Physicochemical and Metagenomic Analysis of Samples from the Roman Baths (Bath, UK) Reveals High Bacterial and Archaeal Diversity and a Potential for Antimicrobial Discovery

Abstract

Antimicrobial resistance of pathogenic bacteria to currently used antibiotics killed an estimated 1.27 million people in 2019 and it is believed that this toll will increase to 10 million per year by 2050. This remains one of the most urgent threats to human health and the hunt for novel antimicrobial natural products (NPs) from microorganisms is essential in efforts to combat this threat, but recent efforts have been unsuccessful. The investigation of extreme ecological niches, such as hot springs, has gained recent interest due to their unique ecosystems, increasing the chance for novel antimicrobial NP discovery. The Roman Baths (Bath) is the UK’s only hot spring and it remains unexplored in terms of microbial diversity. In this study, samples of water, biofilm and sediment were taken from the King’s Bath hot spring and the Great Bath, and 16S rRNA metagenomic sequencing was performed for bacterial and archaeal community exploration. Additionally, samples were used for culture-dependent isolation of antimicrobial NP producing isolates. At the phylum level, data from water samples revealed a shift from an archaeal dominant community in the King’s Bath hot spring (Crenarchaeota, Aenigmarchaeota and Nanoarchaeota) to bacteria in the Great Bath (Cyanobacteria and Proteobacteria). Archaea were still present in the biofilm and sediment of the hot spring but consistently the bacterial phyla Cyanobacteria, Bacteroidota, Proteobacteria and Nitrospirota were dominant at both sites. The antimicrobial NP producing candidate phyla Actinobacteria and Myxobacteria were found in all samples. From initial isolation experiments, 297 isolates were purified, of which 15 showed broad spectrum activity against human pathogens, though interestingly these were not from target genera in the Actinobacteria. From these data, there is clear potential for novel NP discovery from the Roman Baths, as has been demonstrated from other thermal hot springs globally.

Keywords: Hot spring, Prokaryote abundance, 16S rRNA gene sequencing, Antimicrobial discovery, ESKAPE pathogens