Publications by authors named "Jonathan L Klassen"

39 Publications

North American Fireflies Host Low Bacterial Diversity.

Microb Ecol 2021 Feb 20. Epub 2021 Feb 20.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.

Although there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa: Ellychnia corrusca, the Photuris versicolor species complex, Pyractomena borealis, and Pyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other, Ph. versicolor gut and body microbiomes did, with their gut microbiomes being enriched in Pseudomonas and Acinetobacter. Ellychnia corrusca egg and adult microbiomes were unique except for a single egg microbiome that shared a community type with E. corrusca adults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00248-021-01718-7DOI Listing
February 2021

Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities.

Chem Rev 2021 Feb 1;121(4):2648-2712. Epub 2021 Feb 1.

Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States.

The emergence of new pathogens and multidrug resistant bacteria is an important public health issue that requires the development of novel classes of antibiotics. Antimicrobial peptides (AMPs) are a promising platform with great potential for the identification of new lead compounds that can combat the aforementioned pathogens due to their broad-spectrum antimicrobial activity and relatively low rate of resistance emergence. AMPs of multicellular organisms made their debut four decades ago thanks to ingenious researchers who asked simple questions about the resistance to bacterial infections of insects. Questions such as "Do fruit flies ever get sick?", combined with pioneering studies, have led to an understanding of AMPs as universal weapons of the immune system. This review focuses on a subclass of AMPs that feature a metal binding motif known as the amino terminal copper and nickel (ATCUN) motif. One of the metal-based strategies of hosts facing a pathogen, it includes wielding the inherent toxicity of copper and deliberately trafficking this metal ion into sites of infection. The sudden increase in the concentration of copper ions in the presence of ATCUN-containing AMPs (ATCUN-AMPs) likely results in a synergistic interaction. Herein, we examine common structural features in ATCUN-AMPs that exist across species, and we highlight unique features that deserve additional attention. We also present the current state of knowledge about the molecular mechanisms behind their antimicrobial activity and the methods available to study this promising class of AMPs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.chemrev.0c00921DOI Listing
February 2021

Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism.

Front Microbiol 2020 22;11:621041. Epub 2020 Dec 22.

Department of Molecular and Cell Biology, University of Connecticut, Mansfield, CT, United States.

Actinobacteria belonging to the genus have evolved a close relationship with multiple species of fungus-growing ants, where these bacteria produce diverse secondary metabolites that protect the ants and their fungal mutualists from disease. Recent research has charted the phylogenetic diversity of this symbiosis, revealing multiple instances where the ants and have formed stable relationships in which these bacteria are housed on specific regions of the ant's cuticle. Parallel chemical and genomic analyses have also revealed that symbiotic produce diverse secondary metabolites with antifungal and antibacterial bioactivities, and highlighted the importance of plasmid recombination and horizontal gene transfer for maintaining these symbiotic traits. Here, we propose a multi-level model for the evolution of and their secondary metabolites that includes symbiont transmission within and between ant colonies, and the potentially independent movement and diversification of their secondary metabolite biosynthetic genes. Because of their well-studied ecology and experimental tractability, symbionts of fungus-growing ants are an especially useful model system to understand the evolution of secondary metabolites, and also comprise a significant source of novel antibiotic and antifungal agents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.621041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793712PMC
December 2020

Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748, Isolated from a Dragonfly.

Microbiol Resour Announc 2020 Nov 19;9(47). Epub 2020 Nov 19.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA

is a helical bacterium belonging to the class First isolated from a dragonfly, it has the smallest reported genome size of 740 kbp. Here, we report the genome sequence of ATCC 51748.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00422-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679083PMC
November 2020

Cycloheximide-Producing Associated With and Fungus-Farming Ambrosia Beetles.

Front Microbiol 2020 24;11:562140. Epub 2020 Sep 24.

