Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

The protective role of commensal gut microbes and their metabolites against bacterial pathogens

Multidrug-resistant microorganisms have become a major public health concern around the world. The gut microbiome is a gold mine for bioactive compounds that protect the human body from pathogens. We used a multi-omics approach that integrated whole-genome sequencing (WGS) of 74 commensal gut microbiome isolates with metabolome analysis to discover their metabolic interaction with Salmonella and other antibiotic-resistant pathogens. We evaluated differences in the functional potential of these selected isolates based on WGS annotation profiles. Furthermore, the top altered metabolites in co-culture supernatants of selected commensal gut microbiome isolates were identified including a series of dipeptides and examined for their ability to prevent the growth of various antibiotic-resistant bacteria. Our results provide compelling evidence that the gut microbiome produces metabolites, including the compound class of dipeptides that can potentially be applied for anti-infection medication, especially against antibiotic-resistant pathogens. Our established pipeline for the discovery and validation of bioactive metabolites from the gut microbiome as novel candidates for multidrug-resistant infections represents a new avenue for the discovery of antimicrobial lead structures.

Kitasatospora fiedleri sp. nov., a novel antibiotic-producing member of the genus Kitasatospora

Strain TÜ4103T was originally sampled from Java, Indonesia and deposited in the Tübingen strain collection under the name 'Streptomyces sp.'. The strain was found to be an antibiotic producer as strain TÜ4103T showed bioactivity against Gram-positive bacteria, such as Bacillus subtilis and Kocuria rhizophila in bioassays. Strain TÜ4103T showed 16S rRNA gene sequence similarity of 99.65 % to Kitasatospora cheerisanensis DSM 101999T and 98.82 % to Kitasatospora niigatensis DSM 44781T and Kitasatospora cineracea DSM 44780T. Genome-based phylogenetic analysis revealed that strain TÜ4103T is closely related to K. cineracea DSM 44780T and K. niigatensis DSM 44781T. The digital DNA-DNA hybridization values between the genome sequences of strain TÜ4103T and its closest phylogenomic relatives, strains DSM 44780T and DSM 44781T, were 43.0 and 42.9 %, respectively. Average nucleotide identity (ANI) values support this claim, with the highest ANI score of 91.14 % between TÜ4103T and K. niigatensis being closely followed by an ANI value of 91.10 % between K. cineracea and TÜ4103T. The genome of TÜ4103T has a size of 7.91 Mb with a G+C content of 74.05 mol%. Whole-cell hydrolysates of strain TÜ4103T are rich in meso-diaminopimelic acid, and rhamnose, galactose and mannose are characteristic as whole-cell sugars. The phospholipid profile contains phosphatidylethanolamine, diphosphatidylglycerol and glycophospholipid. The predominant menaquinones (>93.5 %) are MK-9(H8) and MK-9(H6). Based on the phenotypic, genotypic and genomic characteristics, strain TÜ4103T (=DSM 114396T=CECT 30712T) merits recognition as the type strain of a novel species of the genus Kitasatospora, for which the name Kitasatospora fiedleri sp. nov. is proposed.

Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis

Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae. They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis, S. parmotrematis and S. rubrisoli; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis, S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.

Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera

The family Streptomycetaceae is a large and diverse family within the phylum Actinomycetota . The members of the family are known for their ability to produce medically important secondary metabolites, notably antibiotics. In this study, 19 type strains showing low 16S rRNA gene similarity (<97.3 %) to other members of the family Streptomycetaceae were identified and their high genetic diversity was reflected in a phylogenomic analysis using conserved universal proteins. This analysis resulted in the identification of six distinct genus-level clades, with two separated from the genus Streptacidiphilus and four separated from the genus Streptomyces . Compared with members of the genera Streptacidiphilus and Streptomyces , average amino acid identity (AAI) analysis of the novel genera identified gave values within the range of 63.9–71.3 %, as has been previously observed for comparisons of related but distinct bacterial genera. The whole-genome phylogeny was reconstructed using PhyloPhlAn 3.0 based on an optimized subset of conserved universal proteins, the results of AAI and percentage of conserved proteins (POCP) analyses indicated that these phylogenetically distinct taxa may be assigned to six novel genera, namely Actinacidiphila gen. nov., Mangrovactinospora gen. nov., Peterkaempfera gen. nov., Phaeacidiphilus gen. nov., Streptantibioticus gen. nov. and Wenjunlia gen. nov.

Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species. IMPORTANCE Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood. Here, we show that the population structure of a ubiquitous Streptomyces species complex matches its habitat distribution and can be defined by gene flow discontinuities. Using comparative genomics and physiological assays, we reveal that gains and losses of specific genomic traits play a significant role in the transition between free-living and host-associated lifestyles, driving speciation of the species. These results provide new insights into the evolutionary trajectory of Streptomyces and the notion of species.

Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria

Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.

Soil actinobacteria inhibit antagonistic fungi of leafcutter ant colonies

Founder females of the leaf-cutting ant species Atta sexdens experience high mortality during the founding and establishment of their colonies. The foundation site is crucial for the success of a new colony. In this study, we isolated and identified actinobacteria from fungus garden chambers of A. sexdens colony growth in soils from (1) forested areas without leafcutter ant nests and (2) open ground areas close to leafcutter ant nests. The inhibitory effect of these isolates on pathogenic fungi and the mutualistic fungus cultivated by leafcutter ants was evaluated. The 16S rRNA gene sequences were employed to identify nine selected actinobacteria species found in the soil: Streptomyces (6), Nocardia (2), and Kitasatospora (1). One Streptomyces and one Kitasatospora isolate inhibited all the tested fungi. Since there is no evidence of actinobacteria cultivation in the workers' cuticle of the Atta genus, our results corroborate the hypothesis that these workers may establish temporary adaptive symbiosis with soil microorganisms that produce antibiotic substances, living in some parts of their nest, or even inside their bodies. Pathogenic fungi are a risk factor that can be controlled by actinobacteria metabolites from soils, with minimal energy cost to the colony.

Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria

Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.

Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42

Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.

Activation of Secondary Metabolism in Red Soil-Derived Streptomycetes via Co-Culture with Mycolic Acid-Containing Bacteria

Our previous research has demonstrated a promising capacity of streptomycetes isolated from red soils to produce novel secondary metabolites, most of which, however, remain to be explored. Co-culturing with mycolic acid-containing bacteria (MACB) has been used successfully in activating the secondary metabolism in Streptomyces. Here, we co-cultured 44 strains of red soil-derived streptomycetes with four MACB of different species in a pairwise manner and analyzed the secondary metabolites. The results revealed that each of the MACB strains induced changes in the metabolite profiles of 35–40 streptomycetes tested, of which 12–14 streptomycetes produced “new” metabolites that were not detected in the pure cultures. Moreover, some of the co-cultures showed additional or enhanced antimicrobial activity compared to the pure cultures, indicating that co-culture may activate the production of bioactive compounds. From the co-culture-induced metabolites, we identified 49 putative new compounds. Taking the co-culture of Streptomyces sp. FXJ1.264 and Mycobacterium sp. HX09-1 as a case, we further explored the underlying mechanism of co-culture activation and found that it most likely relied on direct physical contact between the two living bacteria. Overall, our results verify co-culture with MACB as an effective approach to discover novel natural products from red soil-derived streptomycetes.