Biology subjects

Kwan, J. C.

Publications and source records attributed to Kwan, J. C..

11 recordsLinked to original sources

bioRxiv2024

Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene

The rapid expansion of multi-omics data has transformed biological research, offering unprecedented opportunities to explore complex genomic relationships across diverse organisms. However, the vast volume and heterogeneity of these datasets presents significant challenges for analyses. Here we introduce SocialGene, a comprehensive software suite designed to collect, analyze, and organize multi-omics data into structured knowledge graphs, with the ability to handle small projects to repository-scale analyses. Originally developed to enhance genome mining for natural product drug discovery, SocialGene has been effective across various applications, including functional genomics, evolutionary studies, and systems biology. SocialGenes concerted Python and Nextflow libraries streamline data ingestion, manipulation, aggregation, and analysis, culminating in a custom Neo4j database. The software not only facilitates the exploration of genomic synteny but also provides a foundational knowledge graph supporting the integration of additional diverse datasets and the development of advanced search engines and analyses. This manuscript introduces some of SocialGenes capabilities through brief case studies including targeted genome mining for drug discovery, accelerated searches for similar and distantly related biosynthetic gene clusters in biobank-available organisms, integration of chemical and analytical data, and more. SocialGene is free, open-source, MIT-licensed, designed for adaptability and extension, and available from github.com/socialgene.

bioinformatics↗

bioRxiv2024

A granular view of the traits controlling soil bacterial community reconstruction following a prescribed burn

Prescribed burns and wildfires both cause transient reduction of soil microbiome diversity, which has wide-ranging functions in soil and plant health. However, a genetic basis for understanding the mechanisms behind post-fire microbiome recovery is not well-established. Here, we conducted prescribed burns in multiple plots with paired unburned controls, at two prairie locations, sampling each over 5 months. We assembled >300 bacterial genomes that were conserved in both time and space, then identified genomes that were either enriched or depleted post-fire compared to timepoint controls. On a metagenome level, burned and unburned samples were functionally equivalent, but on a species level we determined that post- fire survival is more nuanced than possession of previously hypothesized pyrophilous traits. Our study therefore advances the understanding of how both function and taxonomy contribute to success during the reconstruction of a complex soil microbiome.

microbiology↗

bioRxiv2024

Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles

Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide and protects the beetles eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.

genomics↗

bioRxiv2023

Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities

In 2019, we developed Autometa, an automated binning pipeline that is able to effectively recover metagenome-assembled genomes from complex environmental and non-model host-associated microbial communities. Autometa has gained widespread use in a variety of environments and has been applied in multiple research projects. However, the genome-binning workflow was at times overly complex and computationally demanding. As a consequence of Autometas diverse application, non-technical and technical researchers alike have noted its burdensome installation and inefficient as well as error-prone processes. Moreover its taxon-binning and genome-binning behaviors have remained obscure. For these reasons we set out to improve its accessibility, efficiency and efficacy to further enable the research community during their exploration of Earths environments. The highly augmented Autometa 2 release, which we present here, has vastly simplified installation, a graphical user interface and a refactored workflow for transparency and reproducibility. Furthermore, we conducted a parameter sweep on standardized community datasets to show that it is possible for Autometa to achieve better performance than any other binning pipeline, as judged by Adjusted Rand Index. Improvements in Autometa 2 enhance its accessibility for non-bioinformatic oriented researchers, scalability for large-scale and highly-complex samples and interpretation of recovered microbial communities. Graphical abstractAutometa: An automated taxon binning and genome binning workflow for single sample resolution of metagenomic communities.