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

Symbiotic microbes help a myriad of insects acquire nutrients. Recent work suggests that insects also frequently associate with actinobacterial symbionts that produce molecules to help defend against parasites and predators. Here we explore a potential association between Actinobacteria and two species of fungus-farming ambrosia beetles, and . We isolated and identified actinobacterial and fungal symbionts from laboratory reared nests, and characterized small molecules produced by the putative actinobacterial symbionts. One 16S rRNA phylotype of (XylebKG-1) was abundantly and consistently isolated from the galleries and adults of and nests. In addition to , the symbiont that cultivates, we also repeatedly isolated a strain of sp. that is an antagonist of this mutualism. Inhibition bioassays between XylebKG-1 and the fungal symbionts from revealed strong inhibitory activity of the actinobacterium toward the fungal antagonist sp. but not the fungal mutualist Bioassay guided HPLC fractionation of XylebKG-1 culture extracts, followed by NMR and mass spectrometry, identified cycloheximide as the compound responsible for the observed growth inhibition. A biosynthetic gene cluster putatively encoding cycloheximide was also identified in XylebKG-1. The consistent isolation of a single 16S phylotype of from two species of ambrosia beetles, and our finding that a representative isolate of this phylotype produces cycloheximide, which inhibits a parasite of the system but not the cultivated fungus, suggests that these actinobacteria may play defensive roles within these systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.562140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7546818PMC
September 2020

Broadening Participation in Scientific Conferences during the Era of Social Distancing.

Trends Microbiol 2020 12 22;28(12):949-952. Epub 2020 Sep 22.

Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA. Electronic address:

Virtual conferences can offer significant benefits but require considerable planning and creativity to be successful. Here we describe the successes and failures of a hybrid in-person/virtual conference model. The COVID-19 epidemic presents the scientific community with an opportunity to pioneer novel models that effectively engage virtual participants to advance conference goals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tim.2020.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7507981PMC
December 2020

Efomycins K and L From a Termite-Associated sp. M56 and Their Putative Biosynthetic Origin.

Front Microbiol 2019 6;10:1739. Epub 2019 Aug 6.

School of Pharmacy, Sungkyunkwan University, Suwon, South Korea.

Two new elaiophylin derivatives, efomycins K () and L (), and five known elaiophylin derivatives () were isolated from the termite-associated sp. M56. The structures were determined by 1D and 2D NMR and HR-ESIMS analyses and comparative CD spectroscopy. The putative gene cluster responsible for the production of the elaiophylin and efomycin derivatives was identified based on significant homology to related clusters. Phylogenetic analysis of gene cluster domains was used to provide a biosynthetic rational for these new derivatives and to demonstrate how a single biosynthetic pathway can produce diverse structures.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.01739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691879PMC
August 2019

Keeping it fresh.

Elife 2019 06 12;8. Epub 2019 Jun 12.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.

Beewolf wasp eggs release nitrogen oxides to provide protection against fungi and other microbes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.48268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561751PMC
June 2019

Evaluation of DESS as a storage medium for microbial community analysis.

PeerJ 2019 5;7:e6414. Epub 2019 Feb 5.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.6414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368006PMC
February 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-08438-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355912PMC
January 2019

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing.

BMC Genomics 2019 Jan 9;20(1):23. Epub 2019 Jan 9.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.

Background: Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have extreme %GC content remains challenging. Long-read, single-molecule sequencing technologies such as the Oxford Nanopore MinION have the potential to overcome these difficulties, although the best approach for harnessing their potential remains poorly evaluated.

Results: We sequenced nine bacterial genomes spanning a wide range of GC contents using Illumina MiSeq and Oxford Nanopore MinION sequencing technologies to determine the advantages of each approach, both individually and combined. Assemblies using only MiSeq reads were highly accurate but lacked contiguity, a deficiency that was partially overcome by adding MinION reads to these assemblies. Even more contiguous genome assemblies were generated by using MinION reads for initial assembly, but these assemblies were more error-prone and required further polishing. This was especially pronounced when Illumina libraries were biased, as was the case for our strains with both high and low GC content. Increased genome contiguity dramatically improved the annotation of insertion sequences and secondary metabolite biosynthetic gene clusters, likely because long-reads can disambiguate these highly repetitive but biologically important genomic regions.

Conclusions: Genome assembly using short-reads is challenged by repetitive sequences and extreme GC contents. Our results indicate that these difficulties can be largely overcome by using single-molecule, long-read sequencing technologies such as the Oxford Nanopore MinION. Using MinION reads for assembly followed by polishing with Illumina reads generated the most contiguous genomes with sufficient accuracy to enable the accurate annotation of important but difficult to sequence genomic features such as insertion sequences and secondary metabolite biosynthetic gene clusters. The combination of Oxford Nanopore and Illumina sequencing can therefore cost-effectively advance studies of microbial evolution and genome-driven drug discovery.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-018-5381-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325685PMC
January 2019

High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants.

