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Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombina- tion in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visuali- zation and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. 

Abstract Sepsis, whole‐body inflammation caused by the contamination of blood by bacteria and endotoxins, affects millions of patients annually with high mortality rates. A recent promising approach to treat sepsis involves the removal of bacteria and endotoxins using extracorporeal blood‐cleansing devices. However, poor specificity, slow recognition of pathogens, and high costs remain the main limitations. Here, the melanin, a biologically derived pigment, is reported for the rapid binding of bacteria and endotoxins from the contaminated blood . This novel approach utilizes the specific binding between Zn²⁺‐loaded melanin and bacteria/endotoxins with minimal nonspecific interactions with human blood components. Melanin contains various chemical functional groups that allow reversible chelation of metallic ions such as Zn²⁺via redox reactions. Zn²⁺enables rapid and specific binding with bacteria/endotoxins due to the strong electrostatic interactions between Zn²⁺and phosphate ions. The presence of various zinc‐binding proteins on the bacterial cell membrane further enhances the binding. The well‐known biocompatibility and low cost make melanin an ideal material to interface with human blood. Zn²⁺‐charged melanin can remove 90% ofE. coliand 100% of endotoxin in PBS and human blood. Zn²⁺‐melanin also demonstrated excellent hemocompatibility shown by protein adsorption, blood coagulation, and hemolysis tests. 

Streptomycesare prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity ofStreptomycesbacteria. We analysed draft genomes of 132Streptomycesisolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree.Streptomycesisolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do withStreptomycesfrom other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of theStreptomycesthat carry them. Each genome carried between 19–65 BGCs (median=42.5) and varied even among members of the sameStreptomycesspecies. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally,Streptomycesgenomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understandingStreptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments. 

Prosocial behavior is ubiquitous in nature despite the relative fitness costs carried by cooperative individuals. However, the stability of cooperation in populations is fragile and often maintained through enforcement. We propose that homologous recombination provides such a mechanism in bacteria. Using an agent-based model of recombination in bacteria playing a public goods game, we demonstrate how changes in recombination rates affect the proportion of cooperating cells. In our model, recombination converts cells to a different strategy, either freeloading (cheaters) or cooperation, based on the strategies of neighboring cells and recombination rate. Increasing the recombination rate expands the parameter space in which cooperators outcompete freeloaders. However, increasing the recombination rate alone is neither sufficient nor necessary. Intermediate benefits of cooperation, lower population viscosity, and greater population size can promote the evolution of cooperation from within populations of cheaters. Our findings demonstrate how recombination influences the persistence of cooperative behavior in bacteria. 

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces . Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces . 

Here we present the important findings related to biologically derived pigments for potential use as antibacterial agents. Melanin biopigments extracted from Equus ferus hair exhibit a homogeneous elliptical microstructure with highly ordered semicrystalline features. Spectroscopic analysis indicates that melanin contains a high degree of redox active catechol groups, which can produce reactive oxygen species. The antibacterial activity of melanins was tested by incubating Escherichia coli and Staphylococcus aureus with melanins. The results showed 100% bacterial growth inhibition within 4 h. This finding suggests that melanin pigments may serve as naturally occurring antibacterial agents with unique redox chemistry and reactive oxygen species generation capability. 

Abstract Streptomycesbacteria are known for their prolific production of secondary metabolites, many of which have been widely used in human medicine, agriculture and animal health. To guide the effective prioritization of specific biosynthetic gene clusters (BGCs) for drug development and targeting the most prolific producer strains, knowledge about phylogenetic relationships ofStreptomycesspecies, genome-wide diversity and distribution patterns of BGCs is critical. We used genomic and phylogenetic methods to elucidate the diversity of major classes of BGCs in 1,110 publicly availableStreptomycesgenomes. Genome mining ofStreptomycesreveals high diversity of BGCs and variable distribution patterns in theStreptomycesphylogeny, even among very closely related strains. The most common BGCs are non-ribosomal peptide synthetases, type 1 polyketide synthases, terpenes, and lantipeptides. We also found that numerousStreptomycesspecies harbor BGCs known to encode antitumor compounds. We observed that strains that are considered the same species can vary tremendously in the BGCs they carry, suggesting that strain-level genome sequencing can uncover high levels of BGC diversity and potentially useful derivatives of any one compound. These findings suggest that a strain-level strategy for exploring secondary metabolites for clinical use provides an alternative or complementary approach to discovering novel pharmaceutical compounds from microbes.