Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces

Abstract

The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus Streptomyces. We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence/absence within Streptomyces, even in strains identical by 16S. Furthermore, we identified key differences in shared ecologically important characters, such as antibiotic resistance, carbohydrate metabolism, biosynthetic gene clusters (BGCs), and other metabolic hallmarks, within 16S identities commonly treated as the same operational taxonomic units (OTUs). Differences between common phylogenetic measures and metabolite-gene annotations confirmed this incongruence. Our results highlight the metabolic diversity and variability within OTUs and add to the growing body of work suggesting 16S-based studies of Streptomyces fail to resolve important ecological and metabolic characteristics.

Streptomyces lydicamycinicus sp. nov. and Its Secondary Metabolite Biosynthetic Gene Clusters for Polyketide and Nonribosomal Peptide Compounds

“…The idea that there is no relation between species classification and secondary metabolites is still widespread. There are two possible reasons why this idea has taken root and continues to persist: (a) only an (or a very limited number of) actually produced secondary metabolite has been investigated and genome information-based comprehensive analyses have not been conducted; (b) the classification of used strains is inaccurate and/or based on only 16S rDNA sequences [26][27][28][29][30][31][32]. If we had focused only on 16S rDNA sequence similarities, we would never have found out about the clear proportionality between phylogenetic distance and RC (Figure 3c).…”

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

“…Within a single hectare of temperate grassland soil, there can be over 1000 kg of microbial biomass and corresponding large microbial population sizes [2]. Recent progress has been made in cataloging the diversity of 16S rRNA genes in soils [3], which is useful for understanding microbial community composition, but this technique is incapable of discerning most genetic variation within populations [4]. In addition, many of the most common soil microorganisms, such as the highly abundant Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla, are underrepresented in or nearly absent from culture collections and genomic databases, even at the level of class or phylum [1,5,6].…”

TheClostridioides difficilespecies problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies

“…Contradicting our ANI and core genome data, 16S rRNA sequences were highly conserved across all 8 clades. This indicates that in C. difficile, 16S rRNA gene similarity correlates poorly with measures of genomic, phenotypic and ecological diversity, as reported in other taxa such as Streptomyces, Bacillus and Enterobacteriaceae 36,37 . Another interesting observation is that C5 and the three cryptic clades had a high proportion (>90%) of MLST alleles that were absent in other clades (Supplementary Data) suggesting minimal exchange of essential housekeeping genes between these clades.…”