Microbiol Resour Announc 2018 Jul 19;7(2). Epub 2018 Jul 19.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.

For their food source, Trachymyrmex septentrionalis ants raise symbiotic fungus gardens that contain bacteria whose functions are poorly understood. Here, we report the genome sequences of eight bacteria isolated from these fungus gardens to better describe the ecology of these strains and their potential to produce secondary metabolites in this niche.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00871-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211366PMC
July 2018

Defining microbiome function.

Nat Microbiol 2018 08 25;3(8):864-869. Epub 2018 Jul 25.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.

Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of 'function' ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of 'who the function is for', in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41564-018-0189-4DOI Listing
August 2018

Propagating annotations of molecular networks using in silico fragmentation.

PLoS Comput Biol 2018 04 18;14(4):e1006089. Epub 2018 Apr 18.

Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America.

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927460PMC
April 2018

Isolation, Biosynthesis and Chemical Modifications of Rubterolones A-F: Rare Tropolone Alkaloids from Actinomadura sp. 5-2.

Chemistry 2017 Jul 21;23(39):9338-9345. Epub 2017 Jun 21.

Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany.

The discovery of six new, highly substituted tropolone alkaloids, rubterolones A-F, from Actinomadura sp. 5-2, isolated from the gut of the fungus-growing termite Macrotermes natalensis is reported. Rubterolones were identified by using fungus-bacteria challenge assays and a HRMS-based dereplication strategy, and characterised by NMR and HRMS analyses and by X-ray crystallography. Feeding experiments and subsequent chemical derivatisation led to a first library of rubterolone derivatives (A-L). Genome sequencing and comparative analyses revealed their putative biosynthetic pathway, which was supported by feeding experiments. This study highlights how gut microbes can present a prolific source of secondary metabolites.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/chem.201701005DOI Listing
July 2017

Linear Peptides Are the Major Products of a Biosynthetic Pathway That Encodes for Cyclic Depsipeptides.

Org Lett 2017 04 22;19(7):1772-1775. Epub 2017 Mar 22.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States.

Three new dentigerumycin analogues are produced by Streptomyces sp. M41, a bacterium isolated from a South African termite, Macrotermes natalensis. The structures of the complex nonribosomal peptide synthetase-polyketide synthase (NRPS/PKS) hybrid compounds were determined by 1D- and 2D-NMR spectroscopy, high-resolution mass spectrometry, and circular dichroism (CD) spectroscopy. Both cyclic and linear peptides are reported, and the genetic organization of the NRPS modules within the biosynthetic gene cluster accounts for the observed structural diversity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.orglett.7b00545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013059PMC
April 2017

Macrotermycins A-D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39.

Org Lett 2017 03 16;19(5):1000-1003. Epub 2017 Feb 16.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States.

Bioassay-guided metabolomic analyses led to the characterization of four new 20-membered glycosylated polyketide macrolactams, macrotermycins A-D, from a termite-associated actinomycete, Amycolatopsis sp. M39. M39's sequenced genome revealed the macrotermycin's putative biosynthetic gene cluster. Macrotermycins A and C had antibacterial activity against human-pathogenic Staphylococcus aureus and, of greater ecological relevance, they also had selective antifungal activity against a fungal parasite of the termite fungal garden.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.orglett.6b03831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006516PMC
March 2017

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.

mSystems 2016 Mar-Apr;1(2). Epub 2016 Mar 29.

Departments of Biological Sciences and Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA.

Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00028-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069740PMC
March 2016

Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche.

Front Microbiol 2016 21;7:1647. Epub 2016 Oct 21.

Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA.

Virtually all multicellular organisms host a community of symbionts composed of mutualistic, commensal, and pathogenic microbes, i.e., their microbiome. The mechanism of selection on host-microbe assemblages remains contentious, particularly regarding whether selection acts differently on hosts and their microbial symbionts. Here, we attempt to reconcile these viewpoints using a model that describes how hosts and their microbial symbionts alter each other's niche and thereby fitness. We describe how host-microbe interactions might change the shape of the host niche and/or reproductive rates within it, which are directly related to host fitness. A host may also alter the niche of a symbiotic microbe, although this depends on the extent to which that microbe is dependent on the host for reproduction. Finally, we provide a mathematical model to test whether interactions between hosts and microbes are necessary to describe the niche of either partner. Our synthesis highlights the phenotypic effects of host-microbe interactions while respecting the unique lifestyles of each partner, and thereby provides a unified framework to describe how selection might act on a host that is associated with its microbiome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2016.01647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073103PMC
October 2016

Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a Tunicate Collected in Long Island Sound.

