Publications by authors named "Marc G Chevrette"

28 Publications

  • Page 1 of 1

Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria.

Nat Commun 2021 03 3;12(1):1422. Epub 2021 Mar 3.

Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.

Trans-acyltransferase polyketide synthases (trans-AT PKSs) are bacterial multimodular enzymes that biosynthesize diverse pharmaceutically and ecologically important polyketides. A notable feature of this natural product class is the existence of chemical hybrids that combine core moieties from different polyketide structures. To understand the prevalence, biosynthetic basis, and evolutionary patterns of this phenomenon, we developed transPACT, a phylogenomic algorithm to automate global classification of trans-AT PKS modules across bacteria and applied it to 1782 trans-AT PKS gene clusters. These analyses reveal widespread exchange patterns suggesting recombination of extended PKS module series as an important mechanism for metabolic diversification in this natural product class. For three plant-associated bacteria, i.e., the root colonizer Gynuella sunshinyii and the pathogens Xanthomonas cannabis and Pseudomonas syringae, we demonstrate the utility of this computational approach for uncovering cryptic relationships between polyketides, accelerating polyketide mining from fragmented genome sequences, and discovering polyketide variants with conserved moieties of interest. As natural combinatorial hybrids are rare among the more commonly studied cis-AT PKSs, this study paves the way towards evolutionarily informed, rational PKS engineering to produce chimeric trans-AT PKS-derived polyketides.
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http://dx.doi.org/10.1038/s41467-021-21163-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930024PMC
March 2021

Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery.

mBio 2021 02 16;12(1). Epub 2021 Feb 16.

Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA

The world faces two seemingly unrelated challenges-a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.
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http://dx.doi.org/10.1128/mBio.03432-20DOI Listing
February 2021

Antileishmanial macrolides from ant-associated Streptomyces sp. ISID311.

Bioorg Med Chem 2021 02 12;32:116016. Epub 2021 Jan 12.

Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, SP, Brazil. Electronic address:

Three antifungal macrolides cyphomycin (1), caniferolide C (2) and GT-35 (3) were isolated from Streptomyces sp. ISID311, a bacterial symbiont associated with Cyphomyrmex fungus-growing ants. The planar structures of these compounds were established by 1 and 2D NMR data and MS analysis. The relative configurations of 1-3 were established using Kishi's universal NMR database method, NOE/ROE analysis and coupling constants analysis assisted by comparisons with NMR data of related compounds. Detailed bioinformatic analysis of cyphomycin biosynthetic gene cluster confirmed the stereochemical assignments. Compounds 1-3 displayed high antagonism against different strains of Escovopsis sp., pathogen fungi specialized to the fungus-growing ant system. Compounds 1-3 also exhibited potent antiprotozoal activity against intracellular amastigotes of the human parasite Leishmania donovani with IC values of 2.32, 0.091 and 0.073 µM, respectively, with high selectivity indexes.
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http://dx.doi.org/10.1016/j.bmc.2021.116016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923958PMC
February 2021

Bacillibactins E and F from a Marine Sponge-Associated sp.

J Nat Prod 2021 01 18;84(1):136-141. Epub 2020 Dec 18.

Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.

Chemical investigation of a marine sponge-associated sp. led to the discovery of bacillibactins E and F ( and ). Despite containing the well-established cyclic triester core of iron-binding natural products such as enterobactin, bacillibactins E and F ( and ) are the first bacterial siderophores that contain nicotinic and benzoic acid moieties. The structures of the new compounds, including their absolute configurations, were determined by extensive spectroscopic analyses and Marfey's method. A plausible biosynthetic pathway to and is proposed; this route bears great similarity to other previously established bacillibactin-like pathways but appears to differentiate itself by a promiscuous DhbE, which likely installs the nicotinic moiety of and the benzoic acid group of .
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http://dx.doi.org/10.1021/acs.jnatprod.0c01170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7856188PMC
January 2021

A marine microbiome antifungal targets urgent-threat drug-resistant fungi.

