Biology subjects

Turkington, C.

Publications and source records attributed to Turkington, C..

2 recordsLinked to original sources

bioRxiv2026

Ratatoskr: A tool for automated retrieval of taxonomic type strain sequences and metadata

Bacterial taxonomic type strains anchor species names to physical and genomic reference material, making them essential for reproducible and comparable prokaryotic research. While reference strains are often well-characterised through curated metadata, nomenclature histories, and sequence records, no single database holds up-to-date information on all these aspects, resulting in fragmented information. Gathering the complete set of information for a type strain is further complicated by inconsistencies in nomenclature between sources due to the often-numerous synonyms that can describe a single strain. As a result, collecting type strain data for taxonomic proposals and emendations can be an onerous task requiring extensive manual curation. To address this issue, we introduce Ratatoskr, a Python-based tool that automates the retrieval of sequences and metadata for bacterial taxonomic type strains. Ratatoskr facilitates this by collecting the latest type strain information of the List of Prokaryotic names with Standing in Nomenclature (LPSN) and using this information to query the BacDive and NCBI databases. By applying known taxonomic synonym information Ratatoskr is able to resolve cross-database inconsistencies and streamline the retrieval process. We show that through its use, Ratatoskr can obtain metadata and sequence data for type strains of bacteria within minutes to seconds, depending on the number of members within the requested taxon. By automating this retrieval, Ratatoskr provides fast, accurate, and readily shareable starting points for studies involving the use of taxonomic type strains and data, such as new taxonomic proposals or emendations. Data summaryRatatoskr was developed using Python 3 and is freely available at https://github.com/Fabian-Bastiaanssen/Ratatoskr under a GPL-3.0 licence.

bioinformatics↗

bioRxiv2024

The relationship between microbial community succession, decay, and anatomical character loss in non-biomineralised animals

A fundamental assumption of hypothesis-driven decay experiments is that, during decay, the loss of anatomy follows a sequence broadly controlled by the intrinsic compositional properties of tissues. Recent work investigating the succession of postmortem endogenous microbial communities (thanatomicrobiome) challenges this assumption. These studies suggest the thanatomicrobiome exhibits a predictable, clock-like succession in response to physical and chemical environmental changes within a carcass. Therefore, it is possible that reproducible sequences of character loss during decay are controlled by thanatomicrobiome succession dynamics. If so, exceptionally preserved fossil anatomy would reflect a succession of ancient contemporaneous microbial communities, about which we know nothing, rendering decay experiments uninformative. Here, we investigate two questions: (1) what is the role of exogenous and endogenous bacteria during formation of the thanatomicrobiome and (2) do thanatomicrobiome successions control the sequence of anatomical character loss within a decaying carcass? Our analysis shows that the thanatomicrobiome is dominated by endogenous bacteria and that, even in the presence of inoculum, exogenous bacteria do not invade the carcass and replace native bacteria (while the carcass is intact). This confirms that the use of environmental inoculum in decay experiments introduces an inadvisable confounding variable. Secondly, we find no correlation between thanatomicrobiome successions and the sequence of anatomical character loss, supporting that fossil non-biomineralised characters correlate with their propensity to decay in extant relatives. These findings indicate that the inability to model ancient bacteria does not invalidate decay experiments. We also present a synthesis of the role of bacteria in non-biomineralised fossilisation.

paleontology↗