Genome Announc 2016 Oct 13;4(5). Epub 2016 Oct 13.

Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA

Streptomyces sp. AVP053U2 is a marine bacterium isolated from Styela clava, a tunicate collected in Long Island Sound. Here, we report a draft genome for this bacterium, which was found to contain a high capacity for secondary metabolite production based on analysis and identification of numerous biosynthetic gene clusters.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.00874-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5064096PMC
October 2016

Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.

Genome Announc 2016 Sep 15;4(5). Epub 2016 Sep 15.

Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA

Streptomyces sp. PTY087I2 is a marine bacterium isolated from Styela canopus, a tunicate collected in Bocas del Toro, Panama. Here, we report a draft genome sequence for this bacterium, found to have 94.7% average nucleotide identity (ANI) with Streptomyces roseosporus NRRL 11379, and containing a diverse suite of secondary metabolite gene clusters.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.00856-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026429PMC
September 2016

Draft Genome Sequence of Shewanella sp. Strain P1-14-1, a Bacterial Inducer of Settlement and Morphogenesis in Larvae of the Marine Hydroid Hydractinia echinata.

Genome Announc 2016 Feb 18;4(1). Epub 2016 Feb 18.

Leibniz Institute for Natural Product Research and Infection Biology e.V., Jena, Germany

The assembly and annotation of the draft genome sequence of Shewanella sp. strain P1-14-1 are reported here to investigate the genes responsible for interkingdom interactions, secondary metabolite production, and microbial electrogenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.00003-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759057PMC
February 2016

Draft Genome Sequences of Six Pseudoalteromonas Strains, P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, Which Induce Larval Settlement and Metamorphosis in Hydractinia echinata.

Genome Announc 2015 Dec 17;3(6). Epub 2015 Dec 17.

Leibniz Institute for Natural Product Research and Infection Biology eV, Jena, Germany

To gain a broader understanding of the importance of a surface-associated lifestyle and morphogenic capability, we have assembled and annotated the genome sequences of Pseudoalteromonas strains P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, isolated from Hydractinia echinata. These genomes will allow detailed studies on bacterial factors mediating interkingdom communication.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.01477-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683232PMC
December 2015

Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata.

Genome Announc 2015 Dec 10;3(6). Epub 2015 Dec 10.

Leibniz Institute for Natural Product Research and Infection Biology e.V., Jena, Germany

The genomes of three Pseudoalteromonas strains (P1-8, P1-11, and P1-30) were sequenced and assembled. These genomes will inform future study of the genes responsible for the production of biologically active compounds responsible for these strains' antimicrobial, biofouling, and algicidal activities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.01380-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675935PMC
December 2015

Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions.

BMC Genomics 2015 Nov 2;16:889. Epub 2015 Nov 2.

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

Background: Xenorhabdus bacteria engage in a beneficial symbiosis with Steinernema nematodes, in part by providing activities that help kill and degrade insect hosts for nutrition. Xenorhabdus strains (members of a single species) can display wide variation in host-interaction phenotypes and genetic potential indicating that strains may differ in their encoded symbiosis factors, including secreted metabolites.

Methods: To discern strain-level variation among symbiosis factors, and facilitate the identification of novel compounds, we performed a comparative analysis of the genomes of 10 Xenorhabdus bovienii bacterial strains.

Results: The analyzed X. bovienii draft genomes are broadly similar in structure (e.g. size, GC content, number of coding sequences). Genome content analysis revealed that general classes of putative host-microbe interaction functions, such as secretion systems and toxin classes, were identified in all bacterial strains. In contrast, we observed diversity of individual genes within families (e.g. non-ribosomal peptide synthetase clusters and insecticidal toxin components), indicating the specific molecules secreted by each strain can vary. Additionally, phenotypic analysis indicates that regulation of activities (e.g. enzymes and motility) differs among strains.

