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Bacteria undergo asexual reproduction, but genetic exchange is common. Current models posit that speciation of sexual bacteria is a gradual and long process, and genetic exchanges decrease but never cease between nascent species. Here, we show that in a panmictic bacterial lineage found in symbiosis with invertebrate hosts across multi-marine ecosystems, a series of speciation events occurred unusually fast with between-species genetic exchange approximating a complete halt. The speciation process is too rapid to sort out ancestral polymorphisms, giving rise to between-species phylogenetic incongruence at a genome-wide scale. This novel bacterial speciation process leads to incomplete lineage sorting, which to date has only been observed in eukaryotes but is 100-1000 times faster. Our finding allows for a more unified understanding of the speciation process across prokaryotes and eukaryotes.

Identifying the mode of action (MOA) of antibacterial compounds is the fundamental basis for the development of new antibiotics, and the challenge increases with the emerging secondary and indirect...

Bioregenerative life-support systems for space have been investigated for 60 years, and plants and other photosynthetic organisms are central to this concept for their ability to produce food and O2, remove CO2, and help recycle wastewater. Many of the studies targeted larger scale systems that might be used for planetary surface missions, with estimates ranging from about 40 to 50 m2(or more) of crop growing area needed per person. But early space missions will not have these volumes available for crop growth. How can plants be used in the interim, where perhaps 2of growing area might be available? One option is to grow plants as supplemental, fresh foods. This could improve the quality and diversity of the meals on the International Space Station or on the Lunar surface, and supply important nutrients to the astronauts for missions like Mars transit, and longer duration Martian surface missions. Although plant chambers for supplemental food production would be relatively small, they could provide the bioregenerative research community with platforms for testing different crops in a space environment and serve as a stepping stone to build larger bioregenerative systems for future missions. Here we review some of NASA’s research and development (ground and spaceflight) targeting fresh food production systems for space. We encourage readers to also look into the extensive work by other space agencies and universities around the world on this same topic.

The current need for novel antibiotics is especially acute for drug-resistant Gram-negative pathogens1,2. These microorganisms have a highly restrictive permeability barrier, which limits the penetration of most compounds3,4. As a result, the last class of antibiotics that acted against Gram-negative bacteria was developed in the 1960s2. We reason that useful compounds can be found in bacteria that share similar requirements for antibiotics with humans, and focus on Photorhabdus symbionts of entomopathogenic nematode microbiomes. Here we report a new antibiotic that we name darobactin, which was obtained using a screen of Photorhabdus isolates. Darobactin is coded by a silent operon with little production under laboratory conditions, and is ribosomally synthesized. Darobactin has an unusual structure with two fused rings that form post-translationally. The compound is active against important Gram-negative pathogens both in vitro and in animal models of infection. Mutants that are resistant to darobactin map to BamA, an essential chaperone and translocator that folds outer membrane proteins. Our study suggests that bacterial symbionts of animals contain antibiotics that are particularly suitable for development into therapeutics.

To better combat the expansion of antibiotic resistance in pathogens, new compounds, particularly those with novel mechanisms-of-action [MOA], represent a major research priority in biomedical science. However, rediscovery of known antibiotics demonstrates a need for approaches that accurately identify potential novelty with higher throughput and reduced labor. Here we describe an explainable artificial intelligence classification methodology that emphasizes prediction performance and human interpretability by using a Hierarchical Ensemble of Classifiers model optimized with a novel feature selection algorithm called Clairvoyance; collectively referred to as a CoHEC model. We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. Our CoHEC model can properly predict the primary MOA of previously unobserved compounds in both purified forms and crude extracts at an accuracy above 99%, while also correctly identifying darobactin, a newly discovered antibiotic, as having a novel MOA. In addition, we deploy our methods on a recent E. coli transcriptomics dataset from a different strain and a Mycobacterium smegmatis metabolomics timeseries dataset showcasing exceptionally high performance; improving upon the performance metrics of the original publications. We not only provide insight into the biological interpretation of our model but also that the concept of MOA is a non-discrete heuristic with diverse effects for different compounds within the same MOA, suggesting substantial antibiotic diversity awaiting discovery within existing MOA., Author summary As antimicrobial resistance is on the rise, the need for compounds with novel targets or mechanisms-of-action [MOA] are of the utmost importance from the standpoint of public health. A major bottleneck in drug discovery is the ability to rapidly screen candidate compounds for precise MOA activity as current approaches are expensive, time consuming, and are difficult to implement in high-throughput. To alleviate this bottleneck in drug discovery, we developed a human interpretable artificial intelligence classification framework that can be used to build highly accurate and flexible predictive models. In this study, we investigated antimicrobial MOA through the transcriptional responses of Escherichia coli challenged with 41 known antibiotic compounds, 9 crude extracts, and a recently discovered (circa 2019) compound, darobactin, with novel MOA activity. We implemented a highly stringent Leave Compound Out Cross-Validation procedure to stress-test our predictive models by simulating the scenario of observing novel compounds. Furthermore, we developed a versatile feature selection algorithm, Clairvoyance, that we apply to our hierarchical ensemble of classifiers framework to build high performance explainable machine-learning models. Although the methods in this study were developed and stress-tested to predict the primary MOA from transcriptomic responses in E. coli, we designed these methods for general application to any classification problem and open-sourced the implementations in our Soothsayer Python package. We further demonstrate the versatility of these methods by deploying them on recent Mycobacterium smegmatis metabolomic and E. coli transcriptomics datasets to predict MOA with high accuracy.