bioinformatics↗

bioRxiv2023

Automappa: An interactive interface for metagenome-derived genome bins

BackgroundStudies attempting to observe microbes commonly considered uncultivable under standard laboratory conditions are turning to so-called "deep" environmental sequencing approaches whereby they may access these unculturable organisms genomes via in silico approaches. A typical workflow involves metagenome assembly, annotation, and binning for reconstruction of each respective organisms genome (or metagenome-assembled genome, MAG). Many automated genome binning approaches have been developed and have displayed a wide range of variation in performance. Therefore, refinement methods have been developed in order to aid manual curation following the automated genome binning process. Current manual curation tools were developed with a focus towards teaching metagenomics concepts and may fail when handling complex datasets containing many microbes. Automappa was developed with a focus on overlaying a variety of annotations such as taxonomy, coverage and marker-gene prevalence while maintaining an implementation that may scale to the complexity of environmental samples. ResultsWe present Automappa, a companion tool and interactive interface for exploration and refinement of Autometa taxon and genome binning results from metagenomes. Selections provide real-time updates of MAG metrics to aid manual curation. Furthermore, researchers may detect unbinned MAGs as well as manually improve their draft-quality MAGs with contigs that closely match the MAGs genome characteristics. Automappas utility has previously been demonstrated on host-associated, marine and terrestrial systems with a total of 242 curated MAGs across fourteen published metagenomes. Of these refined MAGs, the number of high-quality and medium-quality bins increased, consequently lowering the number of low-quality bins and decreasing the amount of data discarded from downstream analyses. The recovery of higher quality MAGs improved the confidence in results and strengthened the resultant conclusions of these respective studies. Automappa consists of three tabs, one for uploading a users metagenome data, another for exploration and refinement and the last for providing an overall summary of the refined MAG results. ConclusionsAutomappa is an open source software package that allows researchers to easily assess and refine undetected or draft-quality MAGs from their respective metagenomes. It is freely available under the GPLv3 license at https://github.com/WiscEvan/Automappa and through Figshare (doi: 10.6084/m9.figshare.22593235).

bioinformatics↗

bioRxiv2023

Elevated Expression of srp RiPPs Across Bacterial Phyla in Marine Sponges

We investigated transcriptional activity, at a genome-resolved level, of bacterial communities in two S. officinalis and two I. felix sponges, both of which are considered high microbial abundance (HMA) sponges that harbor similar bacterial communities. Overlap of metatranscriptional data on genome-resolved metagenomic data showed that genome bins classified within the Chloroflexota and Poribacteria phyla were the most abundant and transcriptionally active. However, abundant bins in general were not the most transcriptionally active, instead less abundant bins of the same phyla were most active indicating that numerical dominance does not imply transcriptional dominance. We found that although some primary metabolic functions appeared upregulated, they were not obviously attributable to any particular bacterial species. However, assessment of transcription levels of biosynthetic gene clusters (BGCs) encoding secondary metabolites revealed a high transcription of ribosomally synthesized and post-translationally modified peptides (RiPPs) in genome bins across diverse bacterial phyla, most of which were likely srp RiPPs encoding brominated azol(in)e-containing compounds. However, the ecological role of these compounds remains elusive. IMPORTANCEMarine sponges and bacteria have formed close associations over several million years with many bacteria performing specialized functions within their sponge host. Previous studies have either assessed the genomes of a given sponge or the expression profile for a sponge holobiont as a whole. Here, we present the first genome-resolved transcriptomic study which gives us a snapshot of the transcriptional activity of individual bacteria in the context of four different sponge holobionts. Using this approach we found that the numerically dominant bacteria were not the most transcriptionally active and that relatively high expression of a ubiquitous biosynthetic gene cluster was evident in many different bacterial phyla in all four sponge samples.

ecology↗

bioRxiv2022

Uncovering Lasonolide A biosynthesis using genome-resolved metagenomics

Invertebrates, in particular sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anti-cancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60 cell line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed this bacterium, herein named Candidatus Thermopylae lasonolidus, only has 88.78% 16S rRNA identity with the closest relative Pedosphaera parvula Ellin514, indicating it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-AT polyketide synthase (PKS) pathway. When compared with its host genome, the las BGC exhibits a significantly different GC content and penta-nucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed including the presence of three insertions, two single-nucleotide polymorphisms and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the Verrucomicrobial producer shows signs of genome-reduction, its genome size is still fairly large (about 5Mbp) and when compared to its closest free-living relative contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. ImportanceWhile sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small amounts by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations and causes premature chromosome condensation, blebbing, cell contraction and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anti-cancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing to uncover how an uncultured bacterium produces LSA. This provides future opportunities for heterologous expression and cultivation efforts that may minimize LSAs supply problem.

microbiology↗

bioRxiv2020

Family matters: The genomes of conserved bacterial symbionts provide insight into specialized metabolic relationships with their sponge host

