Outlining the Hidden Curriculum: Perspectives on Successfully Navigating Scientific Conferences.

Scientific conferences and meetings are valuable opportunities for researchers to network, communicate, and develop knowledge. For early career scientists, conferences can also be intimidating, confusing, and overwhelming, especially without having adequate preparation or experience. In this Perspective, we provide advice based on previous experiences navigating scientific meetings and conferences. These guidelines outline parts of the hidden curriculum around preparing for and attending meetings, navigating conference sessions, networking with other scientists, and participating in social activities while upholding a recommended code of conduct.

Discovery of a New Antibiotic Demethoxytetronasin Using a Dual-Sided Agar Plate Assay (DAPA).

For over a century, researchers have cultured microorganisms together on solid support─typically agar─in order to observe growth inhibition via antibiotic production. These simple bioassays have been critical to both academic researchers that study antibiotic production in microorganisms and to the pharmaceutical industry's global effort to discover drugs. Despite the utility of agar assays to researchers around the globe, several limitations have prevented their widespread adoption in advanced high-throughput compound discovery and dereplication campaigns. To address a list of specific shortcomings, we developed the dual-sided agar plate assay (DAPA), which exists in a 96-well plate format, allows microorganisms to compete through opposing sides of a solid support in individual wells, is amenable to high-throughput screening and automation, is reusable, and is low-cost. Herein, we validate the use of DAPA as a tool for drug discovery and show its utility to discover new antibiotic natural products. From the screening of 217 bacterial isolates on multiple nutrient media against 3 pathogens, 55 hits were observed, 9 known antibiotics were dereplicated directly from agar plugs, and a new antibiotic, demethoxytetronasin (1), was isolated from a Streptomyces sp. These results demonstrate that DAPA is an effective, accessible, and low-cost tool to screen, dereplicate, and prioritize bacteria directly from solid support in the front end of antibiotic discovery pipelines.

A Streptomyces tendae Specialized Metabolite Inhibits Quorum Sensing in Group A Streptococcus.

Quorum sensing (QS) is a means of bacterial communication accomplished by microbe-produced signals and sensory systems. QS systems regulate important population-wide behaviors in bacteria, including secondary metabolite production, swarming motility, and bioluminescence. The human pathogen Streptococcus pyogenes (group A Streptococcus [GAS]) utilizes Rgg-SHP QS systems to regulate biofilm formation, protease production, and activation of cryptic competence pathways. Given their reliance on small-molecule signals, QS systems are attractive targets for small-molecule modulators that would then affect gene expression. In this study, a high-throughput luciferase assay was employed to screen an Actinobacteria-derived secondary metabolite (SM) fraction library to identify small molecule inhibitors of Rgg regulation. A metabolite produced by Streptomyces tendae D051 was found to be a general inhibitor of GAS Rgg-mediated QS. Herein, we describe the biological activity of this metabolite as a QS inhibitor. IMPORTANCE Streptococcus pyogenes, a human pathogen known for causing infections such as pharyngitis and necrotizing fasciitis, uses quorum sensing (QS) to regulate social responses in its environment. Previous studies have focused on disrupting QS as a means to control specific bacterial signaling outcomes. In this work, we identified and described the activity of a naturally derived S. pyogenes QS inhibitor. This study demonstrates that the inhibitor affects three separate but similar QS signaling pathways.

Kaempferol, a Phytoprogestin, Induces a Subset of Progesterone-Regulated Genes in the Uterus.