Identifying the mode of action (MOA) of antibacterial compounds is the fundamental basis for the development of new antibiotics, and the challenge increases with the emerging secondary and indirect effect from antibiotic stress. Although various omics-based system biology approaches are currently available, enhanced throughput, accuracy, and comprehensiveness are still desirable to better define antibiotic MOA. Using label-free quantitative proteomics, we present here a comprehensive reference map of proteomic signatures of

Astrobiology asks three fundamental questions as outlined by the NASA Astrobiology Roadmap: 1. How did Life begin and evolve?; Is there Life elsewhere in the Universe?; and, What is the future of Life on Earth? As we gain perspective on how Life on Earth arose and adapted to its many niches, we too gain insight into how a planet achieves habitability. Here on Earth, microbial Life has evolved to exist in a wide range of habitats from aquatic systems to deserts, the human body, and the International Space Station (ISS). Landers, rovers, and orbiter missions support the search for signatures of Life beyond Earth, by generating data on surface and subsurface conditions of other worlds. These have provided evidence for water activity, supporting the potential for extinct or extant Life. To investigate the putative ecologies of these systems, we study extreme environments on Earth. Several locations on our planet provide analog settings to those we have detected or expect to find on neighboring and distant worlds. Whereas, the field of space biology uses the ISS and low gravity analogs to gain insight on how transplanted Earth-evolved organisms will respond to extraterrestrial environments. Modern genomics allows us to chronicle the genetic makeup of such organisms and provides an understanding of how Life adapts to various extreme environments.

Burkholderia pseudomallei, the causative agent of the severe disease melioidosis, can form persister cells, which can survive under high-dose antibiotic challenge complicating the treatment of the disease. In this review, we discuss our current knowledge on the formation of persister cells in B. pseudomallei. Recent studies suggest that growth-limiting conditions such as nutrient and oxygen limitation, as well as antibiotic challenge, can lead to formation of persister cells. Among the diverse set of genes that can contribute to persister cell formation, toxin-antitoxin pairs are the most studied and have been shown to contribute to persister cell formation in B. pseudomallei. B. pseudomallei infections result in high relapse rate after recovery from melioidosis. Such relapses may be facilitated by reactivation of the B. pseudomallei persister cells. Therefore, understanding the environmental and genetic factors that contribute to persistence is critical to develop effective treatment strategies for melioidosis.