Science 2020 11;370(6519):974-978

Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA.

New antifungal drugs are urgently needed to address the emergence and transcontinental spread of fungal infectious diseases, such as pandrug-resistant Leveraging the microbiomes of marine animals and cutting-edge metabolomics and genomic tools, we identified encouraging lead antifungal molecules with in vivo efficacy. The most promising lead, turbinmicin, displays potent in vitro and mouse-model efficacy toward multiple-drug-resistant fungal pathogens, exhibits a wide safety index, and functions through a fungal-specific mode of action, targeting Sec14 of the vesicular trafficking pathway. The efficacy, safety, and mode of action distinct from other antifungal drugs make turbinmicin a highly promising antifungal drug lead to help address devastating global fungal pathogens such as
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http://dx.doi.org/10.1126/science.abd6919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756952PMC
November 2020

MS-Derived Isotopic Fine Structure Reveals Forazoline A as a Thioketone-Containing Marine-Derived Natural Product.

Org Lett 2020 02 4;22(4):1275-1279. Epub 2020 Feb 4.

Pharmaceutical Sciences Division , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.

Forazoline A is a structurally complex PKS-NRPS hybrid produced by marine-derived sp. During the course of studies highlighting the application of IFS analysis as a powerful tool for natural products analysis, we were alerted to an earlier misinterpretation with respect to forazoline A structure elucidation. In particular, IFS reveals that forazoline A contains a thioketone moiety rarely seen in secondary metabolites and, thus, constitutes an even more intriguing structure than originally thought.
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http://dx.doi.org/10.1021/acs.orglett.9b04535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494057PMC
February 2020

From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome.

Biochemistry 2020 02 24;59(6):729-730. Epub 2020 Jan 24.

Wisconsin Institute for Discovery and Department of Plant Pathology , University of Wisconsin-Madison , Madison , Wisconsin 53715 , United States.

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http://dx.doi.org/10.1021/acs.biochem.0c00033DOI Listing
February 2020

Evolutionary dynamics of natural product biosynthesis in bacteria.

Nat Prod Rep 2020 04 11;37(4):566-599. Epub 2019 Dec 11.

Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.

Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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http://dx.doi.org/10.1039/c9np00048hDOI Listing
April 2020

Local Adaptation of Bacterial Symbionts within a Geographic Mosaic of Antibiotic Coevolution.

Appl Environ Microbiol 2019 12 27;85(24). Epub 2019 Nov 27.

Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA

The geographic mosaic theory of coevolution (GMC) posits that coevolutionary dynamics go beyond local coevolution and are comprised of the following three components: geographic selection mosaics, coevolutionary hot spots, and trait remixing. It is unclear whether the GMC applies to bacteria, as horizontal gene transfer and cosmopolitan dispersal may violate theoretical assumptions. Here, we test key GMC predictions in an antibiotic-producing bacterial symbiont (genus ) that protects the crops of neotropical fungus-farming ants () from a specialized pathogen (genus ). We found that antibiotic inhibition of common pathogens was elevated in colonies from Panama compared to those from Costa Rica. Furthermore, a Panama Canal Zone population of on Barro Colorado Island (BCI) was locally adapted, whereas two neighboring populations were not, consistent with a GMC-predicted selection mosaic and a hot spot of adaptation surrounded by areas of maladaptation. Maladaptation was shaped by incongruent population genetic structure, whereas local adaptation was facilitated by geographic isolation on BCI after the flooding of the Panama Canal. Genomic assessments of antibiotic potential of 29 strains identified diverse and unique biosynthetic gene clusters in BCI strains despite low genetic diversity in the core genome. The strength of antibiotic inhibition was not correlated with the presence/absence of individual biosynthetic gene clusters or with parasite location. Rather, biosynthetic gene clusters have undergone selective sweeps, suggesting that the trait remixing dynamics conferring the long-term maintenance of antibiotic potency rely on evolutionary genetic changes within already-present biosynthetic gene clusters and not simply on the horizontal acquisition of novel genetic elements or pathways. Recently, coevolutionary theory in macroorganisms has been advanced by the geographic mosaic theory of coevolution (GMC), which considers how geography and local adaptation shape coevolutionary dynamics. Here, we test GMC in an ancient symbiosis in which the ant cultivates fungi in an agricultural system analogous to human farming. The cultivars are parasitized by the fungus The ants maintain symbiotic actinobacteria with antibiotic properties that help combat infection. This antibiotic symbiosis has persisted for tens of millions of years, raising the question of how antibiotic potency is maintained over these time scales. Our study tests the GMC in a bacterial defensive symbiosis and in a multipartite symbiosis framework. Our results show that this multipartite symbiotic system conforms to the GMC and demonstrate that this theory is applicable in both microbes and indirect symbiont-symbiont interactions.
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http://dx.doi.org/10.1128/AEM.01580-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881802PMC
December 2019