As the oldest extant metazoans, sponges (Phylum Porifera) have been forming symbiotic relationships with microbes that may date back as far as 700 million years. Most symbionts are conserved within a narrow host range and perform specialized functions. However, there are widely distributed bacterial taxa such as Poribacteria, SAUL and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added eleven new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these broad-host range, sponge-associated bacteria likely perform distinct functions within their hosts and that their respective phylogenies are incongruent with their host phylogenies. These results suggests that ancestors of these bacteria may have undergone multiple association events, rather than a single association event followed by co-evolution. IMPORTANCEMarine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three know bacterial taxa (Entoporibacteria, SAUL and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. Understanding what distinguishes these broad-host range symbionts from specialized symbionts will provide insight into the mechanisms by which sponges form these symbioses. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. This contrasts with specialized symbionts, where function is often a strain-specific trait and have co-evolved with their host following a single association event.

microbiology↗

bioRxiv2019

Metabolic specializations within a bacterial community to create living rocks

Stromatolites are complex microbial mats that form lithified layers and ancient forms are the oldest evidence of life on earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline. Using assembled shotgun metagenomic data we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteriia class (Cyanobacteria phylum), with lower but notable abundances of bacteria classified as Alphaproteobacteria, Gammaproteobacteria and Bacteroidia. We identified functional gene sets in bacterial species conserved across two geographically distinct stromatolite formations, which may promote carbonate precipitation through the reduction of nitrogenous compounds and possible production of calcium ions. We propose that an abundance of extracellular alkaline phosphatases may lead to the formation of phosphatic deposits within these stromatolites. We conclude that the cumulative effect of several conserved bacterial species drives accretion in these two stromatolite formations. ORIGINALITY-SIGNIFICANCEPeritidal stromatolites are unique among stromatolite formations as they grow at the dynamic interface of calcium carbonate-rich groundwater and coastal marine waters. The peritidal space forms a relatively unstable environment and the factors that influence the growth of these peritidal structures is not well understood. To our knowledge, this is the first comparative study that assesses species conservation within the microbial communities of two geographically distinct peritidal stromatolite formations. We assessed the potential functional roles of these communities using genomic bins clustered from metagenomic sequencing data. We identified several conserved bacterial species across the two sites and hypothesize that their genetic functional potential may be important in the formation of pertidal stromatolites. We contrasted these findings against a well-studied site in Shark Bay, Australia and show that, unlike these hypersaline formations, archaea do not play a major role in peritidal stromatolite formation. Furthermore, bacterial nitrogen and phosphate metabolisms of conserved species may be driving factors behind lithification in peritidal stromatolites.

microbiology↗

bioRxiv2019

Horizontal gene transfer to a defensive symbiont with a reduced genome amongst a multipartite beetle microbiome

The loss of functions required for independent life when living within a host gives rise to reduced genomes in obligate bacterial symbionts. Although this phenomenon can be explained by existing evolutionary models, its initiation is not well understood. Here, we describe the microbiome associated with eggs of the beetle Lagria villosa, containing multiple bacterial symbionts related to Burkholderia gladioli including a reduced-genome symbiont thought to produce the defensive compound lagriamide. We find that the putative lagriamide producer is the only symbiont undergoing genome reduction, and that it has already lost most primary metabolism and DNA repair pathways. The horizontal acquisition of the lagriamide biosynthetic gene cluster likely preceded genome reduction, and unexpectedly we found that the symbiont accepted additional genes horizontally during genome reduction, even though it lacks the capacity for homologous recombination. These horizontal gene transfers suggest that absolute genetic isolation is not a requirement for genome reduction.

evolutionary biology↗

bioRxiv2018

Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes

MotivationShotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of \"binning\" where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. Existing methods, however, suffer from: (1) reliance on human pattern recognition, which is inherently unscalable; (2) requirement for multiple co-assembled metagenomes, which degrades assembly quality due to strain variance; and (3) assumption of prior host genome removal not feasible for non-model hosts. We therefore devised a fully-automated pipeline, termed \"Autometa,\" to address these issues. Results: Autometa implements a method for taxonomic partitioning of contigs based on predicted protein homology, and this was shown to vastly improve binning in host-associated and complex metagenomes. Autometas method of automated clustering, based on Barnes-Hut Stochastic Neighbor Embedding (BH-tSNE) and DBSCAN, was shown to be highly scalable, outperforming other binning pipelines in complex simulated datasets.\n\nAvailability and implementationAutometa is freely available at https://bitbucket.org/jasonckwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).\n\nContactjason.kwan@wisc.edu\n\nSupplementary informationSupplementary data are available attached to this article at https://biorxiv.org

bioinformatics↗