Abstract
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
Highlights
Marine sponges [1, 2] contribute significantly to known chemical space [3], accounting for nearly 30% of all specialized metabolites (SMs) reported from the marine environment [1, 4]
Dendrogram at a height of approximately 2 and below represented true species differentiation, not MS artifacts. These results are likely not representative of the relative abundances of in situ bacterial populations [60], rather they represent the populations of culturable bacteria that are accessible to researchers who engage in microbial drug discovery efforts. These results suggest that the readily recoverable bacterial populations from two Eunapius fragilis samples collected in similar location and time windows shared many of the same genera, they varied significantly at the species, and possibly subspecies level
Chryseobacterium metabolite association networks (MANs) (Fig. 3b) showed significant SM overlap aimed to analyze culturable microbial populations that are often that was less correlated to protein spectrum similarity (Fig. 3b and studied by researchers that work in specialized metabolism, S8)
Summary
Marine sponges [1, 2] contribute significantly to known chemical space [3], accounting for nearly 30% of all specialized metabolites (SMs) reported from the marine environment [1, 4]. MALDI-TOF MS protein spectra (3000–15,000 Daltons) mentary techniques revealed that isolates spanned at least four consist primarily of ions of intact ribosomal, cell structure, and phyla commonly associated with sponges: Proteobacteria, Actiregulatory proteins [41, 42] and are often used to group nobacteria, Bacteroidetes, and Firmicutes (Fig. S4) These phyla are microorganisms at the genus, species, and subspecies taxonomic responsible for greater than half of known microbially-produced levels [43–49]. To determine the intra-genus SM variation among our freshwater sponge bacterial isolates, we generated metabolite association networks (MANs) from dendrogram groupings, an embedded function within IDBac. MANs were used to analyze MALDI-TOF SM spectra by linking isolates with shared mass features (Fig. 3) [39]. This correlation aligns well with other recent studies [61, 62, 67–69] and highlights that species-level phylogenetic identity can predict SM diversity
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