Taxonomic and Metabolic Incongruence in the Ancient Genus .

Front Microbiol 2019 20;10:2170. Epub 2019 Sep 20.

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.

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 . We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence/absence within , 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 fail to resolve important ecological and metabolic characteristics.
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http://dx.doi.org/10.3389/fmicb.2019.02170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763951PMC
September 2019

Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code.

ACS Chem Biol 2019 09 3;14(9):2044-2054. Epub 2019 Sep 3.

Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.

Nonribosomal peptides are important natural products biosynthesized by nonribosomal peptide synthetases (NRPSs). Adenylation (A) domains of NRPSs are highly specific for the substrate they recognize. This recognition is determined by 10 residues in the substrate-binding pocket, termed the specificity code. This finding led to the proposal that nonribosomal peptides could be altered by specificity code swapping. Unfortunately, this approach has proven, with few exceptions, to be unproductive; changing the specificity code typically results in broadened specificity or poor function. To enhance our understanding of A domain substrate selectivity, we carried out a detailed analysis of the specificity code from the A domain of EntF, an NRPS involved in enterobactin biosynthesis in . Using directed evolution and a genetic selection, we determined which sites in the code have strict residue requirements and which are tolerant of variation. We showed that the EntF A domain, and other l-Ser-specific A domains, have a functional sequence space for l-Ser recognition, rather than a single code. This functional space is more expansive than the aggregate of all characterized l-Ser-specific A domains: we identified 152 new l-Ser specificity codes. Together, our data provide essential insights into how to overcome the barriers that prevent rational changes to A domain specificity.
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http://dx.doi.org/10.1021/acschembio.9b00532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800085PMC
September 2019

Madurastatin D1 and D2, Oxazoline Containing Siderophores Isolated from an

Org Lett 2019 08 5;21(16):6275-6279. Epub 2019 Aug 5.

Pharmaceutical Sciences Division , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States.

Two new siderophores, madurastatin D1 and D2, together with (-)-madurastatin C1, the enantiomer of a known compound, were isolated from marine-derived sp. The presence of an unusual 4-imidazolidinone ring in madurastatins D1 and D2 inspired us to sequence the sp. genome and to identify the biosynthetic gene cluster, knowledge of which enables us to now propose a biosynthetic pathway. Madurastatin D1 and D2 are moderately active in antimicrobial assays with .
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http://dx.doi.org/10.1021/acs.orglett.9b02159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941472PMC
August 2019

Experimental Microbiomes: Models Not to Scale.

mSystems 2019 Jul 30;4(4). Epub 2019 Jul 30.

Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA

Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static "screenshots" derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (-, -Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.
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http://dx.doi.org/10.1128/mSystems.00175-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667727PMC
July 2019

The antimicrobial potential of Streptomyces from insect microbiomes.

Nat Commun 2019 01 31;10(1):516. Epub 2019 Jan 31.

Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA.