Progesterone functions as a steroid hormone involved in female reproductive physiology. While some reproductive disorders manifest with symptoms that can be treated by progesterone or synthetic progestins, recent data suggest that women also seek botanical supplements to alleviate these symptoms. However, botanical supplements are not regulated by the U.S. Food and Drug Administration and therefore it is important to characterize and quantify the inherent active compounds and biological targets of supplements within cellular and animal systems. In this study, we analyzed the effect of two natural products, the flavonoids, apigenin and kaempferol, to determine their relationship to progesterone treatment in vivo. According to immunohistochemical analysis of uterine tissue, kaempferol and apigenin have some progestogenic activity, but do not act in exactly the same manner as progesterone. More specifically, kaempferol treatment did not induce HAND2, did not change proliferation, and induced ZBTB16 expression. Additionally, while apigenin treatment did not appear to dramatically affect transcripts, kaempferol treatment altered some transcripts (44%) in a similar manner to progesterone treatment but had some unique effects as well. Kaempferol regulated primarily unfolded protein response, androgen response, and interferon-related transcripts in a similar manner to progesterone. However, the effects of progesterone were more significant in regulating thousands of transcripts making kaempferol a selective modifier of signaling in the mouse uterus. In summary, the phytoprogestins, apigenin and kaempferol, have progestogenic activity in vivo but also act uniquely.

Automated Microbial Library Generation Using the Bioinformatics Platform IDBac.

Libraries of microorganisms have served as a cornerstone of therapeutic drug discovery, though the continued re-isolation of known natural product chemical entities has remained a significant obstacle to discovery efforts. A major contributing factor to this redundancy is the duplication of bacterial taxa in a library, which can be mitigated through the use of a variety of DNA sequencing strategies and/or mass spectrometry-informed bioinformatics platforms so that the library is created with minimal phylogenetic, and thus minimal natural product overlap. IDBac is a MALDI-TOF mass spectrometry-based bioinformatics platform used to assess overlap within collections of environmental bacterial isolates. It allows environmental isolate redundancy to be reduced while considering both phylogeny and natural product production. However, manually selecting isolates for addition to a library during this process was time intensive and left to the researcher's discretion. Here, we developed an algorithm that automates the prioritization of hundreds to thousands of environmental microorganisms in IDBac. The algorithm performs iterative reduction of natural product mass feature overlap within groups of isolates that share high homology of protein mass features. Employing this automation serves to minimize human bias and greatly increase efficiency in the microbial strain prioritization process.

Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges.

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.

The Flavonoid Baicalein Negatively Regulates Progesterone Target Genes in the Uterus in Vivo.

Baicalein is a flavonoid extracted from the root of Scutellaria baicalensis (Chinese skullcap) and is consumed as part of this botanical dietary supplement to reduce oxidative stress, pain, and inflammation. We previously reported that baicalein can also modify receptor signaling through the progesterone receptor (PR) and glucocorticoid receptor (GR) in vitro, which is interesting due to the well-established roles of both PR and GR in reducing inflammation. To understand the effects of baicalein on PR and GR signaling in vivo in the uterus, ovariectomized CD-1 mice were treated with DMSO, progesterone (P4), baicalein, P4 with baicalein, and P4 with RU486, a PR antagonist, for a week. The uteri were collected for histology and RNA sequencing. Our results showed that baicalein attenuated the antiproliferative effect of P4 on luminal epithelium as well as on the PR target genes HAND2 and ZBTB16. Baicalein did not change levels of PR or GR RNA or protein in the uterus. RNA sequencing data indicated that many transcripts significantly altered by baicalein were regulated in the opposite direction by P4. Similarly, a large portion of GO/KEGG terms and GSEA gene sets were altered in the opposite direction by baicalein as compared to P4 treatment. Treatment of baicalein did not change body weight, organ weight, or blood glucose level. In summary, baicalein functioned as a PR antagonist in vivo and therefore may oppose P4 action under certain conditions such as uterine hyperplasia, fibroids, and uterine cancers.

Irilone, a Red Clover Isoflavone, Combined with Progesterone Enhances PR Signaling through the Estrogen and Glucocorticoid Receptors.