Conclusions: The analyses presented here demonstrate that while general mechanisms by which X. bovienii bacterial strains interact with their invertebrate hosts are similar, the specific molecules mediating these interactions differ. Our data support that adaptation of individual bacterial strains to distinct hosts or niches has occurred. For example, diverse metabolic profiles among bacterial symbionts may have been selected by dissimilarities in nutritional requirements of their different nematode hosts. Similarly, factors involved in parasitism (e.g. immune suppression and microbial competition factors), likely differ based on evolution in response to naturally encountered organisms, such as insect hosts, competitors, predators or pathogens. This study provides insight into effectors of a symbiotic lifestyle, and also highlights that when mining Xenorhabdus species for novel natural products, including antibiotics and insecticidal toxins, analysis of multiple bacterial strains likely will increase the potential for the discovery of novel molecules.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-2000-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630870PMC
November 2015

Minimum Information about a Biosynthetic Gene cluster.

Authors:
Marnix H Medema Renzo Kottmann Pelin Yilmaz Matthew Cummings John B Biggins Kai Blin Irene de Bruijn Yit Heng Chooi Jan Claesen R Cameron Coates Pablo Cruz-Morales Srikanth Duddela Stephanie Düsterhus Daniel J Edwards David P Fewer Neha Garg Christoph Geiger Juan Pablo Gomez-Escribano Anja Greule Michalis Hadjithomas Anthony S Haines Eric J N Helfrich Matthew L Hillwig Keishi Ishida Adam C Jones Carla S Jones Katrin Jungmann Carsten Kegler Hyun Uk Kim Peter Kötter Daniel Krug Joleen Masschelein Alexey V Melnik Simone M Mantovani Emily A Monroe Marcus Moore Nathan Moss Hans-Wilhelm Nützmann Guohui Pan Amrita Pati Daniel Petras F Jerry Reen Federico Rosconi Zhe Rui Zhenhua Tian Nicholas J Tobias Yuta Tsunematsu Philipp Wiemann Elizabeth Wyckoff Xiaohui Yan Grace Yim Fengan Yu Yunchang Xie Bertrand Aigle Alexander K Apel Carl J Balibar Emily P Balskus Francisco Barona-Gómez Andreas Bechthold Helge B Bode Rainer Borriss Sean F Brady Axel A Brakhage Patrick Caffrey Yi-Qiang Cheng Jon Clardy Russell J Cox René De Mot Stefano Donadio Mohamed S Donia Wilfred A van der Donk Pieter C Dorrestein Sean Doyle Arnold J M Driessen Monika Ehling-Schulz Karl-Dieter Entian Michael A Fischbach Lena Gerwick William H Gerwick Harald Gross Bertolt Gust Christian Hertweck Monica Höfte Susan E Jensen Jianhua Ju Leonard Katz Leonard Kaysser Jonathan L Klassen Nancy P Keller Jan Kormanec Oscar P Kuipers Tomohisa Kuzuyama Nikos C Kyrpides Hyung-Jin Kwon Sylvie Lautru Rob Lavigne Chia Y Lee Bai Linquan Xinyu Liu Wen Liu Andriy Luzhetskyy Taifo Mahmud Yvonne Mast Carmen Méndez Mikko Metsä-Ketelä Jason Micklefield Douglas A Mitchell Bradley S Moore Leonilde M Moreira Rolf Müller Brett A Neilan Markus Nett Jens Nielsen Fergal O'Gara Hideaki Oikawa Anne Osbourn Marcia S Osburne Bohdan Ostash Shelley M Payne Jean-Luc Pernodet Miroslav Petricek Jörn Piel Olivier Ploux Jos M Raaijmakers José A Salas Esther K Schmitt Barry Scott Ryan F Seipke Ben Shen David H Sherman Kaarina Sivonen Michael J Smanski Margherita Sosio Evi Stegmann Roderich D Süssmuth Kapil Tahlan Christopher M Thomas Yi Tang Andrew W Truman Muriel Viaud Jonathan D Walton Christopher T Walsh Tilmann Weber Gilles P van Wezel Barrie Wilkinson Joanne M Willey Wolfgang Wohlleben Gerard D Wright Nadine Ziemert Changsheng Zhang Sergey B Zotchev Rainer Breitling Eriko Takano Frank Oliver Glöckner

Nat Chem Biol 2015 Sep;11(9):625-31

1] Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany. [2] Jacobs University Bremen gGmbH, Bremen, Germany.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio.1890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714517PMC
September 2015

Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts.

mBio 2015 Jun 4;6(3):e00076. Epub 2015 Jun 4.

