimicrobial-resistance (AMR) genes, and other adaptations of medical or environmental interest. While microbial genome sequencing has become rapid and inexpensive, current computational methods for GI analysis are not amenable for rapid, accurate, user-friendly and scalable comparative analysis of sets of related genomes. To help fill this gap, we have developed IslandCompare, an open-source computational pipeline for GI prediction and comparison across several to hundreds of bacterial genomes. A dynamic and interactive visualization strategy displays a bacterial core-genome phylogeny, with bacterial genomes linearly displayed at the phylogenetic tree leaves. Genomes are overlaid with GI predictions and AMR determinants from the Comprehensive Antibiotic Resistance Database (CARD), and regions of similarity between the genomes are also displayed. GI predictions are performed using Sigi-HMM and IslandPath-DIMOB, the two most precise GI prediction tools based on nucleotide composition biases, as well as a novel blast-based consistency step to improve cross-genome prediction consistency. GIs across genomes sharing sequence similarity are grouped into clusters, further aiding comparative analysis and visualization of acquisition and loss of mobile GIs in specific sub-clades. IslandCompare is an open-source software that is containerized for local use, plus available via a user-friendly, web-based interface to allow direct use by bioinformaticians, biologists and clinicians (at https://islandcompare.ca)

Panbiogeography of Nothofagus (Nothofagaceae): analysis of the main species massings

Aim  The aim of this paper is to analyse the biogeography of Nothofagus and its subgenera in the light of molecular phylogenies and revisions of fossil taxa. Location  Cooler parts of the South Pacific: Australia, Tasmania, New Zealand, montane New Guinea and New Caledonia, and southern South America. Methods  Panbiogeographical analysis is used. This involves comparative study of the geographic distributions of the Nothofagus taxa and other organisms in the region, and correlation of the main patterns with historical geology. Results  The four subgenera of Nothofagus have their main massings of extant species in the same localities as the main massings of all (fossil plus extant) species. These main massings are vicariant, with subgen. Lophozonia most diverse in southern South America (north of Chiloé I.), subgen. Fuscospora in New Zealand, subgen. Nothofagus in southern South America (south of Valdivia), and subgen. Brassospora in New Guinea and New Caledonia. The main massings of subgen. Brassospora and of the clade subgen. Brassospora/subgen. Nothofagus (New Guinea–New Caledonia–southern South America) conform to standard biogeographical patterns. Main conclusions  The vicariant main massings of the four subgenera are compatible with largely allopatric differentiation and no substantial dispersal since at least the Upper Cretaceous (Upper Campanian), by which time the fossil record shows that the four subgenera had evolved. The New Guinea–New Caledonia distribution of subgenus Brassospora is equivalent to its total main massing through geological time and is explained by different respective relationships of different component terranes of the two countries. Global vicariance at family level suggests that Nothofagaceae/Nothofagus evolved largely as the South Pacific/Antarctic vicariant in the breakup of a world-wide Fagales ancestor