The opportunistic pathogensBurkholderia cepaciaandBurkholderia contaminans, both genomovars of theBurkholderia cepaciacomplex (BCC), are frequently cultured from the potable water system (PWS) of the International Space Station (ISS). Here, we sequenced the genomes and conducted phenotypic assays to characterize theseBurkholderiaisolates. All recovered isolates of the two species fall within monophyletic clades based on phylogenomic trees of conserved single-copy core genes. Within species, the ISS PWS strains all demonstrate greater than 99% average nucleotide identity (ANI), suggesting that they are of a highly similar genomic lineage and both individually may have stemmed from the two founding clonal strains before diverging into two unique sub strain populations. No evidence for horizontal gene transfer between the populations was observed. Differences between the recovered isolates can be observed at the pangenomic level, particularly within putative plasmids identified within theB. cepaciagroup. Phenotypically, the ISS-derivedB. cepaciaisolates generally exhibit a trend of lower rates and shorter duration of macrophage intracellularization compared to the selected terrestrial reference strain (though not significantly), and significantly lower rates of cellular lysis in 7 of the 19 isolates. ISS-derivedB. contaminansisolates displayed no difference in rates of macrophage intracellularization compared to the selected reference, though generally increased rates lysis, with 2 of the 5 significantly increased at 12-hours post inoculation. We additionally find that ISS-isolatedB. contaminansdisplay hemolytic activity at 37°C not demonstrated by the terrestrial control, and greater antifungal capacity in the more recently collected isolates. Thankfully, the ISS-derived isolates generally exhibit 1-4 times greater sensitivity to common antibiotics used in their clinical treatments. Thus, despite their infection potential, therapeutic treatment should still have efficacy.Author SummaryThe International Space Station (ISS) is a unique built environment due to its isolation and recycling of air and water. Both microbes and astronauts inhabit the ISS, and the potential pathogenicity of the former is of great concern for the safety of the latter. The potable water dispenser (PWD) of the potable water system (PWS) on board the ISS was assembled in a cleanroom facility and then primed on Earth using an extensive process to ensure no gas bubbles existed within the lines that could lock the apparatus upon installation in orbit. The primed system sat dormant for 6 months before installation on the ISS. Microbial surveillance was conducted on the system after installation and the bacterial load was 85 CFU/mL, which exceeded the 50 CFU/mL limits set for ISS potable water. Over a microbial surveillance spanning 4.5 years, numerous strains of the potential pathogenBurkholderiahave been isolated from the PWD. Here we sequenced and analyzed the genomes of these strains while also characterizing their potential pathogenicity. The genome analysis indicates it is likely that there were only two strains that were introduced on Earth that have subsequently undergone minimal diverging evolution. These strains retain pathogenicity, but remain susceptible to antibiotics, providing a potential therapeutic intervention in the event of infection.

Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread of drug-resistant bacterial pathogens is causing a global health crisis. To facilitate the drug discovery processes, we present a large-scale study of reference antibiotic challenge bacterial transcriptome profiles, which included 37 antibiotics across 6 mechanisms of actions (MOAs) and provide an economical approach to aid in antimicrobial dereplication in the discovery process., Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread of drug-resistant bacterial pathogens is causing a global health crisis. To facilitate the drug discovery processes, we present a large-scale study of reference antibiotic challenge bacterial transcriptome profiles, which included 37 antibiotics across 6 mechanisms of actions (MOAs) and provide an economical approach to aid in antimicrobial dereplication in the discovery process. We demonstrate that classical MOAs can be sorted based upon the magnitude of gene expression profiles despite some overlap in the secondary effects of antibiotic exposures across MOAs. Additionally, using gene subsets, we were able to subdivide broad MOA classes into subMOAs. Furthermore, we provide a biomarker gene set that can be used to classify most antimicrobial challenges according to their canonical MOA. We also demonstrate the ability of this rapid MOA diagnostic tool to predict and classify the expression profiles of pure compounds and crude extracts to their expression profile-associated MOA class.

Viruses are underrepresented as targets in pharmacological screening efforts, given the difficulties of devising suitable cell-based and biochemical assays. In this study we found that a pre-fractionated organic extract of the Red Sea sponge Amphimedon chloros was able to inhibit the West Nile Virus NS3 protease (WNV NS3). Using liquid chromatography&ndash, mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy, the identity of the bioactive compound was determined as a 3-alkylpyridinium with m/z = 190.16. Diffusion Ordered Spectroscopy (DOSY) NMR and NMR relaxation rate analysis suggest that the bioactive compound forms oligomers of up to 35 kDa. We observed that at 9.4 &mu, g/mL there was up to 40&ndash, 70% inhibitory activity on WNV NS3 protease in orthogonal biochemical assays for solid phase extracts (SPE) of A. chloros. However, the LC-MS purified fragment was effective at inhibiting the protease up to 95% at an approximate amount of 2 &micro, g/mL with negligible cytotoxicity to HeLa cells based on a High-Content Screening (HCS) cytological profiling strategy. To date, 3-alkylpyridinium type natural products have not been reported to show antiviral activity since the first characterization of halitoxin, or 3-alkylpyridinium, in 1978. This study provides the first account of a 3-alkylpyridinium complex that exhibits a proposed antiviral activity by inhibiting the NS3 protease. We suggest that the here-described compound can be further modified to increase its stability and tested in a cell-based assay to explore its full potential as a potential novel antiviral capable of inhibiting WNV replication.

Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. We examined the transcriptomic response of the coral Orbicella faveolata in the presence (symbiotic) and absence (aposymbiotic) of Symbiodinium minutum, one of its associated symbionts. 9 days post-metamorphic aposymbiotic coral polyps of O. faveolata were compared to symbiotic coral polyps and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into control of pathways as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.