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

Unlabelled: Microbial symbionts provide benefits that contribute to the ecology and fitness of host plants and animals. Therefore, the evolutionary success of plants and animals fundamentally depends on long-term maintenance of beneficial associations. Most work investigating coevolution and symbiotic maintenance has focused on species-level associations, and studies are lacking that assess the impact of bacterial strain diversity on symbiotic associations within a coevolutionary framework. Here, we demonstrate that fitness in mutualism varies depending on bacterial strain identity, and this is consistent with variation shaping phylogenetic patterns and maintenance through fitness benefits. Through genome sequencing of nine bacterial symbiont strains and cophylogenetic analysis, we demonstrate diversity among Xenorhabdus bovienii bacteria. Further, we identified cocladogenesis between Steinernema feltiae nematode hosts and their corresponding X. bovienii symbiont strains, indicating potential specificity within the association. To test the specificity, we performed laboratory crosses of nematode hosts with native and nonnative symbiont strains, which revealed that combinations with the native bacterial symbiont and closely related strains performed significantly better than those with more divergent symbionts. Through genomic analyses we also defined potential factors contributing to specificity between nematode hosts and bacterial symbionts. These results suggest that strain-level diversity (e.g., subspecies-level differences) in microbial symbionts can drive variation in the success of host-microbe associations, and this suggests that these differences in symbiotic success could contribute to maintenance of the symbiosis over an evolutionary time scale.

Importance: Beneficial symbioses between microbes and plant or animal hosts are ubiquitous, and in these associations, microbial symbionts provide key benefits to their hosts. As such, host success is fundamentally dependent on long-term maintenance of beneficial associations. Prolonged association between partners in evolutionary time is expected to result in interactions in which only specific partners can fully support symbiosis. The contribution of bacterial strain diversity on specificity and coevolution in a beneficial symbiosis remains unclear. In this study, we demonstrate that strain-level differences in fitness benefits occur in beneficial host-microbe interactions, and this variation likely shapes phylogenetic patterns and symbiotic maintenance. This highlights that symbiont contributions to host biology can vary significantly based on very-fine-scale differences among members of a microbial species. Further, this work emphasizes the need for greater phylogenetic resolution when considering the causes and consequences of host-microbe interactions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00076-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462624PMC
June 2015

Microbial secondary metabolites and their impacts on insect symbioses.

Curr Opin Insect Sci 2014 Oct 19;4:15-22. Epub 2014 Aug 19.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA. Electronic address:

All insects host communities of microbes that interact both with the insect and each other. Secondary metabolites are understood to mediate many of these interactions, although examples having robust genetic, chemical and/or ecological evidence are relatively rare. Here, I review secondary metabolites mediating community interactions in the beewolf, entomopathogenic nematode and fungus-growing ant symbioses, using the logic of Koch's postulates to emphasize well-validated symbiotic functions mediated by these metabolites. I especially highlight how these interaction networks are structured by both ecological and evolutionary processes, and how selection acting on secondary metabolite production can be multidimensional.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cois.2014.08.004DOI Listing
October 2014

ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis.

PLoS One 2013 6;8(3):e58387. Epub 2013 Mar 6.

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

The high-throughput annotation of open reading frames (ORFs) required by modern genome sequencing projects necessitates computational protocols that sometimes annotate orthologous ORFs inconsistently. Such inconsistencies hinder comparative analyses by non-uniformly extending or truncating 5' and/or 3' sequence ends, causing ORFs that are in fact identical to artificially diverge. Whereas strategies exist to correct such inconsistencies during whole-genome annotation, equivalent software designed to correct subsets of these data without genome reannotation is lacking. We therefore developed ORFcor, which corrects annotation inconsistencies using consensus start and stop positions derived from sets of closely related orthologs. ORFcor corrects inconsistent ORF annotations in diverse test datasets with specificities and sensitivities approaching 100% when sufficiently related orthologs (e.g., from the same taxonomic family) are available for comparison. The ORFcor package is implemented in Perl, multithreaded to handle large datasets, includes related scripts to facilitate high-throughput phylogenomic analyses, and is freely available at www.currielab.wisc.edu/downloads.html.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058387PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590147PMC
September 2013