Trifolium pratense L. (red clover) is a popular botanical supplement used for women's health. Irilone isolated from red clover previously demonstrated progestogenic potentiation activity. In this study, irilone enhanced progesterone signaling was determined to not occur due to post-translational phosphorylation or by reducing progesterone receptor (PR) protein levels but instead increased PR protein levels in T47D breast cancer cells, which could be blocked by estrogen receptor (ER) antagonists, suggesting an ER dependent effect. Further, irilone increased luciferase activity from a hormone responsive element in a cell line that lacked ER and PR but expressed the glucocorticoid receptor (GR). A siRNA knockdown of GR in Ishikawa PR-B endometrial cancer cells reduced irilone's ability to enhance progesterone signaling. In an ovariectomized CD-1 mouse model, irilone did not induce uterine epithelial cell proliferation. The mechanism of action of irilone gives insight into PR crosstalk with other steroid hormone receptors, which can be important for understanding botanicals that are used for women's health.

Evaluating the Distribution of Bacterial Natural Product Biosynthetic Genes across Lake Huron Sediment.

Environmental microorganisms continue to serve as a major source of bioactive natural products (NPs) and as an inspiration for many other scaffolds in the toolbox of modern medicine. Nearly all microbial NP-inspired therapies can be traced to field expeditions to collect samples from the environment. Despite the importance of these expeditions in the search for new drugs, few studies have attempted to document the extent to which NPs or their corresponding production genes are distributed within a given environment. To gain insights into this, the geographic occurrence of NP ketosynthase (KS) and adenylation (A) domains was documented across 53 and 58 surface sediment samples, respectively, covering 59,590 square kilometers of Lake Huron. Overall, no discernible NP geographic distribution patterns were observed for 90,528 NP classes of nonribosomal peptides and polyketides detected in the survey. While each sampling location harbored a similar number of A domain operational biosynthetic units (OBUs), a limited overlap of OBU type was observed, suggesting that at the sequencing depth used in this study, no single location served as a NP "hotspot". These data support the hypothesis that there is ample variation in NP occurrence between sampling sites and suggest that extensive sample collection efforts are required to fully capture the functional chemical diversity of sediment microbial communities on a regional scale.

Secoiridoids from Dogwood (Cornus officinalis) Potentiate Progesterone Signaling.

The use of botanical dietary supplements for the alleviation of conditions such as hot flashes, premenstrual syndrome, and fertility is prolific worldwide. Estrogen and progesterone receptors (ER and PR) and their corresponding steroid hormones are critical for the relief of hot flashes and the treatment of patients who develop endometriosis, and these pathways can influence the development of endometrial, ovarian, and breast cancers. However, few studies have investigated or identified the natural product components in herbal supplements that act on the PR. In the current study, a new secoiridoid, demethoxy-cornuside (1), along with six known secoiridoids (2-7) were isolated from the twigs of dogwood (Cornus officinalis) by bioassay-guided isolation with a progesterone response element (PRE)/luciferase (Luc) reporter assay in Ishikawa cells. Four phytoprogestins (1, 2, 6, 7) potentiated the effect of progesterone in the PRE/Luc assay. This study demonstrates that C. officinalis components might potentiate progesterone signaling in the presence of progesterone, which could modify progesterone receptor action in hormone-responsive tissues such as the uterus and mammary gland.

The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia.

The question of whether culturable microorganisms will continue to be a viable source of new drug leads is inherently married to the strategies used to collect samples from the environment, the methods used to cultivate microorganisms from these samples, and the processes used to create microbial libraries. An academic microbial natural products (NP) drug discovery program with the latest innovative chromatographic and spectroscopic technology, high-throughput capacity, and bioassays will remain at the mercy of the quality of its microorganism source library. This viewpoint will discuss limitations of sample collection and microbial strain library generation practices. Additionally, it will offer suggestions to innovate these areas, particularly through the targeted cultivation of several understudied bacterial phyla and the untargeted use of mass spectrometry and bioinformatics to generate diverse microbial libraries. Such innovations have potential to impact downstream therapeutic discovery, and make its front end more informed, efficient, and less reliant on serendipity. This viewpoint is not intended to be a comprehensive review of contributing literature and was written with a focus on bacteria. Strategies to discover NPs from microbial libraries, including a variety of genomics and "OSMAC" style approaches, are considered downstream of sample collection and library creation, and thus are out of the scope of this viewpoint.