Antimicrobial resistance is a global health crisis and few novel antimicrobials have been discovered in recent decades. Natural products, particularly from Streptomyces, are the source of most antimicrobials, yet discovery campaigns focusing on Streptomyces from the soil largely rediscover known compounds. Investigation of understudied and symbiotic sources has seen some success, yet no studies have systematically explored microbiomes for antimicrobials. Here we assess the distinct evolutionary lineages of Streptomyces from insect microbiomes as a source of new antimicrobials through large-scale isolations, bioactivity assays, genomics, metabolomics, and in vivo infection models. Insect-associated Streptomyces inhibit antimicrobial-resistant pathogens more than soil Streptomyces. Genomics and metabolomics reveal their diverse biosynthetic capabilities. Further, we describe cyphomycin, a new molecule active against multidrug resistant fungal pathogens. The evolutionary trajectories of Streptomyces from the insect microbiome influence their biosynthetic potential and ability to inhibit resistant pathogens, supporting the promise of this source in augmenting future antimicrobial discovery.
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http://dx.doi.org/10.1038/s41467-019-08438-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355912PMC
January 2019

Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota.

Appl Environ Microbiol 2019 05 2;85(10). Epub 2019 May 2.

Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA

Resources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed coculture inhibition assays between nasal and spp. We found that isolates of coagulase-negative staphylococci (CoNS) were sensitive to growth inhibition by but that isolates were resistant to inhibition. Among , we observed that spp. were variable in their ability to inhibit CoNS. We sequenced the genomes of 10 species isolates, including 3 isolates that strongly inhibited CoNS and 7 other species isolates that only weakly inhibited CoNS. Using a comparative genomics approach, we found that the genomes were enriched in genes for iron acquisition and harbored a biosynthetic gene cluster (BGC) for siderophore production, absent in the noninhibitory species genomes. Using a chrome azurol S assay, we confirmed that produced siderophores. We demonstrated that iron supplementation rescued CoNS from inhibition by , suggesting that inhibition was due to iron restriction through siderophore production. Through comparative metabolomics and molecular networking, we identified the siderophore produced by as dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressed by analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project. Together, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness. Within the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasal species strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and posttranslationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by hindering access to or depleting essential nutrients. As the nasal cavity is a nutrient-limited environment, we hypothesized that exploitation competition occurs in this system. We determined that produces an iron-chelating siderophore, and this iron-sequestering molecule correlates with the ability to inhibit the growth of coagulase-negative staphylococci. Furthermore, we found that the genes required for siderophore production are expressed Thus, although siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.
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http://dx.doi.org/10.1128/AEM.02406-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498180PMC
May 2019

Emerging evolutionary paradigms in antibiotic discovery.

J Ind Microbiol Biotechnol 2019 Mar 29;46(3-4):257-271. Epub 2018 Sep 29.

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.

Antibiotics revolutionized medicine and remain its cornerstone. Despite their global importance and the continuous threat of resistant pathogens, few antibiotics have been discovered in recent years. Natural products, especially the secondary metabolites of Actinobacteria, have been the traditional discovery source of antibiotics. In nature, the chemistry of antibiotic natural products is shaped by the unique evolution and ecology of their producing organisms, yet these influences remain largely unknown. Here, we highlight the ecology of antibiotics employed by microbes in defensive symbioses and review the evolutionary processes underlying the chemical diversity and activity of microbe-derived antibiotics, including the dynamics of vertical and lateral transmission of biosynthetic pathways and the evolution of efficacy, targeting specificity, and toxicity. We argue that a deeper understanding of the ecology and evolution of microbial interactions and the metabolites that mediate them will allow for an alternative, rational approach to discover new antibiotics.
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http://dx.doi.org/10.1007/s10295-018-2085-6DOI Listing
March 2019

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite.

ISME J 2019 01 16;13(1):104-117. Epub 2018 Aug 16.

Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

Plant cell-wall polysaccharides constitute the most abundant but recalcitrant organic carbon source in nature. Microbes residing in the digestive tract of herbivorous bilaterians are particularly efficient at depolymerizing polysaccharides into fermentable sugars and play a significant support role towards their host's lifestyle. Here, we combine large-scale functional screening of fosmid libraries, shotgun sequencing, and biochemical assays to interrogate the gut microbiota of the wood-feeding "higher" termite Globitermes brachycerastes. A number of putative polysaccharide utilization gene clusters were identified with multiple fibrolytic genes. Our large-scale functional screening of 50,000 fosmid clones resulted in 464 clones demonstrating plant polysaccharide-degrading activities, including 267 endoglucanase-, 24 exoglucanase-, 72 β-glucosidase-, and 101 endoxylanase-positive clones. We sequenced 173 functionally active clones and identified ~219 genes encoding putative carbohydrate-active enzymes (CAZymes) targeting cellulose, hemicellulose and pectin. Further analyses revealed that 68 of 154 contigs encode one or more CAZyme, which includes 35 examples of putative saccharolytic operons, suggesting that clustering of CAZymes is common in termite gut microbial inhabitants. Biochemical characterization of a representative xylanase cluster demonstrated that constituent enzymes exhibited complementary physicochemical properties and saccharolytic capabilities. Furthermore, diverse cellobiose-metabolizing enzymes include β-glucosidases, cellobiose phosphorylases, and phopho-6-β-glucosidases were identified and functionally verified, indicating that the termite gut micro-ecosystem utilizes diverse metabolic pathways to interconnect hydrolysis and central metabolism. Collectively, these results provide an in-depth view of the adaptation and digestive strategies employed by gut microbiota within this tiny-yet-efficient host-associated ecosystem.
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http://dx.doi.org/10.1038/s41396-018-0255-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298952PMC
January 2019

Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium.

Genome Announc 2018 Feb 22;6(8). Epub 2018 Feb 22.

Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA

sp. strain WMMA1996 was isolated in 2013 off the coast of the Florida Keys, United States, from a marine sponge as part of bacterial coculture-based drug discovery initiatives. Analysis of the ∼6.44-Mb genome reveals this microbe's potential role in the discovery of new drugs.
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http://dx.doi.org/10.1128/genomeA.00077-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823995PMC
February 2018

Complete Genome Sequence of sp. Strain WMMA184, a Marine Coral-Associated Bacterium.

Genome Announc 2018 Feb 1;6(5). Epub 2018 Feb 1.

Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA

sp. strain WMMA184 was isolated from the marine coral as part of ongoing drug discovery efforts. Analysis of the 4.16-Mb genome provides information regarding interspecies interactions as it pertains to the regulation of secondary metabolism and natural product biosynthesis potential.
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http://dx.doi.org/10.1128/genomeA.01582-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794961PMC
February 2018

Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin.

ACS Chem Biol 2017 12 22;12(12):3093-3102. Epub 2017 Nov 22.

Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin , Madison, Wisconsin 53705, United States.

Advances in genomics and metabolomics have made clear in recent years that microbial biosynthetic capacities on Earth far exceed previous expectations. This is attributable, in part, to the realization that most microbial natural product (NP) producers harbor biosynthetic machineries not readily amenable to classical laboratory fermentation conditions. Such "cryptic" or dormant biosynthetic gene clusters (BGCs) encode for a vast assortment of potentially new antibiotics and, as such, have become extremely attractive targets for activation under controlled laboratory conditions. We report here that coculturing of a Rhodococcus sp. and a Micromonospora sp. affords keyicin, a new and otherwise unattainable bis-nitroglycosylated anthracycline whose mechanism of action (MOA) appears to deviate from those of other anthracyclines. The structure of keyicin was elucidated using high resolution MS and NMR technologies, as well as detailed molecular modeling studies. Sequencing of the keyicin BGC (within the Micromonospora genome) enabled both structural and genomic comparisons to other anthracycline-producing systems informing efforts to characterize keyicin. The new NP was found to be selectively active against Gram-positive bacteria including both Rhodococcus sp. and Mycobacterium sp. E. coli-based chemical genomics studies revealed that keyicin's MOA, in contrast to many other anthracyclines, does not invoke nucleic acid damage.
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http://dx.doi.org/10.1021/acschembio.7b00688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973552PMC
December 2017

Complexity of Complement Resistance Factors Expressed by Needed for Survival in Human Serum.