Addition of insoluble fiber to isolation media allows for increased metabolite diversity of lab-cultivable microbes derived from zebrafish gut samples.

There is a gap in measured microbial diversity when comparing genomic sequencing techniques versus cultivation from environmental samples in a laboratory setting. Standardized methods in artificial environments may not recapitulate the environmental conditions that native microbes require for optimal growth. For example, the intestinal tract houses microbes at various pH values as well as minimal oxygen and light environments. These microbes are also exposed to an atypical source of carbon: dietary fiber compacted in fecal matter. To investigate how the addition of insoluble fiber to isolation media could affect the cultivation of microbes from zebrafish intestines, an isolate library was built and analyzed using the bioinformatics pipeline IDBac. While all isolation media encouraged the growth of species from several phyla, the extent of growth was greater with the addition of fiber allowing for easier isolation. Furthermore, fiber addition altered the metabolism of the cultivated gut-derived microbes and induced the production of unique metabolites that were not produced when microbes were otherwise grown on standard isolation media. Addition of this inexpensive carbon source to the media supported the cultivation of a diverse community whose secondary metabolite production may more closely replicate their metabolite production in vivo.

Antimicrobial Lavandulylated Flavonoids from a Sponge-Derived Streptomyces sp. G248 in East Vietnam Sea.

Three new lavandulylated flavonoids, (2S,2''S)-6-lavandulyl-7,4'-dimethoxy-5,2'-dihydroxylflavanone (1), (2S,2''S)-6-lavandulyl-5,7,2',4'-tetrahydroxylflavanone (2), and (2''S)-5'-lavandulyl-2'-methoxy-2,4,4',6'-tetrahydroxylchalcone (3), along with seven known compounds 4-10 were isolated from culture broth of Streptomyces sp. G248. Their structures were established by spectroscopic data analysis, including 1D and 2D nuclear magnetic resonance (NMR), and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). The absolute configurations of 1-3 were resolved by comparison of their experimental and calculated electronic circular dichroism spectra. Compounds 1-3 exhibited remarkable antimicrobial activity. Whereas, two known compounds 4 and 5 exhibited inhibitory activity against Mycobacterium tuberculosis H37Rv with minimum inhibitory concentration (MIC) values of 6.0 µg/mL and 11.1 µg/mL, respectively.

Viral composition and context in metagenomes from biofilm and suspended growth municipal wastewater treatment plants.

Wastewater treatment plants (WWTPs) contain high density and diversity of viruses which can significantly impact microbial communities in aquatic systems. While previous studies have investigated viruses in WWTP samples that have been specifically concentrated for viruses and filtered to exclude bacteria, little is known about viral communities associated with bacterial communities throughout wastewater treatment systems. Additionally, differences in viral composition between attached and suspended growth wastewater treatment bioprocesses are not well characterized. Here, shotgun metagenomics was used to analyse wastewater and biomass from transects through two full-scale WWTPs for viral composition and associations with bacterial hosts. One WWTP used a suspended growth activated sludge bioreactor and the other used a biofilm reactor (trickling filter). Myoviridae, Podoviridae and Siphoviridae were the dominant viral families throughout both WWTPs, which are all from the order Caudovirales. Beta diversity analysis of viral sequences showed that samples clustered significantly both by plant and by specific sampling location. For each WWTP, the overall bacterial community structure was significantly different than community structure of bacterial taxa associated with viral sequences. These findings highlight viral community composition in transects through different WWTPs and provide context for dsDNA viral sequences in bacterial communities from these systems.

Minimizing Taxonomic and Natural Product Redundancy in Microbial Libraries Using MALDI-TOF MS and the Bioinformatics Pipeline IDBac.