J Immunol 2017 10 30;199(8):2803-2814. Epub 2017 Aug 30.

Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and

is a bacterial pathogen with increasing impact in healthcare settings, due in part to this organism's resistance to many antimicrobial agents, with pneumonia and bacteremia as the most common manifestations of disease. A significant proportion of clinically relevant strains are resistant to killing by normal human serum (NHS), an observation supported in this study by showing that 12 out of 15 genetically diverse strains of are resistant to NHS killing. To expand our understanding of the genetic basis of serum resistance, a transposon (Tn) sequencing (Tn-seq) approach was used to identify genes contributing to this trait. An ordered Tn library in strain AB5075 with insertions in every nonessential gene was subjected to selection in NHS. We identified 50 genes essential for the survival of in NHS, including already known serum resistance factors, and many novel genes not previously associated with serum resistance. This latter group included the maintenance of lipid asymmetry genetic pathway as a key determinant in protecting from the bactericidal activity of NHS via the alternative complement pathway. Follow-up studies validated the role of eight additional genes identified by Tn-seq in resistance to killing by NHS but not by normal mouse serum, highlighting the human species specificity of serum resistance. The identification of a large number of genes essential for serum resistance in indicates the degree of complexity needed for this phenotype, which might reflect a general pattern that pathogens rely on to cause serious infections.
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http://dx.doi.org/10.4049/jimmunol.1700877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5636677PMC
October 2017

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

Bioinformatics 2017 Oct;33(20):3202-3210

Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands.

Summary: Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool.

Availability And Implementation: SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3).

Contact: [email protected] or [email protected]

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btx400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860034PMC
October 2017

Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations.

Mar Drugs 2017 Jun 6;15(6). Epub 2017 Jun 6.

Department of Genetics, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction. Finally, to explore sequencing parameters that affect the recovery and contiguity of large and repetitive BGCs assembled , we simulate Illumina and PacBio sequencing of the genome focusing on assembly of the salinilactam () BGC.
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http://dx.doi.org/10.3390/md15060165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484115PMC
June 2017

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Nucleic Acids Res 2017 07;45(W1):W36-W41

Bioinformatics Group, Wageningen University, 6708PB Wageningen, Netherlands.

Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
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http://dx.doi.org/10.1093/nar/gkx319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570095PMC
July 2017

Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium.

Genome Announc 2017 Jan 12;5(2). Epub 2017 Jan 12.

Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA

Micromonospora sp. strain WMMB235 was isolated in 2011 off the coast of the Florida Keys, USA, from a marine ascidian as part of an ongoing drug discovery project. Analysis of the ~7.1-Mb genome provides insight into this strain's biosynthetic potential, means of regulation, and response to coculturing conditions.
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http://dx.doi.org/10.1128/genomeA.01369-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5256203PMC
January 2017

Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium.

Genome Announc 2016 Dec 15;4(6). Epub 2016 Dec 15.

Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA

The Rhodococcus strain WMMA185 was isolated from the marine sponge Chondrilla nucula as part of ongoing drug discovery efforts. Analysis of the 4.44-Mb genome provides information regarding interspecies interactions as pertains to regulation of secondary metabolism and natural product biosynthetic potentials.
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http://dx.doi.org/10.1128/genomeA.01406-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159585PMC
December 2016

Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.

Annu Rev Microbiol 2016 09;70:235-54

Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; email:

The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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http://dx.doi.org/10.1146/annurev-micro-102215-095748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703056PMC
September 2016
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