Libraries of microorganisms have been a cornerstone of drug discovery efforts since the mid-1950s, but strain duplication in some libraries has resulted in unwanted natural product redundancy. In the current study, we implemented a workflow that minimizes both the natural product overlap and the total number of bacterial isolates in a library. Using a collection expedition to Iceland as an example, we purified every distinct bacterial colony off isolation plates derived from 86 environmental samples. We employed our mass spectrometry (MS)-based IDBac workflow on these isolates to form groups of taxa based on protein MS fingerprints (3-15 kDa) and further distinguished taxa subgroups based on their degree of overlap within corresponding natural product spectra (0.2-2 kDa). This informed the decision to create a library of 301 isolates spanning 54 genera. This process required only 25 h of data acquisition and 2 h of analysis. In a separate experiment, we reduced the size of an existing library based on the degree of metabolic overlap observed in natural product MS spectra of bacterial colonies (from 833 to 233 isolates, a 72.0% size reduction). Overall, our pipeline allows for a significant reduction in costs associated with library generation and minimizes natural product redundancy entering into downstream biological screening efforts.

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data.

In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac-a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.

Genome Sequence of Marine-Derived Streptomyces sp. Strain F001, a Producer of Akashin A and Diazaquinomycins.

We report the 9.7-Mb genome sequence of Streptomyces sp. strain F001, isolated from a marine sediment sample from Raja Ampat, Indonesia. F001 produces diazaquinomycins, which exhibit potent and selective antituberculosis activity. In addition, it is also known to produce akashin A, a blue pigment that has shown cytotoxic activity.

Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes.

Tuberculosis is an infectious disease of global concern. Members of the diazaquinomycin (DAQ) class of natural products have shown potent and selective activity against drug-resistant Mycobacterium tuberculosis. However, poor solubility has prevented further development of this compound class. Understanding DAQ biosynthesis may provide a viable route for the generation of derivatives with improved properties. We have sequenced the genomes of two actinomycete bacteria that produce distinct DAQ derivatives. While software tools for automated biosynthetic gene cluster (BGC) prediction failed to detect DAQ BGCs, comparative genomics using MAUVE alignment led to the identification of putative BGCs in the marine Streptomyces sp. F001 and in the freshwater Micromonospora sp. B006. Deletion of the identified daq BGC in strain B006 using CRISPR-Cas9 genome editing abolished DAQ production, providing experimental evidence for BGC assignment. A complete model for DAQ biosynthesis is proposed based on the genes identified. Insufficient knowledge of natural product biosynthesis is one of the major challenges of productive genome mining approaches. The results reported here fill a gap in knowledge regarding the genetic basis for the biosynthesis of DAQ antibiotics. Moreover, identification of the daq BGC shall enable future generations of improved derivatives using biosynthetic methods.

Irilone from Red Clover ( Trifolium pratense) Potentiates Progesterone Signaling.

The use of botanical dietary supplements is becoming increasingly popular for the alleviation of hormonal-based conditions such as hot flashes, premenstrual syndrome, and fertility. Estrogen and progesterone receptors (ER and PR) play an essential role in these processes. However, despite the fact that many therapies used to alleviate gynecological conditions act through PR-mediated mechanisms, few studies have investigated or identified any herbal natural product components that act on this receptor. In the current study, we used a progesterone response element (PRE)-luciferase (Luc) reporter assay to identify four phytoprogestins present in a standardized red clover ( Trifolium pratense) extract. We found that the component irilone (1) potentiated the effect of progesterone in both endometrial and ovarian cancer cell lines. In these cancers, progesterone action is generally associated with positive outcomes; thus the potentiating effect of 1 may provide entirely new strategies for enhancing progesterone signaling as a means of mitigating conditions such as fibroids and endometriosis. Formononetin (3) and biochanin A (4) exhibited mixed agonist activity, while prunetin (2) acted only as an antagonist. Collectively, these results suggest that the effects of red clover extract repeatedly observed in cultured cells and the inverse correlation between risk of various cancers and flavonoid intake may be due, in part, to altered progesterone signaling.